MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Biophysical Chemistry' source. Thu, 09 Feb 2012 13:01:28 +0100 http://www.medworm.com/index.php?rid=5671562&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22285312%26dopt%3DAbstract This study also observed that all PolyHbs could potentially improve tissue oxygenation under hypoxic conditions, while low O(2) affinity PolyHbs were more effective in oxygenating tissues under normoxic conditions compared with high O(2) affinity PolyHbs. In addition, all ultrahigh molecular weight PolyHbs displayed higher O(2) transfer rates than the commercial HBOC Oxyglobin® and cell-free bHb. Therefore, these results suggest that ultrahigh molecular weight PolyHb solutions could be used as safe and efficacious O(2) carriers for use in transfusion medicine. It also suggests that future generations of PolyHb solutions should possess lower NO dioxygenation reaction rate constants in order to reduce NO scavenging, while maintaining high solution viscosity to take advantage of wall shear s... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5671562 Mon, 09 Jan 2012 05:00:00 +0100 5671562 http://www.medworm.com/index.php?rid=5671563&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22284904%26dopt%3DAbstract In this study we present a mathematical model to determine the relevance of feedback regulators (Arkadia, Smad7, Smurf1, Smurf2, SnoN and Ski) on TGF-β target gene expression and the potential to initiate stable oscillations within a realistic parameter space. We employed massive sampling of the parameters space to pinpoint crucial players for potential oscillations as well as transcriptional product levels. We identified Smad7 and Smurf2 with the highest impact on the dynamics. Based on these findings, we conducted preliminary time course experiments. PMID: 22284904 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5671563 Thu, 05 Jan 2012 05:00:00 +0100 5671563 http://www.medworm.com/index.php?rid=5671564&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22284903%26dopt%3DAbstract We examined the roles of residues in the glutamate-binding and cleft-closing mechanisms by molecular dynamics (MD) simulations. A glutamate entered the cleft deeply within the order of nanoseconds and the cleft locked the glutamate completely at 15ns in an MD run. TYR450 seemed to regulate the orientation of the glutamate upon binding by cation-π interaction. A semi-open state was identified in the free energy profile evaluated with the structures on the spontaneously glutamate-bound and cleft-closed pathway by the unbiased MD simulations for the first time to our knowledge. In the semi-open state, the two sub-domains were bridged by two hydrogen bonds of GLU705 in the sub-domain 2 with TYR732 in the sub-domain 1 and with the glutamate bound to the sub-domain 1 until the transition to the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5671564 Wed, 28 Dec 2011 05:00:00 +0100 5671564 http://www.medworm.com/index.php?rid=5618552&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22245249%26dopt%3DAbstract Authors: Arseneault M, Dumont M, Otis F, Voyer N Abstract We have prepared fluorescent analogs of known ion-channel-forming synthetic peptide nanostructures. These analogs were designed as probes to gain insight about the mechanism by which self-assembling amphiphilic peptides interact with lipid membranes. Conformational studies demonstrated that the labeled analogs retain their propensity to adopt a strong helical conformation in 2,2,2-trifluoroethanol and lipid bilayers. Attenuated total reflectance results indicated that the fluorescent peptide nanostructures are under an incorporation equilibrium between two forms, adsorbed at the surface or incorporated within the bilayer, similar to their unlabeled counterparts. However, when using a HeLa mimicking membrane, the proportion o... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5618552 Sat, 24 Dec 2011 05:00:00 +0100 5618552 http://www.medworm.com/index.php?rid=5618551&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22257976%26dopt%3DAbstract Authors: Meunier A, Fulcrand R, Darchen F, Guille Collignon M, Lemaître F, Amatore C Abstract The microfabrication and successful testing of a series of three ITO (Indium Tin Oxide) microsystems for amperometric detection of cells exocytosis are reported. These microdevices have been optimized in order to simultaneously (i) enhance signal-to-noise ratios, as required electrochemical monitoring, by defining appropriate electrodes geometry and size, and (ii) provide surface conditions which allow cells to be cultured over during one or two days, through apposite deposition of a collagen film. The intrinsic electrochemical quality of the microdevices as well as the effect of different collagen treatments were assessed by investigating the voltammetric responses of two classical redox... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5618551 Sat, 24 Dec 2011 05:00:00 +0100 5618551 http://www.medworm.com/index.php?rid=5544480&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22197349%26dopt%3DAbstract Authors: Mimura S, Yamato T, Kamiyama T, Gekko K Abstract The evolution of structural fluctuations of proteins was examined by calculating the isothermal compressibility (β(T)) values of chicken lysozyme and its six evolutionary mutants at Thr40, Ile55, and Ser91 (a ternary mutant corresponding to bobwhite lysozyme) from their X-ray structures by normal-mode analysis at 300K. The β(T) values of the two extant lysozymes from chicken and bobwhite were 1.61 and 1.59Mbar(-1), respectively, but five other evolutionary mutants showed larger β(T) values of up to 2.17Mbar(-1). These results suggest that ancestral lysozymes exhibit larger volume fluctuations than extant ones, and hence that the molecular evolution of lysozymes has followed a nonneutral evolutionary pathway. The evolution... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5544480 Wed, 07 Dec 2011 05:00:00 +0100 5544480 http://www.medworm.com/index.php?rid=5544479&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22197350%26dopt%3DAbstract Authors: Beauchamp DL, Khajehpour M Abstract Salt ions affect protein stability in a variety of ways. In general, these effects have either been interpreted from a charge solvation/charge screening standpoint or they have been considered to be the result of ion-specific interactions with a particular protein. Recent theoretical work suggests that a major contribution to salt effects on proteins is through the interaction of salt ions that are located near the protein surface and their induced point image charges that are located in the low-dielectric protein cavity. These interactions form the basis of "salting-out" interactions. Salt ions induce an image charge of the same sign in the low dielectric protein medium. The interaction between the induced charge and its mirror charge i... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5544479 Fri, 02 Dec 2011 05:00:00 +0100 5544479 http://www.medworm.com/index.php?rid=5293631&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816534%26dopt%3DAbstract Authors: Kitagawa Y, Matsuda K, Hasegawa JY Abstract The excited states of the chlorophyll 6-mer in the photosystem II (PSII) reaction center (RC) were investigated theoretically using ab initio quantum chemical calculations, and the results are compared with those of the bacterial reaction center (bRC). A significant difference in the peak at the lowest energy in the absorption spectra arises from the structural asymmetry of the special pair (SP). The origin can be traced back to the structural difference in the CD helix. The low-lying excited states are characterized as a linear combination of the excited states of the chlorophyll monomers, which verifies the applicability of exciton theory. Analysis of the molecular interactions clearly explains the cause of the constructive/des... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5293631 Fri, 07 Oct 2011 22:26:33 +0100 5293631 http://www.medworm.com/index.php?rid=5293630&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21840115%26dopt%3DAbstract Authors: Boeckx B, Ramaekers R, Maes G Abstract A combined experimental matrix-isolation FT-IR and theoretical study has been performed to investigate the conformational behavior of N-acetylproline. The conformational landscape of N-acetylproline was explored using successively higher computational methods, i.e. HF, DFT(B3LYP) and finally MP2. The exploration resulted in 10 conformations with a relative energy difference smaller than 22kJ.mol(-1) at the HF/3-21G level of theory. These conformations led to six different conformations after DFT(B3LYP) optimizations. Further optimization at the MP2/6-31++G** level of theory resulted in the same six conformations, all of them with an energy difference smaller than 11.5kJ.mol(-1). One conformation with an intramolecular H-bond was found... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5293630 Fri, 07 Oct 2011 22:26:15 +0100 5293630 http://www.medworm.com/index.php?rid=5293629&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21962489%26dopt%3DAbstract Authors: Bonnist EY, Liebert K, Dryden DT, Jeltsch A, Jones AC Abstract The EcoRV DNA methyltransferase methylates the first adenine in the GATATC recognition sequence. It is presumed that methylation proceeds by a nucleotide flipping mechanism but no crystal structure is available to confirm this. A popular solution-phase assay for nucleotide flipping employs the fluorescent adenine analogue, 2-aminopurine (2AP), substituted at the methylation target site; a substantial increase in fluorescence intensity on enzyme binding indicates flipping. However, this appeared to fail for M.EcoRV, since 2AP substituted for the non-target adenine in the recognition sequence showed a much greater intensity increase than 2AP at the target site. This anomaly is resolved by recording the fluorescen... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5293629 Sat, 10 Sep 2011 04:00:00 +0100 5293629 http://www.medworm.com/index.php?rid=5272701&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21945664%26dopt%3DAbstract Authors: Powell LR, Dukes KD, Lammi RK Abstract One avenue for prevention and treatment of Alzheimer's disease involves inhibiting the aggregation of amyloid-β peptide (Aβ). Given the deleterious effects reported for Aβ dimers and trimers, it is important to investigate inhibition of the earliest association steps. We have employed quantized photobleaching of dye-labeled Aβ peptides to characterize four peptide-based inhibitors of fibrillogenesis and/or cytotoxicity, assessing their ability to inhibit association in the smallest oligomers (n=2-5). Inhibitors were tested at acidic pH and in the presence of zinc, conditions that may promote oligomerization in vivo. Distributions of peptide species were constructed by examining dozens of surface-tethered monomers and oligomers, on... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5272701 Thu, 08 Sep 2011 04:00:00 +0100 5272701 http://www.medworm.com/index.php?rid=5240379&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21924540%26dopt%3DAbstract Authors: Renthal R, Brancaleon L, Peña I, Silva F, Chen LY Abstract To probe structural changes that occur when a membrane protein is transferred from lipid bilayers to SDS micelles, a fragment of bacteriorhodopsin containing transmembrane helical segments A and B was studied by fluorescence spectroscopy, molecular dynamics (MD) simulation, and stopped flow kinetics. In lipid bilayers, Förster resonance energy transfer (FRET) was observed between tyrosine 57 on helix B and tryptophans 10 and 12 on helix A. FRET efficiency decreased substantially when the peptide was transferred to SDS. MD simulation showed no evidence for significant disruption of helix-helix interactions in SDS micelles. However, a cluster of water molecules was observed to form a hydrogen-bonded network with th... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5240379 Sat, 27 Aug 2011 04:00:00 +0100 5240379 http://www.medworm.com/index.php?rid=5240378&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21924541%26dopt%3DAbstract Authors: Winter PW, McPhee JT, Van Orden AK, Roess DA, Barisas BG Abstract We used fluorescence correlation spectroscopy to examine the binding of insulin, insulin-like growth factor 1 (IGF1) and anti-receptor antibodies to insulin receptors (IR) and IGF1 receptors (IGF1R) on individual 2H3 rat basophilic leukemia cells. Experiments revealed two distinct classes of insulin binding sites with K(D) of 0.11nM and 75nM, respectively. IGF1 competes with insulin for a portion of the low-affinity insulin binding sites with K(D) of 0.14nM and for the high-affinity insulin binding sites with K(D) of 10nM. Dissociation rate constants of insulin and IGF1 were determined to be 0.015min(-1) and 0.013min(-1), respectively, allowing estimation of ligand association rate constants. Combined, our r... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5240378 Tue, 23 Aug 2011 04:00:00 +0100 5240378 http://www.medworm.com/index.php?rid=5225574&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21920659%26dopt%3DAbstract Authors: Ghadami SA, Khodarahmi R, Ghobadi S, Ghasemi M, Pirmoradi S Abstract The misfolding and extracellular amyloid deposition of specific proteins are associated with a large family of human pathologies, often called protein conformational diseases. Despite the many efforts expended to characterize amyloid formation in vitro, there is no deep knowledge about the environment (in which aggregation occurs) as well as mechanism of this type of protein aggregation. Recently, β-lactoglobulin (β-lg) was driven toward amyloid aggregation under specific extreme conditions. In the present study, citraconylation was employed to neutralize the charges on accessible lysine residues of β-lg and different approaches such as turbidimetry, thermodynamic analysis, extrinsic fluorimetry and th... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5225574 Tue, 23 Aug 2011 04:00:00 +0100 5225574 http://www.medworm.com/index.php?rid=5215500&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21908094%26dopt%3DAbstract We report Ca(2+) oscillations in response to several stimuli in RTL-W1 cells and to a lesser extent in primary hepatocytes. Moreover, these Ca(2+) oscillations are amplitude-encoded in contrast to their mammalian counterpart. Bioinformatics and computational analysis were employed to identify key players of Ca(2+) signaling in fish and to determine likely causes for the experimentally observed differences between the Ca(2+) dynamics in fish cells compared to those in mammalian liver cells. PMID: 21908094 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5215500 Thu, 18 Aug 2011 04:00:00 +0100 5215500 http://www.medworm.com/index.php?rid=5187030&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21885181%26dopt%3DAbstract Authors: Gabellieri E, Bucciantini M, Stefani M, Cioni P Abstract The bacterial redox protein azurin has been shown to be able to enter into cancer cells and induce apoptosis by stabilizing p53. Although the formation of a complex between the two proteins has been demonstrated, little is known about their binding features. We investigated the interaction between the transcription activation domain of p53 (p53(1-63)) and Pseudomonas aeruginosa azurin using fluorescence and phosphorescence spectroscopic techniques. Trp phosphorescence lifetime measurements revealed conformational changes in azurin induced by the interaction with p53(1-63). Acrylamide quenching of Trp phosphorescence also indicated a significant increase in the overall flexibility of azurin upon binding to p53(1-63). ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5187030 Tue, 09 Aug 2011 23:00:00 +0100 5187030 http://www.medworm.com/index.php?rid=5171035&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21868145%26dopt%3DAbstract Authors: do Canto AM, Carvalho AJ, Ramalho JP, Loura LM Abstract T-20 (also known as enfuvirtide) is a fusion inhibitor peptide known to have some effectiveness in the control of progression of HIV infection by inhibiting the fusion of the HIV envelope with the target cell membrane. Recent results indicate that T-20 is able to interact with membranes in the liquid disordered state but not with membranes in an ordered state, which could be linked to its effectiveness. A detailed molecular picture of the interaction of these molecules with membranes is still lacking. To this effect, extensive molecular dynamics simulations (100ns) were carried out to investigate the interaction between T-20 and bilayers of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and POPC/cholesterol (1:1). Me... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5171035 Fri, 05 Aug 2011 23:00:00 +0100 5171035 http://www.medworm.com/index.php?rid=5138734&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21840114%26dopt%3DAbstract Authors: Casares-Atienza S, Weininger U, Cámara-Artigas A, Balbach J, Garcia-Mira MM Onconase is a member of the ribonuclease A superfamily currently in phase IIIb clinical trials as a treatment for malign mesothelioma due to its cytotoxic activity selective against tumor-cells. In this work, we have studied the equilibrium thermal unfolding of onconase using a combination of several structural and biophysical techniques. Our results indicate that at least one significantly populated intermediate, which implies the exposure of hydrophobic surface and significant changes in the environment around Trp3, occurs during the equilibrium unfolding process of this protein. The intermediate begins to populate at about 30° below the global unfolding temperature, reaching a maximum population o... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5138734 Sat, 23 Jul 2011 23:00:00 +0100 5138734 http://www.medworm.com/index.php?rid=5138750&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21840113%26dopt%3DAbstract Authors: Shea MA, Correia JJ, Brenowitz MD In 2011, the Gibbs Conference on Biothermodynamics will celebrate its 25th anniversary. Since the inaugural meeting in 1987, it has brought together laboratories that lived, breathed and argued about the molecular logic of macromolecular machines. The participants have a deep commitment to understanding the nature of physico-chemical forces that govern regulation of biological systems, and share a passion for applying linkage theory. The collective goal is to understand how ligand binding, subunit assembly and conformational change drive what we observe as physiological processes such as regulated transport, enzyme cascades, gene regulation, membrane permeability, viral infection, intracellular trafficking and folding of macromolecules. In thi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5138750 Wed, 20 Jul 2011 23:00:00 +0100 5138750 http://www.medworm.com/index.php?rid=5088456&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21807453%26dopt%3DAbstract Authors: Wako H, Endo S The conformational change of a protein upon ligand binding was examined by normal mode analysis (NMA) based on an elastic-network model (ENM) for a full-atom system using dihedral angles as independent variables. Specifically, we investigated the extent to which conformational change vectors of atoms from an apo form to a holo form of a protein can be represented by a linear combination of the displacement vectors of atoms in the apo form calculated for the lowest-frequency m normal modes (m=1, 2, …, 20). In this analysis, the latter vectors were best fitted to the former ones by the least-squares method. Twenty-two paired proteins in the holo and apo forms, including three dimer pairs, were examined. The results showed that, in most cases, the conformational ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5088456 Wed, 20 Jul 2011 23:00:00 +0100 5088456 http://www.medworm.com/index.php?rid=5088457&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21802827%26dopt%3DAbstract Authors: Takayama Y, Nakasako M The structures of proteins in crystals are fixed by molecular interactions with neighboring molecules, except in non-contacting flexible regions. Thus, it is difficult to imagine what conformational changes occur in solution. However, if molecular interactions can be changed by manipulating molecular packing in crystals, it may be possible to visualize conformational responses of proteins at atomic resolution by diffraction experiments. For this purpose, it is suitable to control the molecular packing in protein crystals by changing the volume of solvent channels through variation of the environmental relative humidity. Here, we studied conformational responses of hen egg white lysozyme (HEWL) in the tetragonal crystal by X-ray diffraction experiments us... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5088457 Tue, 12 Jul 2011 23:00:00 +0100 5088457 http://www.medworm.com/index.php?rid=5088458&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21802194%26dopt%3DAbstract Authors: Bell-Upp P, Robinson AC, Whitten ST, Wheeler EL, Lin J, Stites WE, E BG The general thermodynamic principles behind pH driven conformational transitions of biological macromolecules are well understood. What is less obvious is how they can be used to engineer pH switches in proteins. The acid unfolding of staphylococcal nuclease (SNase) was used to illustrate different factors that can affect pH-driven conformational transitions. Acid unfolding is a structural transition driven by preferential H(+) binding to the acid unfolded state (U) over the native (N) state of a protein. It is the result of carboxylic groups that titrate with more normal pK(a) values in the U state than in the N state. Acid unfolding profiles of proteins reflect a balance between electrostatic and non-ele... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5088458 Wed, 06 Jul 2011 23:00:00 +0100 5088458 http://www.medworm.com/index.php?rid=5088460&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21782315%26dopt%3DAbstract Authors: Danoff EJ, Fleming KG OmpA is one of only a few transmembrane proteins whose folding and stability have been investigated in detail. However, only half of the OmpA mass encodes its transmembrane β-barrel; the remaining sequence is a soluble domain that is localized to the periplasmic side of the outer membrane. To understand how the OmpA periplasmic domain contributes to the stability and folding of the full-length OmpA protein, we cloned, expressed, purified and studied the OmpA periplasmic domain independently of the OmpA transmembrane β-barrel region. Our experiments showed that the OmpA periplasmic domain exists as an independent folding unit with a free energy of folding equal to -6.2 (±0.1) kcalmol(-1) at 25°C. Using circular dichroism, we determined that the OmpA pe... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5088460 Tue, 05 Jul 2011 23:00:00 +0100 5088460 http://www.medworm.com/index.php?rid=5088459&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21782316%26dopt%3DAbstract In this study, the stability of these various CRP species in the presence of GuHCl was monitored by three spectroscopic techniques, namely, CD, tryptophan fluorescence and FT-IR which could provide data on the stability of α-helices and β-strands separately. Results of this study led to the following conclusions: 1. The α-helices can be grouped into two families with different stabilities. Mutations exert a differential effect on the stability of helices as demonstrated by a biphasic unfolding curve for the helices. 2. Regardless of the locations of mutations, the effects can be communicated to the other domain resulting in a perturbation of the stability of both domains, although the effects are more significantly expressed in the stability of the helices. 3. Although in an earlier stu... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5088459 Sat, 02 Jul 2011 23:00:00 +0100 5088459 http://www.medworm.com/index.php?rid=5038777&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21763060%26dopt%3DAbstract Authors: Gmajner D, Grabnar PA, Znidarič MT, Strus J, Sentjurc M, Ulrih NP The physicochemical properties of binary lipid mixtures of diether C(25,25) lipids and dipalmitoyl-L-α-phosphatidylcholine (DPPC) were studied using photon correlation, fluorescence and electron paramagnetic resonance spectroscopy, and transmission electron microscopy. These two types of lipids can be mixed at all molar ratios to form unilamellar and multilamellar liposomes. Fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatrien in mixed liposomes indicates that the abrupt changes in order parameter in the hydrophobic part of bilayer membranes made of DPPC lipids disappears with increasing mol%C(25,25) lipids. Electron paramagnetic resonance spectroscopy shows that at temperatures below 50°C, the interfacial... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038777 Wed, 29 Jun 2011 23:00:00 +0100 5038777 http://www.medworm.com/index.php?rid=5038776&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21764207%26dopt%3DAbstract Authors: Gray RD, Chaires JB Formation of DNA quadruplexes requires monovalent cation binding. To characterize the cation binding stoichiometry and linkage between binding and folding, we carried out KCl titrations of Tel22 (d[A(GGGTTA)(3)]), a model of the human telomere sequence, using a fluorescent indicator to determine [K(+)](free) and circular dichroism to assess the extent of folding. At [K(+)](free)=5mM (sufficient for >95% folding), the apparent binding stoichiometry is 3K(+)/Tel22; at [K(+)](free)=20mM, it increased to 8-10K(+)/Tel22. Thermodynamic analysis shows that at [K(+)](free)=5mM, K(+) binding contributes approximately -4.9kcal/mol for folding Tel22. The overall folding free energy is -2.4kcal/mol, indicating that there are energetically unfavorable contributions t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038776 Mon, 27 Jun 2011 23:00:00 +0100 5038776 http://www.medworm.com/index.php?rid=5038783&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21741753%26dopt%3DAbstract Authors: Rivolta I, Panariti A, Collini M, Lettiero B, D'Alfonso L, Sironi L, Miserocchi G, Chirico G We have measured in human alveolar cells the cytoplasmic distribution of the fluorophore coumarin-6 carried by Solid Lipid Nanoparticles (SLNs) and observed a perinuclear accumulation of the fluorescence that can be described by a single exponential growth along an ideal line joining the plasma membrane to the nuclear border and by a sigmoidal relationship as a function of time. Intracellular distribution was affected by lowering the temperature from 37 to 4°C and by the disruption of cytoskeleton by cytochalasin D, but it was minimally perturbed by the inhibition of ATP dependent molecular motors. A biophysical model was developed for an accumulation of loaded particles against a dif... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038783 Thu, 23 Jun 2011 23:00:00 +0100 5038783 http://www.medworm.com/index.php?rid=5038782&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21741754%26dopt%3DAbstract Authors: Niedzwiecka A, Lekka M, Nilsson P, Virtanen A Deadenylation is the initial and often rate-limiting step in the main pathways of eukaryotic mRNA decay. Poly(A)-specific ribonuclease (PARN) is a eukaryotic enzyme that efficiently degrades mRNA poly(A) tails. Structural and functional studies have shown that human PARN is composed of at least three functional domains, i.e. the catalytic nuclease domain and two RNA binding domains, the R3H and the RNA recognition motif (RRM), respectively. However, the complete structure of the full length protein is still unknown. We have investigated the global architecture of human PARN by atomic force microscopy (AFM) imaging in buffered milieu and report for the first time the dimensions of the full length protein at subnanometer resolution. ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038782 Thu, 23 Jun 2011 23:00:00 +0100 5038782 http://www.medworm.com/index.php?rid=5038781&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21742429%26dopt%3DAbstract In this study we examine if two Pol I family polymerases from evolutionarily distant organisms also differ in their preferences for replication versus repair substrates. The DNA binding preferences of Klenow and Klentaq DNA polymerases, from Escherichia coli and Thermus aquaticus respectively, have been studied using a fluorescence competition binding assay. Klenow polymerase binds primed-template DNA (the replication substrate) with up to 50× higher affinity than it binds to nicked DNA, DNA with a 2 base single-stranded gap, blunt-ended DNA, or to a DNA end with a 3' overhang. In contrast, Klentaq binds all of these DNAs almost identically, indicating that Klenow has a stronger ability to discriminate between replication and repair substrates than Klentaq. In contrast, both polymerases b... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038781 Thu, 23 Jun 2011 23:00:00 +0100 5038781 http://www.medworm.com/index.php?rid=5038778&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21757287%26dopt%3DAbstract Authors: Evans TI, Hell JW, Shea MA Calmodulin (CaM) binding to the intracellular C-terminal tail (CTT) of the cardiac L-type Ca(2+) channel (Ca(V)1.2) regulates Ca(2+) entry by recognizing sites that contribute to negative feedback mechanisms for channel closing. CaM associates with Ca(V)1.2 under low resting [Ca(2+)], but is poised to change conformation and position when intracellular [Ca(2+)] rises. CaM binding Ca(2+), and the domains of CaM binding the CTT are linked thermodynamic functions. To better understand regulation, we determined the energetics of CaM domains binding to peptides representing pre-IQ sites A(1588), and C(1614) and the IQ motif studied as overlapping peptides IQ(1644) and IQ'(1650) as well as their effect on calcium binding. (Ca(2+))(4)-CaM bound to all four ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038778 Thu, 23 Jun 2011 23:00:00 +0100 5038778 http://www.medworm.com/index.php?rid=5038779&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21752532%26dopt%3DAbstract In this report, we adopt an atomistic molecular dynamics (MD) simulation approach, comparing the complexation of 21-bp siRNA with low-generation polyamidoamine (PAMAM) dendrimers (G0 and G1) at both neutral and acidic pHs, the latter of which mimics the degradative environment within maturing 'late-endosomes'. Our simulations reveal that the time taken for the dendrimer-gene complex (dendriplex) to reach equilibrium is appreciably longer at low pH and this is accompanied by more compact packaging of the dendriplex, as compared to simulations performed at neutral pH. We also note larger absolute values of calculated binding free energies of the dendriplex at low pH, indicating a higher dendrimer-nucleic acid affinity in comparison with neutral pH. These novel simulations provide a more deta... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038779 Tue, 21 Jun 2011 23:00:00 +0100 5038779 http://www.medworm.com/index.php?rid=5038775&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21764506%26dopt%3DAbstract Authors: Vieux EF, Barrick D Mapping the stability distributions of proteins in their native folded states provides a critical link between structure, thermodynamics, and function. Linear repeat proteins have proven more amenable to this kind of mapping than globular proteins. C-terminal deletion studies of YopM, a large, linear leucine-rich repeat (LRR) protein, show that stability is distributed quite heterogeneously, yet a high level of cooperativity is maintained [1]. Key components of this distribution are three interfaces that strongly stabilize adjacent sequences, thereby maintaining structural integrity and promoting cooperativity. To better understand the distribution of interaction energy around these critical interfaces, we studied internal (rather than terminal) deletions o... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038775 Tue, 21 Jun 2011 23:00:00 +0100 5038775 http://www.medworm.com/index.php?rid=5038780&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21752531%26dopt%3DAbstract Authors: Maiti S, Kankia B, Khutsishvili I, Marky LA We use a variety of biophysical techniques to determine thermodynamic profiles, including hydration, for the unfolding of DNA stem-loop motifs (hairpin, a three-way junction and a pseudoknot) and their interaction with netropsin and random cationic copolymers. The unfolding thermodynamic data show that their helix-coil transition takes place according to their melting domains or sequences of their stems. All hairpins adopted the B-like conformation and their loop(s) contribute with an immobilization of structural water. The thermodynamic data of netropsin binding to the (5')-AAATT-(3')/TTTAA site of each hairpin show affinities of ~10(6-7)M(-1), 1:1 stoichiometries, exothermic enthalpies of -7 to -12kcal mol(-1) (-22kcal mol(-1) for ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038780 Mon, 20 Jun 2011 23:00:00 +0100 5038780 http://www.medworm.com/index.php?rid=5038784&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21715082%26dopt%3DAbstract In this study, the correlation between thermodynamic measurements of in vitro DNA binding affinity with in vivo transcription repression was investigated for two transcription repressors. In the first system, which comprised an engineered LacI/GalR homolog, mutational changes altered the equilibrium constant for binding DNA. Changes correlated with altered repression, but estimates of in vivo repressor concentration suggest a ≥25-fold discrepancy with in vitro conditions. In the second system, changes in ligand binding to BirA altered dimerization and subsequent DNA occupancy. Again, these changes correlate with altered in vivo repression, but comparison with in vitro measurements reveals a ~10-fold discrepancy. Further analysis of each system suggests that the observed discrepancies bet... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038784 Tue, 14 Jun 2011 23:00:00 +0100 5038784 http://www.medworm.com/index.php?rid=5038785&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21704443%26dopt%3DAbstract The objective was to characterize the structure of surfactant films using endogenous rat surfactant. Solid-support surfactant films, at different surface pressures, were obtained using a Langmuir balance and were analyzed using atomic force microscopy. The results showed a lipid film structure with three distinct phases: liquid expanded, liquid ordered and liquid condensed. The area covered by the liquid condensed domains increased as surface pressure increased. The presence of liquid ordered phase within these structures correlated with the cholesterol content. At a surface pressure of 50mN/m, stacks of bilayers appeared. Several structural details of these films differ from previous observations made with goat and exogenous surfactants. Overall, the data indicate that surfactant films de... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038785 Sun, 12 Jun 2011 23:00:00 +0100 5038785 http://www.medworm.com/index.php?rid=5038787&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21684672%26dopt%3DAbstract Authors: Wrabl JO, Gu J, Liu T, Schrank TP, Whitten ST, Hilser VJ It is now well-known that proteins exist at equilibrium as ensembles of conformational states rather than as unique static structures. Here we review from an ensemble perspective important biological effects of such spontaneous fluctuations on protein allostery, function, and evolution. However, rather than present a thorough literature review on each subject, we focus instead on connecting these phenomena through the ensemble-based experimental, theoretical, and computational investigations from our laboratory over the past decade. Special emphasis is given to insights that run counter to some of the prevailing ideas that have emerged over the past 40years of structural biology research. For instance, when proteins are ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038787 Mon, 30 May 2011 23:00:00 +0100 5038787 http://www.medworm.com/index.php?rid=5038786&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21703752%26dopt%3DAbstract Authors: Cole JL, Correia JJ, Stafford WF For 25years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980s this approach was extended to the use of sedimentation veloc... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=5038786 Thu, 26 May 2011 23:00:00 +0100 5038786 http://www.medworm.com/index.php?rid=4945795&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21652139%26dopt%3DAbstract Authors: Topol I, Collins J, Savitsky A, Nemukhin A Computational methods of quantum chemistry are used to characterize structures and vertical excitation energies of the S(0)-S(1) optical transitions in the chromophore binding pockets of the red fluorescent proteins DsRed and of its artificial mutant mCherry. As previously shown, optimizing the equilibrium geometry configurations with B3LYP density functional theory, followed by ZINDO calculations of the electronic excitations, yields positions of the optical bands in good agreement with experimental data. These large scale quantum calculations elucidate the role of the hydrogen bonded network as well as point mutations in the absorption spectra of the DsRed and mCherry proteins. The effect of an external electric field applied to the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945795 Thu, 26 May 2011 23:00:00 +0100 4945795 http://www.medworm.com/index.php?rid=4945794&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21652140%26dopt%3DAbstract Authors: Wang M, Jiji RD The mechanism by which flavonoids prevent formation of amyloid-β (Aβ) fibrils, as well as how they associate with non-fibrillar Aβ is still unclear. Fresh, un-oxidized myricetin exhibited excitation and emission fluorescence maxima at 481 and 531nm, respectively. Introduction of either Aβ(1-42) or Aβ(25-40) resulted in a fluorescence decrease, when measured at 481nm, suggesting formation of a myricetin-Aβ complex. Circular dichroism (CD) and ultraviolet resonance Raman (UVRR) studies indicate that the association of myricetin with the Aβ peptide or its hydrophobic fragment, Aβ(25-40), leads to subtle changes in each peptide's conformation. Aβ(25-40) formed amyloid fibrils at a similar rate, when compared to the full-length peptide, Aβ(1-42), using thi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945794 Thu, 26 May 2011 23:00:00 +0100 4945794 http://www.medworm.com/index.php?rid=4945793&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21665349%26dopt%3DAbstract Authors: Bhattacharjee N, Biswas P Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945793 Thu, 26 May 2011 23:00:00 +0100 4945793 http://www.medworm.com/index.php?rid=4945791&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21665351%26dopt%3DAbstract Authors: Murciano-Calles J, Cobos ES, Mateo PL, Camara-Artigas A, Martinez JC Equilibrium unfolding at neutral pH of the third PDZ domain of PSD95 is well described by the presence of a partly unfolded intermediate that presents association phenomena. After some days' incubation annular and fibrillar structures form from the oligomers. At pH values below 3, however, differential scanning calorimetry shows that PDZ3 seems to unfold under a two-state scheme. Kinetic measurements followed by dynamic light scattering, ThT and ANS fluorescence reveal that the misfolding pathway still exists despite the absence of any populated intermediates and shows an irreversible assembling of the supramacromolecular structures as well as an appreciable lag-phase, contrary to what is found in similar exp... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945791 Thu, 26 May 2011 23:00:00 +0100 4945791 http://www.medworm.com/index.php?rid=4945790&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21676530%26dopt%3DAbstract Authors: Bolean M, Simão AM, Favarin BZ, Millán JL, Ciancaglini P Tissue-nonspecific alkaline phosphatase (TNAP) is associated to the plasma membrane via a GPI-anchor and plays a key role in the biomineralization process. In plasma membranes, most GPI-anchored proteins are associated with "lipid rafts", ordered microdomains enriched in sphingolipids, glycosphingolipids and cholesterol. In order to better understand the role of lipids present in rafts and their interactions with GPI-anchored proteins, the insertion of TNAP into different lipid raft models was studied using dipalmitoylphosphatidylcholine (DPPC), cholesterol (Chol), sphingomyelin (SM) and ganglioside (GM1). Thus, the membrane models studied were binary systems (9:1 molar ratio) containing DPPC:Chol, DPPC:SM and DPPC:GM1... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945790 Thu, 26 May 2011 23:00:00 +0100 4945790 http://www.medworm.com/index.php?rid=4945792&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21665350%26dopt%3DAbstract Authors: Henzl MT, Reed MA, Tan A Phl p 7 exhibits atypical conformational stability and a diminutive denaturational heat capacity increment, ΔC(p). Because exposure of apolar surface largely dictates the magnitude of ΔC(p), a depressed value could signify an unusually compact unfolded state. The volume of the denatured state ensemble (DSE) is evidently inversely correlated with mean hydrophobicity [Pace et al., Protein Sci. 19 (2010) 929-943]. Interestingly, apolar residues replace more polar ones at four positions in Phl p 7. We herein examine the consequences of replacing those residues with the corresponding ones from Bra n 1, a related isoform. All four mutations - M4H, L21A, I60T, and C63A - destabilize Phl p 7. Our analysis suggests that the DSE of Phl p 7 is indeed highly com... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945792 Wed, 25 May 2011 23:00:00 +0100 4945792 http://www.medworm.com/index.php?rid=4945796&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21645959%26dopt%3DAbstract Authors: Schipper JL, Mackenzie SH, Sharma A, Clark AC The dimer interface of caspase-3 contains a bifunctional allosteric site in which the enzyme can be activated or inactivated, depending on the context of the protein. In the mature caspase-3, the binding of allosteric inhibitors to the interface results in an order-to-disorder transition in the active site loops. In procaspase-3, by contrast, the binding of allosteric activators to the interface results in a disorder-to-order transition in the active site. We have utilized the allosteric site to identify a small molecule activator of procaspase and to characterize its binding to the protease. The data suggest that an efficient activator must stabilize the active conformer of the zymogen by expelling the intersubunit linker from the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945796 Tue, 24 May 2011 23:00:00 +0100 4945796 http://www.medworm.com/index.php?rid=4945797&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21640469%26dopt%3DAbstract Authors: Martin DJ, Ramirez-Alvarado M Amyloid formation occurs when a precursor protein misfolds and aggregates, forming a fibril nucleus that serves as a template for fibril growth. Glycosaminoglycans are highly charged polymers known to associate with tissue amyloid deposits that have been shown to accelerate amyloidogenesis in vitro. We studied two immunoglobulin light chain variable domains from light chain amyloidosis patients with 90% sequence identity, analyzing their fibril formation kinetics and binding properties with different glycosaminoglycan molecules. We find that the less amyloidogenic of the proteins shows a weak dependence on glycosaminoglycan size and charge, while the more amyloidogenic protein responds only minimally to changes in the glycosaminoglycan. These glyc... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4945797 Tue, 17 May 2011 23:00:00 +0100 4945797 http://www.medworm.com/index.php?rid=4897129&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21621902%26dopt%3DAbstract Authors: Sztiller-Sikorska M, Heyduk E, Heyduk T Bacterial RNA polymerase (RNAP) interacts with conserved -10 and -35 promoter elements to recognize the promoter and to form an open complex in which DNA duplex around transcription start site melts. Using model DNA constructs (fork junction DNA) that mimic DNA structure found in the open complex we observed that the consequences of mutations in -10 promoter element for RNAP binding exhibited a striking dependence on the presence or absence of a functional -35 promoter element. A role of spacer DNA (a non-conserved DNA sequence connecting -10 and -35 promoter elements) in this phenomenon was probed with a series of fork junction DNA constructs containing perturbations to the spacer DNA. In the absence of a physical connection between the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897129 Thu, 12 May 2011 23:00:00 +0100 4897129 http://www.medworm.com/index.php?rid=4897128&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21621903%26dopt%3DAbstract This study describes experimental folding/unfolding equilibrium and kinetic studies of the engineered protein Ubq-UIM, consisting of ubiquitin (Ubq) fused to the sequence of the ubiquitin interacting motif (UIM) via a short linker. Urea-induced folding/unfolding profiles of Ubq-UIM were monitored by far-UV circular dichroism and fluorescence spectroscopies and compared to those of the isolated Ubq domain. It was found that the equilibrium data for Ubq-UIM is inconsistent with a two-state model. Analysis of the kinetics of folding shows similarity in the folding transition state ensemble between Ubq and Ubq-UIM, suggesting that formation of Ubq domain is independent of UIM. The major contribution to the stabilization of Ubq-UIM, relative to Ubq, was found to be in the rates of unfolding. Mo... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897128 Thu, 12 May 2011 23:00:00 +0100 4897128 http://www.medworm.com/index.php?rid=4897127&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21624765%26dopt%3DAbstract Authors: Sharp KA Allostery, the modulation of function of a protein at one site by the binding of a ligand at a different site, is a property of many proteins. Two kinetically distinct models have been proposed: i) The induced fit model in which the ligand binds to the protein and then induces the conformational change. ii) The population selection model, in which the protein spontaneously undergoes a conformational change, which is then 'captured' by the ligand. Using measured kinetic constants for the lac repressor the contribution of population selection vs. induced dissociation is quantified by simulating the kinetics of allostery. At very low inducer concentration, both mechanisms contribute significantly. Total induction, though, is small under these conditions. At increasing le... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897127 Wed, 11 May 2011 23:00:00 +0100 4897127 http://www.medworm.com/index.php?rid=4897126&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21636209%26dopt%3DAbstract Authors: Kozlov AG, Lohman TM We have previously shown that formation of a 1:1 fully wrapped complex of Escherichia coli SSB tetramer with (dT)(70) displays a temperature-dependent sign reversal of the binding heat capacity (ΔC(P)). Here we examine SSB binding to shorter oligodeoxynucleotides ((dX)(35)) to probe whether this effect requires binding of one or two (dX)(35) molecules per SSB tetramer. We find that the ΔC(P) for the first molecule of (dX)(35) is always negative. However, a sign reversal of ΔC(P) from negative to positive occurs with increasing temperature for binding of the second (dX)(35). This striking behavior of ΔC(P) for the second (dX)(35) appears linked to conformational changes within the ssDNA-SSB complex that are required to form a fully wrapped (SSB)(65) bin... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897126 Wed, 11 May 2011 23:00:00 +0100 4897126 http://www.medworm.com/index.php?rid=4897124&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21636210%26dopt%3DAbstract Authors: Banik SD, Nandi N The relation between the conservation of active site residues and the molecular mechanism of aminoacylation reaction is an unexplored problem. In the present paper, the influences of the conserved active site residues on the reaction mechanism as well as the electrostatic potential near the reaction center are analyzed for Histidyl tRNA synthetase from Escherichia coli, Thermus thermophilus and Staphylococcus aureus. While the primary structures show both convergence as well as divergence, the secondary level structures of the active sites of the three species show considerable conservation in the respective structural organizations. The conserved active site residues near the reaction center, which have a major role in the reaction mechanism and catalysis, r... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897124 Wed, 11 May 2011 23:00:00 +0100 4897124 http://www.medworm.com/index.php?rid=4897136&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605933%26dopt%3DAbstract Authors: Sassi P, Giugliarelli A, Paolantoni M, Morresi A, Onori G The unfolding of hen egg-white lysozyme dissolved both in D(2)O and CH(3)CH(2)OD/D(2)O was studied by Fourier Transform Infrared (FTIR) absorption spectroscopy at different protein concentrations. A detailed description of the local and global rearrangement of the secondary structure upon a temperature increase, in the range 295 to 365K, was obtained through the analysis of the amide I band. Thermodynamic parameters for the melting, and the effect of the co-solvent in determining a change in thermal stability of the protein were evaluated. The protein-protein interactions were also followed as a function of temperature: a strong dependence of the cluster stability and aggregation yield on the solvent composition was obs... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897136 Thu, 05 May 2011 23:00:00 +0100 4897136 http://www.medworm.com/index.php?rid=4897134&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605935%26dopt%3DAbstract Authors: Zhang R, Xiao T, Hou Z The effect of internal noise in a delayed circadian oscillator is studied by using both chemical Langevin equations and stochastic normal form theory. It is found that internal noise can induce circadian oscillation even if the delay time τ is below the deterministic Hopf bifurcation τ(h). We use signal-to-noise ratio (SNR) to quantitatively characterize the performance of such noise induced oscillations and a threshold value of SNR is introduced to define the so-called effective oscillation. Interestingly, the τ-range for effective stochastic oscillation, denoted as Δτ(EO), shows a bell-shaped dependence on the intensity of internal noise which is inversely proportional to the system size. We have also investigated how the rates of synthesis and de... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897134 Thu, 05 May 2011 23:00:00 +0100 4897134 http://www.medworm.com/index.php?rid=4897130&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21621319%26dopt%3DAbstract Authors: Nyarko A, Hall J, Hall A, Hare M, Kremerskothen J, Barbar E A highly conserved and ubiquitous protein known as LC8 binds over twenty different partners, characteristic of a molecular hub (Barbar, 2008 Biochemistry, 47, 503-508). Structural studies of LC8 complexes with binding partners having diverse recognition sequences show that the same binding groove of LC8 accommodates the various binding motifs. Here we use thermodynamics and dynamics measurements of LC8 complexes to group LC8 binding partners in two categories: those whose binding is enthalpically driven and those that are entropically favored. Peptides that are enthalpically driven completely silence the millisecond-microsecond relaxation signal, suggesting a significant rigidifying of the binding groove, while peptid... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897130 Thu, 05 May 2011 23:00:00 +0100 4897130 http://www.medworm.com/index.php?rid=4897135&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605934%26dopt%3DAbstract Authors: Khrapunov S, Brenowitz M MfpA from Mycobacterium tuberculosis is a founding member of the pentapeptide repeat class of proteins (PRP) that is believed to confer bacterial resistance to the drug fluoroquinolone by mimicking the size, shape and surface charge of duplex DNA. We show that phenylalanine side chain stacking stabilizes the N-terminus of MfpA's pentapeptide thus extending the DNA mimicry analogy. The Lumry-Eyring model was applied to multiple spectral measures of MfpA denaturation revealing that the MfpA dimer dissociates to monomers which undergo a structural transition that leads to aggregation. MfpA retains high secondary and tertiary structure content under denaturing conditions. Dimerization stabilizes MfpA's pentapeptide repeat fold. The high Arrhenius activatio... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897135 Wed, 04 May 2011 23:00:00 +0100 4897135 http://www.medworm.com/index.php?rid=4897164&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21601346%26dopt%3DAbstract Authors: Jang YJ, Yeo GY, Park B, Kim SK The binding modes of the [Ru(II)(1,10-phenanthroline)(L(1)L(2)) dipyrido[3,2-a:2',3'-c]phenazine](2+) {[Ru(phen)(py) Cl dppz](+) (L(1)=Cl, L(2)=pyridine) and ([Ru(phen)(py)(2)dppz](2+) (L(1)=L(2)=pyridine)} to native DNA is compared to that of the [Ru(II)(1,10-phenanthroline)(2)dipyrido[3,2-a:2',3'-c]phenazine](2+) complex ([Ru(phen)(2)dppz](2+)) by various spectroscopic and hydrodynamic methods including electric absorption, linear dichroism (LD), fluorescence spectroscopy, and viscometric titration. All measured properties, including red-shift and hypochromism in the dppz absorption band, nearly perpendicular molecular plane of the dppz ligand with respect to the local DNA helix axis, prohibition of the ethidium binding, the light switch effec... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897164 Sat, 30 Apr 2011 23:00:00 +0100 4897164 http://www.medworm.com/index.php?rid=4897154&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21601347%26dopt%3DAbstract Authors: Jezewska MJ, Szymanski MR, Bujalowski W Interactions of the polymerase X from the African Swine Fever Virus with the ssDNA have been studied, using quantitative fluorescence titration and fluorescence resonance energy transfer techniques. The primary DNA-binding subsite of the enzyme, independent of the DNA conformation, is located on the C-terminal domain. Association of the bound DNA with the catalytic N-terminal domain finalizes the engagement of the total DNA-binding site of the enzyme and induces a large topological change in the structure of the bound ssDNA. The free energy of binding includes a conformational transition of the protein. Large positive enthalpy changes accompanying the ASFV pol X-ssDNA association indicate that conformational changes of the complex are in... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897154 Wed, 27 Apr 2011 23:00:00 +0100 4897154 http://www.medworm.com/index.php?rid=4897143&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605932%26dopt%3DAbstract Authors: Jezewska MJ, Szymanski MR, Bujalowski W Kinetic mechanism of the ssDNA recognition by the polymerase X of African Swine Fever Virus (ASFV) and energetics of intermediate formations have been examined, using the fluorescence stopped-flow method. The association is a minimum three-step processThe nucleic acid makes the initial contact through the C-terminal domain, which generates most of the overall ΔG°. In the second step the nucleic acid engages the N-terminal domain, assuming the bent structure. In equilibrium, the complex exists in at least two different states. Apparent enthalpy and entropy changes, characterizing formations of intermediates, reflect association of the DNA with the C-terminal domain and gradual engagement of the catalytic domain by the nucleic acid. The ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4897143 Wed, 27 Apr 2011 23:00:00 +0100 4897143 http://www.medworm.com/index.php?rid=4851039&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21550711%26dopt%3DAbstract Authors: Wills PR, Winzor DJ Theory is developed for the characterization of protein interactions by spectral techniques, where the constraints of constant temperature and pressure demand that thermodynamic activity be defined on the molal concentration scale. The customary practice of defining the equilibrium constant (K) on a molar basis is accommodated by developing expressions to convert those experimental values (K(molar)) to their thermodynamically more rigorous counterparts (K(molal)). Such procedures are illustrated by reanalysis of published results for the effects of molecular crowding agents on the isomerisation of α-chymotrypsin and reversible complex formation between catalase and superoxide dismutase. Although those reanalyses have led to only minor refinements of the qu... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4851039 Mon, 18 Apr 2011 23:00:00 +0100 4851039 http://www.medworm.com/index.php?rid=4851038&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21550712%26dopt%3DAbstract Authors: Galburt EA, Parrondo JM, Grill SW Molecular motors can exhibit Brownian ratchet or power stroke mechanisms. These mechanistic categories are related to transition state position: An early transition state suggests that chemical energy is stored and then released during the step (stroke) while a late transition state suggests that the release of chemical energy rectifies thermally activated motion that has already occurred (ratchet). Cellular RNA polymerases are thought to be ratchets that can push each other forward to reduce pausing during elongation. Here, by constructing a two-dimensional energy landscape from the individual landscapes of active and backtracked enzymes, we identify a new pushing mechanism which is the result of a saddle trajectory that arises in the two-dim... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4851038 Fri, 15 Apr 2011 23:00:00 +0100 4851038 http://www.medworm.com/index.php?rid=4851040&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21550710%26dopt%3DAbstract Authors: Yi M, Zhao Q, Tang J, Wang C It is known that Ca(2+) signal regulates mitogen-activated protein kinase (MAPK) cascade by a central Ras protein in GTPase-cycle. Therefore, we construct an integrated theoretical model comprising Ca(2+) oscillations, GTPase-cycle and MAPK cascade modules sequentially. Meanwhile, based on multiple feedback regulations in MAPK cascade, three operation modes of this model are introduced. An extended version of this model is further built when spatial heterogeneity is involved. These models allow us to investigate the very interesting and broad question about the effects of Ca(2+) oscillations on the activation of MAPK cascade in both the homogeneous and heterogeneous systems. When the Li-Rinzel model is adopted to simulate endogenous Ca(2+) oscillat... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4851040 Tue, 12 Apr 2011 23:00:00 +0100 4851040 http://www.medworm.com/index.php?rid=4797699&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21531495%26dopt%3DAbstract Authors: Bosisio C, Quercioli V, Chirico G, D'Alfonso L, Bettati S, Raboni S, Campanini B, Collini M We have used fluorescence spectroscopy techniques such as fluorescence correlation spectroscopy and fluorescence anisotropy decay on a wide time range, from nanoseconds to seconds, to investigate the unfolding kinetics induced by guanidinium chloride of GFPMut2 and its point mutation H148G, which has proved to be relevant for GFP photochemistry and photophysics. The mutation affects the unfolding kinetics of GFP leading to a much faster process at alkaline pH values, where protonation dynamics is negligible, that can be ascribed to a twofold role of His148, either as a proton shutter towards the chromophore and as a conformation stabiliser. For both mutants a soft region located near be... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4797699 Tue, 12 Apr 2011 23:00:00 +0100 4797699 http://www.medworm.com/index.php?rid=4797701&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21530061%26dopt%3DAbstract Authors: Vitalis A, Pappu RV Polyglutamine aggregation is associated with neurodegeneration in nine different disorders. The effects of polyglutamine length and peptide concentration on the kinetics of aggregation were previously analyzed using a homogeneous nucleation model that assumes the presence of a single bottleneck along the free energy profile G(n), where n denotes the number of polyglutamine molecules. The observation of stable, soluble oligomers as intermediates along aggregation pathways is refractory to the assumptions of homogeneous nucleation. Furthermore, the analysis of in vitro kinetic data using a specific variant of homogeneous nucleation leads to confounding observations such as fractional and/or negative values for estimates of the critical nucleus size. Here, we ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4797701 Mon, 11 Apr 2011 23:00:00 +0100 4797701 http://www.medworm.com/index.php?rid=4797700&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21530062%26dopt%3DAbstract In this study, isothermal titration calorimetry was used to probe the binding energetics of G-site (glutathione and glutathione sulfonate) and H-site (ethacrynic acid) ligands to wild-type and a Y9F mutant of human glutathione transferase A1-1. Although previous studies have reported a favourable entropic component to the binding of conjugates occupying both sites, our data reveal that ligand binding is enthalpically driven when either the G- or H-site is occupied independently. Also, heat capacity changes demonstrate that α9 is fully localised by H-site but not G-site occupation. The Tyr-9 hydroxyl group contributes significantly to ligand binding energetics, although the effect differs between the two binding sites. G-site binding is made slightly enthalpically more favourable and entro... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4797700 Mon, 11 Apr 2011 23:00:00 +0100 4797700 http://www.medworm.com/index.php?rid=4797698&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21536369%26dopt%3DAbstract Authors: Pozzi N, Chen R, Chen Z, Bah A, Di Cera E Binding of Na(+) to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na(+) is weak due to large heat capacity and enthalpy changes associated with binding, and the K(d)=80mM ensures only 64% saturation of the site at the concentration of Na(+) in the blood (140mM). Residues controlling Na(+) binding and activation have been identified. Yet, attempts to improve the interaction of Na(+) with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4797698 Mon, 11 Apr 2011 23:00:00 +0100 4797698 http://www.medworm.com/index.php?rid=4797703&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21514034%26dopt%3DAbstract Authors: Lee KH, Kuczera K, Holl MM We have carried out stochastic boundary molecular dynamics simulations to estimate free energy changes for substitutions of Gly with Val, Arg and Trp residues in a collagen-like peptide. The relative free energy change differences of mutants containing a Val, an Arg and a Trp relative to the wild type are 5.7, 8.1 and 9.5kcal/mol, respectively. The corresponding free energy change differences of mutants containing two mutated residues are on average 7.6, 10.5 and 14.7kcal/mol, respectively. We show that the free energy change differences are correlated with the severity of OI from statistical analysis and mechanical properties of the individual tropocollagen molecules. This simulation result indicates an atomistic-level mechanistic understanding of t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4797703 Thu, 07 Apr 2011 23:00:00 +0100 4797703 http://www.medworm.com/index.php?rid=4797702&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21514036%26dopt%3DAbstract Authors: Sasamori E, Kato M, Maki K, Tagawa Y, Hanyu Y We studied the role of the 2 salt bridges (Asp143-Arg147 and Asp146-Arg150) in helix 1 of mouse prion protein (PrP) on the formation of the complex between PrP and the monoclonal antibody T2. We introduced 6 charge-changing mutations to the amino acid residues associated with the salt bridges. Analysis of the circular dichroism spectra of the mutant PrPs showed that the salt bridge mutations did not change the secondary structures. We analyzed the kinetics of the association and dissociation of the PrPs with the T2 antibody. The results showed that the association kinetics were not significantly different among the variants except Arg150Lys, while the dissociation rate of the neutralized-charge variants was 2 orders of magnitude hi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4797702 Thu, 07 Apr 2011 23:00:00 +0100 4797702 http://www.medworm.com/index.php?rid=4744946&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21482020%26dopt%3DAbstract Authors: Scipioni A, De Santis P In eukaryotic genomes, nucleosomes are responsible for packaging DNA and controlling gene expression. For this reason, an increasing interest is arising on computational methods capable of predicting the nucleosome positioning along genomes. In this review we describe and compare bioinformatic and physical approaches adopted to predict nucleosome occupancy along genomes. Computational analyses attempt at decoding the experimental nucleosome maps of genomes in terms of certain dinucleotide step periodicity observed along DNA. Such investigations show that highly significant information about the occurrence of a nucleosome along DNA is intrinsic in certain features of the sequence suggesting that DNA of eukaryotic genomes encodes nucleosome organization. ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4744946 Wed, 06 Apr 2011 23:00:00 +0100 4744946 http://www.medworm.com/index.php?rid=4744945&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21511390%26dopt%3DAbstract Authors: Reyes-Caballero H, Campanello GC, Giedroc DP Prokaryotic organisms have evolved the capacity to quickly adapt to a changing and challenging microenvironment in which the availability of both biologically required and non-essential transition metal ions can vary dramatically. In all bacteria, a panel of metalloregulatory proteins controls the expression of genes encoding membrane transporters and metal trafficking proteins that collectively manage metal homeostasis and resistance. These "metal sensors" are specialized allosteric proteins, in which the direct binding of a specific or small number of "cognate" metal ion(s) drives a conformational change in the regulator that allosterically activates or inhibits operator DNA binding, or alternatively, distorts the promoter structu... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4744945 Mon, 04 Apr 2011 23:00:00 +0100 4744945 http://www.medworm.com/index.php?rid=4690836&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21458909%26dopt%3DAbstract Authors: Harris RC, Bredenberg JH, Silalahi AR, Boschitsch AH, Fenley MO The predictions of the derivative of the electrostatic binding free energy of a biomolecular complex, ΔG(el), with respect to the logarithm of the 1:1 salt concentration, d(ΔG(el))/d(ln[NaCl]), SK, by the Poisson-Boltzmann equation, PBE, are very similar to those of the simpler Debye-Hückel equation, DHE, because the terms in the PBE's predictions of SK that depend on the details of the dielectric interface are small compared to the contributions from long-range electrostatic interactions. These facts allow one to obtain predictions of SK using a simplified charge model along with the DHE that are highly correlated with both the PBE and experimental binding data. The DHE-based model developed here, which was de... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4690836 Wed, 30 Mar 2011 23:00:00 +0100 4690836 http://www.medworm.com/index.php?rid=4690837&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21458141%26dopt%3DAbstract Authors: Shanmugam G, Phambu N, Polavarapu PL VP1 peptide, an active domain of m-calpain enzyme with antimicrobial activity is found to undergo an unusual conformational transition in trifluoroethanol (TFE) solvent. The nature of, and time dependent variations in, circular dichroism associated with the amide I vibrations, suggest that VP1 undergoes self-aggregation forming anti-parallel β-sheet structure in TFE. Transmission electron micrograph (TEM) images revealed that β-sheet aggregates formed by VP1 possess fibril-like assemblies. PMID: 21458141 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4690837 Tue, 29 Mar 2011 23:00:00 +0100 4690837 http://www.medworm.com/index.php?rid=4690841&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21435774%26dopt%3DAbstract Authors: Kelley S, Boroda S, Musier-Forsyth K, Kankia BI Short guanine-rich sequences have a tendency to form quadruplexes that are stabilized by G-quartets with specific cation coordination. Quadruplexes are part of telomeres at the ends of chromosomes and play an important role in the regulation of gene expression. In addition, there is a strong interest in the therapeutic and biotechnological potential of quadruplex oligonucleotides. The HIV-integrase aptamer, d(GGGT)(4), demonstrated unusually favorable van't Hoff thermodynamics, and based on NMR studies the aptamer was proposed to fold into an antiparallel structure. Here we probed an apparent discrepancy between the NMR structure and the quadruplex topology suggested by circular dichroism (CD). Systematic thermodynamic analyses o... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4690841 Tue, 22 Mar 2011 00:00:00 +0100 4690841 http://www.medworm.com/index.php?rid=4690840&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21440362%26dopt%3DAbstract Authors: Liu H, Ge H, Peng Y, Xiao P, Xu J Recently, reversible antagonists of the P2Y(12) receptor have been reported. However, the mechanisms of binding have not been elucidated. To this end, a number of homology models were built by means of three programs from four templates. A consensus model was derived from those initial models. The final model was created by refining the consensus model with molecular dynamics simulations. The agonist and antagonists of P2Y(12) have been docked in the final model. For the agonist, the Arg256, Lys280, and Phe252 are "hot" residues. For the antagonists, the Lys280 and Phe252 are "hot" residues that have hydrogen bonding contacts and π-π interactions, respectively. These results can explain the observations of mutation experiments and can guide ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4690840 Sun, 06 Mar 2011 00:00:00 +0100 4690840 http://www.medworm.com/index.php?rid=4690839&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21440980%26dopt%3DAbstract Authors: Ananyan G, Avetisyan A, Aloyan L, Dalyan Y The complex formation of porphyrins with DNA leads to changes of stability of DNA. In the present study we investigated binding properties and the thermodynamic parameters of a water-soluble, cationic planar Cu(II)-containing meso-tetrakis(4-N-butyl-pyridiniumyl)porphyrin [CuTButPyP4] and nonplanar Co(II)-containing meso-tetrakis(4-N-butyl-pyridiniumyl)porphyrin [CoButPyP4] with calf thymus DNA in the presence of divalent manganese ions. For displaying the changes of thermodynamic parameters (T(m) and ΔT) the melting curves of DNA-porphyrin complexes in the presence of Mn(2+) ions have been obtained. The enthalpy (ΔH) of helix-coil transition has been also evaluated. It was shown that the binding of ions to DNA proceeds in two stage... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4690839 Sun, 06 Mar 2011 00:00:00 +0100 4690839 http://www.medworm.com/index.php?rid=4690838&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21450392%26dopt%3DAbstract Authors: Völker J, Winter R PMID: 21450392 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4690838 Sat, 05 Mar 2011 00:00:00 +0100 4690838 http://www.medworm.com/index.php?rid=4632929&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21402435%26dopt%3DAbstract Authors: Mező G, Herényi L, Habdas J, Majer Z, Myśliwa-Kurdziel B, Tóth K, Csík G Recently cationic porphyrin-peptide conjugates were synthesized to enhance the cellular uptake of porphyrins or deliver the peptide moiety to the close vicinity of nucleic acids. DNA binding of such compounds was not systematically studied yet. We synthesized two new porphyrin-tetrapeptide conjugates which can be considered as a typical monomer unit corresponding to the branches of porphyrin-polymeric branched chain polypeptide conjugates. Tetra-peptides were linked to the tri-cationic meso-tri(4-N-methylpyridyl)-mono-(4-carboxyphenyl)porphyrin and bi-cationic meso-5,10-bis(4-N-methylpyridyl)-15,20-di-(4-carboxyphenyl)porphyrin. DNA binding of porphyrin derivatives, and their peptide conjugates was i... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4632929 Sat, 26 Feb 2011 00:00:00 +0100 4632929 http://www.medworm.com/index.php?rid=4632927&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21411219%26dopt%3DAbstract Authors: Muhlrad A, Grintsevich EE, Reisler E Three polycations, polylysine, the polyamine spermine and the polycationic protein lysozyme were used to study the formation, structure, ionic strength sensitivity and dissociation of polycation-induced actin bundles. Bundles form fast, simultaneously with the polymerization of MgATP-G-actins, upon the addition of polycations to solutions of actins at low ionic strength conditions. This indicates that nuclei and/or nascent filaments bundle due to attractive, electrostatic effect of polycations and the neutralization of repulsive interactions of negative charges on actin. The attractive forces between the filaments are strong, as shown by the low (in nanomolar range) critical concentration of their bundling at low ionic strength. These bundl... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4632927 Sat, 26 Feb 2011 00:00:00 +0100 4632927 http://www.medworm.com/index.php?rid=4570939&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21349631%26dopt%3DAbstract We present results from the theoretical simulations of catalytic mechanism at the two-step successive surface redox reaction under conditions of square-wave voltammetry. This mechanism is assigned as a surface EEC', and it can be presented by the following simplified scheme: A(ads)+ne-⇄B(ads)+ne-⇄C(ads)+Substrate→k(cat)B(ads). Our attention is focused on several phenomena of this complex protein-film mechanism, while we give set of qualitative criteria to distinguish this mechanism from similar ones studied under voltammetric conditions. Moreover, we also provide hints to use methodologies for the determination of thermodynamic and kinetic parameters relevant to the protein-film EEC' mechanism. The considered protein-film EEC' mechanism is applicable to all lipophilic redox proteins ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4570939 Tue, 22 Feb 2011 00:00:00 +0100 4570939 http://www.medworm.com/index.php?rid=4570938&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21367514%26dopt%3DAbstract Authors: Kamatari YO, Smith LJ, Dobson CM, Akasaka K We have used low temperatures (down to -20°C) and high pressures (up to 2000bar) to populate low-lying excited state conformers of hen lysozyme, and have analyzed their structures site-specifically using (15)N/(1)H two-dimensional HSQC NMR spectroscopy. The resonances of a number of residues were found to be selectively broadened, as the temperature was lowered at a pressure of 2000bar. The resulting disappearance of cross-peaks includes those of residues in the β-domain of the protein and the cleft between the β- and α-domains, both located close to water-containing cavities. The results indicate that low-lying excited state conformers of hen lysozyme are characterized by slowly fluctuating local conformations around these cavit... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4570938 Thu, 03 Feb 2011 00:00:00 +0100 4570938 http://www.medworm.com/index.php?rid=4517377&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21334803%26dopt%3DAbstract Authors: Gorbenko G, Trusova V The ability of oligomeric lysozyme to modify the molecular organization of the model bilayer membranes composed of phosphatidylcholine (PC) and its mixtures with phosphatidylglycerol (PG) or cholesterol (Chol) was assessed using fluorescent probes 6-propionyl-2-dimethylaminonaphthalene (Prodan), 4-dimethylaminochalcone (DMC), pyrene and 1,6-diphenyl-1,3,5-hexatriene (DPH). The observed changes in the fluorescence characteristics of polarity-sensitive probes Prodan and DMC, located in interfacial bilayer region, were interpreted due to the partial dehydration of the glycerol backbone, which was under the influence of aggregated protein. Cholesterol was found to prevent the perturbations of membrane polar part by lysozyme aggregates. Analysis of the pyrene ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4517377 Thu, 03 Feb 2011 00:00:00 +0100 4517377 http://www.medworm.com/index.php?rid=4459590&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21255902%26dopt%3DAbstract Authors: Vongsutilers V, Phillips DJ, Train BC, McKelvey GR, Thomsen NM, Shaughnessy KH, Lewis JP, Gannett PM The B form of DNA exists in equilibrium with the Z form and is mainly affected by sequence, electrostatic interactions, and steric effects. C8-purine substitution shifts the equilibrium toward the Z form though how this interaction overcomes the unfavorable electrostatic interactions and decrease in stacking in the Z form has not been determined. Here, a series of C8-arylguanine derivatives, bearing a para-substituent were prepared and the B/Z equilibrium determined. B/Z ratios were measured by CD and conformational effects of the aryl substitution determined by NMR spectroscopy and molecular modeling. The para-substituent was found to have a significant effect on the B/Z DNA e... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4459590 Tue, 01 Feb 2011 00:00:00 +0100 4459590 http://www.medworm.com/index.php?rid=4459587&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21288629%26dopt%3DAbstract Authors: Hallen MA, Liang ZY, Endow SA The nonprocessive kinesin-14 Ncd motor binds to microtubules and hydrolyzes ATP, undergoing a single displacement before releasing the microtubule. A lever-like rotation of the coiled-coil stalk is thought to drive Ncd displacements or steps along microtubules. Crystal structures and cryoelectron microscopy reconstructions imply that stalk rotation is correlated with ADP release and microtubule binding by the motor. Here we report FRET assays showing that the end of the stalk is more than ~9nm from the microtubule when wild-type Ncd binds microtubules without added nucleotide, but the stalk is within ~6nm of the microtubule surface when the microtubule-bound motor binds an ATP analogue, matching the rotated state observed in crystal structures. We... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4459587 Thu, 13 Jan 2011 00:00:00 +0100 4459587 http://www.medworm.com/index.php?rid=4459589&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21255903%26dopt%3DAbstract Authors: Zhai Y, Okoro L, Cooper A, Winter R Pressure perturbation calorimetry (PPC) is a relatively new and efficient technique, to study the volumetric properties of biomolecules in solution. In PPC, the coefficient of thermal expansion of the partial volume of the biomolecule is deduced from the heat consumed or produced after small isothermal pressure jumps (typically±5bar). This strongly depends on the interaction of the biomolecule with the solvent or cosolvent as well as on its packing and internal dynamic properties. This technique, complemented by ultrasound velocity and densitometry, provides valuable insight into the basic thermodynamic properties of solvation and volume effects accompanying phase transitions and interactions of biomolecular systems. Here we review data on ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4459589 Tue, 04 Jan 2011 00:00:00 +0100 4459589 http://www.medworm.com/index.php?rid=4459588&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21266296%26dopt%3DAbstract Authors: Andrews MN, Winter R Conformational properties of the full-length human and rat islet amyloid polypeptide 1-37 (amyloidogenic hIAPP and non-amyloidogenic rIAPP, respectively) were studied at 310 and 330K by MD simulations both for the cysteine (reduced IAPP) and cystine (oxidized IAPP) moieties. At all temperatures studied, IAPP does not adopt a well-defined conformation and is essentially random coil in solution, although transient helices appear forming along the peptide between residues 8 and 22, particularly in the reduced form. Above the water percolation transition (at 320K), the reduced hIAPP moiety presents a considerably diminished helical content remaining unstructured, while the natural cystine moiety reaches a rather compact state, presenting a radius of gyration t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4459588 Fri, 31 Dec 2010 00:00:00 +0100 4459588 http://www.medworm.com/index.php?rid=4459586&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21295397%26dopt%3DAbstract Authors: Kamal MZ, Ahmad S, Rao NM In studies on polyol-mediated protein stabilization, the polyols are the preferred variable and less importance is given to the intrinsic properties of the protein used. We investigated the stabilizing effects of glycerol on three in vitro evolved lipase mutants with varying stabilities and also in a broad pH range of 3.3-12.1. Significant linear negative correlation between increment in stability due to glycerol and prior stability suggests that stabilizing effects of glycerol depend on the prior stability of the protein. Polar/nonpolar surface area and charge do not have a bearing on the stabilizing effects of glycerol. PMID: 21295397 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4459586 Thu, 30 Dec 2010 00:00:00 +0100 4459586 http://www.medworm.com/index.php?rid=4392371&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21236557%26dopt%3DAbstract Authors: Chalikian TV Interactions of proteins and protein groups with water-soluble cosolvents have been studied for the last 50years with a variety of theoretical and experimental methods. The contribution of volumetric techniques to these studies is relatively modest, although volumetric properties of solutes are sensitive to the entire spectrum of solute-solvent and solute-cosolvent interactions. This deficiency is partly related to formidable experimental difficulties related to conducting volumetric measurements at high cosolvent concentrations and partly to the lack of the theoretical framework within which volumetric results can be rationalized in terms of solute-solvent and solute-cosolvent interactions. However, recent years have witnessed a revival of interest in application... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4392371 Fri, 24 Dec 2010 00:00:00 +0100 4392371 http://www.medworm.com/index.php?rid=4392463&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21215508%26dopt%3DAbstract Authors: Lin C, Chinnappan R, Acharya K, Pellequer JL, Jankowiak R It has been shown that anti-PAH mAb can bind a particular cross-reactant by adopting two distinct "red" and "blue" conformations of its binding sites [N.M. Grubor et al. PNAS 102, 2005, 7453-7458]. In the case of red conformation of pyrene (Py)/anti-PAH mAb (with a broad fluorescence (0,0)-band with fwhm ~140cm(-1)), the central role in complex formation was played by π-π interactions. The nature of the blue-shifted conformation with very narrow fluorescence (0,0)-band (fwhm ~75cm(-1)) was left unclear due to the lack of suitable data for comparison. In this work, we suggest spectroscopic and modeling results obtained for the blue conformation of Py in several mAb (including 4D5 mAb) are consistent with π-cation inte... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4392463 Wed, 22 Dec 2010 00:00:00 +0100 4392463 http://www.medworm.com/index.php?rid=4392462&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21227568%26dopt%3DAbstract Authors: Skjevik AA, Haug BE, Lygre H, Teigen K Local anesthetics (LAs) are drugs that cause reversible loss of nociception during surgical procedures. Articaine is a commonly used LA in dentistry that has proven to be exceptionally effective in penetrating bone tissue and induce anesthesia on posterior teeth in maxilla and mandibula. In the present study, our aim was to gain a deeper understanding of the penetration of articaine through biological membranes by studying the interactions of articaine with a phospholipid membrane. Our approach involves Langmuir monolayer experiments combined with molecular dynamics simulations. Membrane permeability of LAs can be modulated by pH due to a titratable amine group with a pKa value close to physiological pH. A change in protonation state is t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4392462 Thu, 16 Dec 2010 00:00:00 +0100 4392462 http://www.medworm.com/index.php?rid=4392461&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21232842%26dopt%3DAbstract Authors: Chaudhuri S, Chakraborty S, Sengupta PK Steady state and time resolved fluorescence spectroscopy, combined with molecular modeling computations, have been used to explore the interactions of two therapeutically important flavonoids, fisetin (3,7,3',4'-OH-flavone) and 3-hydroxyflavone (3-HF), with normal human hemoglobin (HbA). Distinctive 'two color' fluorescence signatures and fairly high fluorescence anisotropy (r=0.12-0.28) of fisetin and 3-HF reveal their specific interactions with HbA. Binding constants estimated from the fluorescence studies were ≈4.00×10(4)M(-1) and 9.83×10(3)M(-1) for fisetin and 3-HF respectively. Specific interactions with HbA were further confirmed from flavonoid-induced static quenching of the protein tryptophan fluorescence as indicated by: (a... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4392461 Thu, 16 Dec 2010 00:00:00 +0100 4392461 http://www.medworm.com/index.php?rid=4392464&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21211898%26dopt%3DAbstract We report here that 2,6-bis(1H-benzimidazol-2-yl)pyridine (BBP), which is almost non-fluorescent in aqueous solutions, reveals a strong emission enhancement in a hydrophobic environment of a phospholipid bilayer, making it interesting for fluorescence probing of water content in a lipid membrane. Comparing the fluorescence behavior of BBP in a wide variety of solvents with those in phospholipid vesicles, we suggest that the hydrogen bonding interactions between a BBP fluorophore and water molecules play a crucial role in the observed "light switch effect". Therefore, the loss of water-induced fluorescence quenching inside a membrane are thought to be due to deep penetration of BBP into the hydrophobic, water-free region of a bilayer. Characterized by strong quenching by transition metal io... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4392464 Mon, 13 Dec 2010 00:00:00 +0100 4392464 http://www.medworm.com/index.php?rid=4305146&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21183271%26dopt%3DAbstract Authors: Jalili S, Akhavan M The interaction of the Alzheimer's amyloid beta peptide, Aβ40, with sodium dodecyl sulfate (SDS) micelles, together with the self-assembly of SDS molecules around the peptide from an initial random distribution were studied using atomistic and coarse-grained (CG) molecular dynamics simulations. In atomistic simulations, the peptide structure in the micelle was characterized by two helical regions connected through a short hinge. The initial structure of the system was shown to affect the simulation results. The atomistic self-assembly of SDS molecules resulted in a 38-molecule micelle around the peptide, along with some globules and individual molecules. Coarse-grained simulation results, however, did not show such a difference, and at the end of all CG si... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4305146 Fri, 03 Dec 2010 00:00:00 +0100 4305146 http://www.medworm.com/index.php?rid=4305147&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21167630%26dopt%3DAbstract Authors: Mogami G, Wazawa T, Morimoto N, Kodama T, Suzuki M Hydration properties of adenine nucleotides and orthophosphate (Pi) in aqueous solutions adjusted to pH=8 with NaOH were studied by high-resolution microwave dielectric relaxation (DR) spectroscopy at 20°C. The dielectric spectra were analyzed using a mixture theory combined with a least-squares Debye decomposition method. Solutions of Pi and adenine nucleotides showed qualitatively similar dielectric properties described by two Debye components. One component was characterized by a relaxation frequency (f(c)=18.8-19.7GHz) significantly higher than that of bulk water (17GHz) and the other by a much lower f(c) (6.4-7.6GHz), which are referred to here as hyper-mobile water and constrained water, respectively. By contrast, a hyd... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4305147 Mon, 29 Nov 2010 00:00:00 +0100 4305147 http://www.medworm.com/index.php?rid=4269847&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21146283%26dopt%3DAbstract Authors: Ravich VL, Masso M, Vaisman II The development of drug resistance to antiretroviral medications used to treat infection with HIV-1 is a major concern. Given the cost and time constraints associated with phenotypic resistance testing, computational approaches leading to accurate predictive models of resistance based on a patient's mutational patterns in the target protein would provide a welcome alternative. A combined sequence-structure computational mutagenesis procedure is used to generate attribute vectors for each of 222 mutational patterns of HIV-1 reverse transcriptase that were isolated and sequenced from patients. Phenotypic fold-levels of resistance to the non-nucleoside inhibitor Nevirapine are known for over 25% of these mutants, whose values are used to assign each... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4269847 Tue, 23 Nov 2010 00:00:00 +0100 4269847 http://www.medworm.com/index.php?rid=4269848&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21146282%26dopt%3DAbstract Authors: Kruse S, Krapf S, Lampe B, Koslowski T We approach the problem of optical excitations in molecular aggregates in complex biochemical environments from a computational, all-atom perspective. The system is divided into a π orbital part described by a Pariser-Parr-Pople model with configuration interaction using singly excited Slater determinants (PPP-CIS). It is coupled to the protein and water charges of a classical force field. Strategies for a high-accuracy reparameterization and an efficient computational solution are presented. For γD-crystallin, a band edge consisting of charge-transfer states emerges for a coupled molecular aggregate compared to the uncoupled residues. The energies of some charge-transfer states strongly depend on the dielectric properties of the model,... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4269848 Fri, 19 Nov 2010 00:00:00 +0100 4269848 http://www.medworm.com/index.php?rid=4269849&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21145159%26dopt%3DAbstract Authors: Bechinger B, Resende JM, Aisenbrey C Solid-state NMR spectroscopy is a powerful technique for the investigation of membrane-associated peptides and proteins as well as their interactions with lipids, and a variety of conceptually different approaches have been developed for their study. The technique is unique in allowing for the high-resolution investigation of liquid disordered lipid bilayers representing well the characteristics of natural membranes. Whereas magic angle solid-state NMR spectroscopy follows approaches that are related to those developed for solution NMR spectroscopy the use of static uniaxially oriented samples results in angular constraints which also provide information for the detailed analysis of polypeptide structures. This review introduces this latter... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4269849 Fri, 12 Nov 2010 00:00:00 +0100 4269849 http://www.medworm.com/index.php?rid=4214008&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21093143%26dopt%3DAbstract Authors: Montanha EA, Caseli L, Kaczmarek O, Liebscher J, Huster D, Oliveira ON Liponucleosides may assist the anchoring of nucleic acid nitrogen bases into biological membranes for tailored nanobiotechnological applications. To this end precise knowledge about the biophysical and chemical details at the membrane surface is required. In this paper, we used Langmuir monolayers as simplified cell membrane models and studied the insertion of five lipidated nucleosides. These molecules varied in the type of the covalently attached lipid group, the nucleobase, and the number of hydrophobic moieties attached to the nucleoside. All five lipidated nucleosides were found to be surface-active and capable of forming stable monolayers. They could also be incorporated into dipalmitoylphosphatidylch... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4214008 Fri, 29 Oct 2010 00:00:00 +0100 4214008 http://www.medworm.com/index.php?rid=4121645&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20980090%26dopt%3DAbstract Authors: Mohan PM, Chakraborty S, Hosur RV Local structural and dynamic modulations due to small environmental perturbations reflect the adaptability of the protein to different interactors. We have investigated here the preferential local perturbations in Dynein light chain protein (DLC8), a cargo adapter, by sub-denaturing urea concentrations. Equilibrium unfolding experiments by optical spectroscopic methods indicated a two state like unfolding of DLC8 dimer, with the transition mid-point occurring around 8.6M urea. NMR studies identified the β3 and β4 strands, N-, C- terminal regions, loops connecting β1 to α1, α1 to α2 and β3 to β4 as the soft targets of urea perturbation and thus indicated potential unfolding initiation sites. Native-state hydrogen exchange studies sugges... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4121645 Mon, 25 Oct 2010 00:00:00 +0100 4121645 http://www.medworm.com/index.php?rid=4106985&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20952122%26dopt%3DAbstract Cytochromes: Reactivity of the "dark side" of the heme. Biophys Chem. 2010 Oct 15; Authors: Ascenzi P, Santucci R, Coletta M, Polticelli F Ligand binding to the heme distal side is a paradigm of heme-protein biochemistry, the proximal axial ligand being in most cases a His residue. NO binds to the ferrous heme-Fe-atom giving rise to hexa-coordinated adducts (as in myoglobin and hemoglobin) with His and NO as proximal and distal axial ligands, respectively, or to penta-coordinated adducts (as in soluble guanylate cyclase) with NO as the axial distal ligand. Recently, the ferrous derivative of Alcaligenes xylosoxidans cytochrome c' (Axcyt c') and of cardiolipin-bound horse heart cytochrome c (CL-hhcyt c) have been reported to bind NO to the "dark side" of the heme (i.e., as the p... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4106985 Thu, 14 Oct 2010 23:00:00 +0100 4106985 http://www.medworm.com/index.php?rid=4075130&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20943306%26dopt%3DAbstract Authors: Zubrienė A, Gutkowska M, Matulienė J, Chaleckis R, Michailovienė V, Voroncova A, Venclovas C, Zylicz A, Zylicz M, Matulis D Radicicol is a natural antibiotic that specifically inhibits chaperone Hsp90 activity and binds to its active site with nanomolar affinity. Radicicol has been widely used as a lead compound to generate synthetic analogs with reduced toxicity and increased stability that could be employed clinically. Here we present a detailed thermodynamic description of radicicol binding to human Hsp90 and yeast Hsc82 studied by isothermal titration calorimetry and thermal shift assay. Titrations as a function of pH showed a linked protonation event upon radicicol binding. The intrinsic binding constant and the thermodynamic parameters (including the enthalpy, entropy... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4075130 Sun, 10 Oct 2010 23:00:00 +0100 4075130 http://www.medworm.com/index.php?rid=4040095&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20888119%26dopt%3DAbstract Authors: Falvo MR, Gorkun OV, Lord ST When normal blood circulation is compromised by damage to vessel walls, clots are formed at the site of injury. These clots prevent bleeding and support wound healing. To sustain such physiological functions, clots are remarkably extensible and elastic. Fibrin fibers provide the supporting framework of blood clots, and the properties of these fibers underlie the mechanical properties of clots. Recent studies, which examined individual fibrin fibers or cylindrical fibrin clots, have shown that the mechanical properties of fibrin depend on the mechanical properties of the individual fibrin monomers. Within the fibrin monomer, three structures could contribute to these properties: the coiled-coil connectors the folded globular nodules and the relative... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4040095 Wed, 29 Sep 2010 23:00:00 +0100 4040095 http://www.medworm.com/index.php?rid=4025313&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20875698%26dopt%3DAbstract Authors: Santiago PS, Carvalho JW, Domingues MM, Santos NC, Tabak M Glossoscolex paulistus hemoglobin (HbGp) was studied by dynamic light scattering (DLS), optical absorption spectroscopy (UV-VIS) and differential scanning calorimetry (DSC). At pH 7.0, cyanomet-HbGp is very stable, no oligomeric dissociation is observed, while denaturation occurs at 56°C, 4°C higher as compared to oxy-HbGp. The oligomeric dissociation of HbGp occurs simultaneously with some protein aggregation. Kinetic studies for oxy-HbGp using UV-VIS and DLS allowed to obtain activation energy (E(a)) values of 278-262kJ/mol (DLS) and 333kJ/mol (UV-VIS). Complimentary DSC studies indicate that the denaturation is irreversible, giving endotherms strongly dependent upon the heating scan rates, suggesting a kinetic... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=4025313 Mon, 06 Sep 2010 23:00:00 +0100 4025313 http://www.medworm.com/index.php?rid=3776710&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20637975%26dopt%3DAbstract Authors: Karabencheva T, Donev R, Balali-Mood K, Christov C Class A beta-lactamases are enzymes which are responsible for the bacterial resistance against antibiotics and therefore are of great importance in rational inhibitor design. In this paper we comparatively analyze all the individual contributions of the aromatic chromophores in three class A beta-lactamases (from Staphylococcus aureus, Streptomyces albus and Bacillus licheniformis) to their near-UV Circular Dichroism. The analysis is performed using recently developed procedure based on established theoretical method. We found that in beta-lactamase from S. albus the most significant contributions to the total near-UV CD intensity exhibit Y251 and Y229. In the tryptophan-containing beta-lactamases from B. licheniformis and S. ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3776710 Thu, 22 Jul 2010 10:06:08 +0100 3776710 http://www.medworm.com/index.php?rid=3672730&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20542200%26dopt%3DAbstract Authors: Garidel P, Kerth A, Winter R PMID: 20542200 [PubMed - in process] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3672730 Fri, 18 Jun 2010 18:36:06 +0100 3672730 http://www.medworm.com/index.php?rid=3554241&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20456856%26dopt%3DAbstract Authors: Berhanu WM, Masunov AE Amyloid-like fibrils had been associated with many fatal diseases, and the rational design of the fibrillization inhibitors holds the great promise of finding the prevention and treatment options. The understanding of the mechanisms by which the small molecules can inhibit the aggregation plays the key role in such design. Here we present the results of MD simulations that provide the atomistic details of the process, by which the small molecules may destabilize the ordered amyloid oligomers formed by the model hexapeptide. We select a heptapeptide fragment (GNNQQNY) from Sup-35 yeast prion protein, which is capable to form both amyloid fibrils and microcrystals. Atomic-resolution structures of its crystals were reported by Eisenberg et al. (Nature 447:4... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3554241 Wed, 12 May 2010 13:38:14 +0100 3554241 http://www.medworm.com/index.php?rid=3545780&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20444536%26dopt%3DAbstract Authors: Scott DJ, Wills PR, Winzor DJ This theoretical investigation explores the use of statistical-mechanical approaches to characterize the reversible tetramerization of a protein monomer with the size and charge characteristics of serum albumin under conditions where consideration of nearest-neighbor interactions suffices to describe effects of thermodynamic non-ideality. Such analysis of simulated sedimentation equilibrium distributions points to the adequacy of both the scaled particle theory and potential-of-mean-force methods for determining the self-association constant. Although the latter method usually entails the assignment of a magnitude to monomer net charge, this requirement can be obviated to some extent by repeating the analysis for a range of monomer charges and ide... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3545780 Sun, 02 May 2010 23:00:00 +0100 3545780 http://www.medworm.com/index.php?rid=3538805&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20442006%26dopt%3DAbstract We describe the excitation energy spectrum of the cyan mTFP1 fluorescent protein with the original chromophore and with chromophore mutants Tyr67His and Tyr67Trp. PMID: 20442006 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3538805 Fri, 09 Apr 2010 23:00:00 +0100 3538805 http://www.medworm.com/index.php?rid=3530551&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20435400%26dopt%3DAbstract Authors: Bonomo J, Welsh JP, Manthiram K, Swartz JR The Hsp70 family of molecular chaperones is an essential class of chaperones that is present in many different cell types and cellular compartments. We have compared the bioactivities of the prokaryotic cytosolic Hsp70, DnaK, to that of the eukaryotic Hsp70, BiP, located in the endoplasmic reticulum (ER). Both chaperones helped to prevent protein aggregation. However, only DnaK provided enhanced refolding of denatured proteins. We also tested chaperone folding assistance during translation in the context of cell-free protein synthesis reactions for several protein targets and show that both DnaK and BiP can provide folding assistance under these conditions. Our results support previous reports suggesting that DnaK provides both post-t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3530551 Fri, 09 Apr 2010 23:00:00 +0100 3530551 http://www.medworm.com/index.php?rid=3530550&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20435401%26dopt%3DAbstract Authors: Jeppesen MD, Hein K, Nissen P, Westh P, Otzen DE We explore the thermodynamic properties of three different fibrils of the peptide hormone glucagon, formed under different salt conditions (glycine, sulfate and NaCl, respectively), and differing considerably in compactness. The three fibrils display a large variation in the specific heat capacity DeltaC(p) determined by isothermal titration calorimetry. Sulfate fibrils show a negative DeltaC(p) expected from a folding reaction, while the DeltaC(p) for glycine fibrils is essentially zero. NaCl fibrils, which are less stable than the other fibrils, have a large and positive C(p). The predicted change in solvent accessible area is not a useful predictor of fibrillar DeltaC(p) unlike the case for globular proteins. We speculate tha... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3530550 Thu, 08 Apr 2010 23:00:00 +0100 3530550 http://www.medworm.com/index.php?rid=3512380&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20421142%26dopt%3DAbstract Authors: Schmidt P, Berger C, Scheidt HA, Berndt S, Bunge A, Beck-Sickinger AG, Huster D Although highly resolved crystal structures of G protein-coupled receptors have become available within the last decade, the need for studying these molecules in their natural membrane environment, where the molecules are rather dynamic, has been widely appreciated. Solid-state NMR spectroscopy is an excellent method to study structure and dynamics of membrane proteins in their native lipid environment. We developed a reconstitution protocol for the uniformly (15)N labeled Y(2) receptor into a bicelle-like lipid structure with high yields suitable for NMR studies. Milligram quantities of target protein were expressed in Escherichia coli using an optimized fermentation process in defined medium yiel... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3512380 Wed, 07 Apr 2010 23:00:00 +0100 3512380 http://www.medworm.com/index.php?rid=3480282&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20395035%26dopt%3DAbstract Authors: Asagi M, Toyama A, Takeuchi H Distamycin A (Dst) is an antibiotic which binds to the minor groove of double-stranded DNA at A/T-rich regions. We have examined the affinity and mode of Dst binding to DNA duplexes containing a conserved A/T core and variable terminal A/T regions by using circular dichroism spectroscopy. The observed circular dichroism spectra were analyzed by singular value decomposition and fitted to a two-step binding model. The result clearly shows a correlation between the affinity for Dst and the preference for Dst-DNA 1:1 binding over 2:1 binding. The A/T stretches that prefer 1:1 binding form high-affinity 1:1 complexes, whereas those preferring 2:1 binding form stable 2:1 complex with low overall affinities. The terminal A/T residues of the Dst binding r... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3480282 Sat, 27 Mar 2010 00:00:00 +0100 3480282 http://www.medworm.com/index.php?rid=3480284&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20392557%26dopt%3DAbstract Authors: Krylova OO, Jahnke N, Keller S We have studied the solubilisation and reconstitution of lipid membranes composed of either synthetic phosphatidylcholine or Escherichia. coli polar lipid extract by the non-ionic detergent octylglucoside. For both lipid systems, composition-dependent transformations of unilamellar vesicles into micelles or vice versa were followed by high-sensitivity isothermal titration calorimetry. Data obtained over a range of detergent and lipid concentrations could be rationalised in terms of a three-stage phase separation model involving bilayer, bilayer/micelle coexistence, and micellar ranges, yielding the detergent/lipid phase diagrams and the bilayer-to-micelle partition coefficients of both detergent and lipid. The most notable difference between the ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3480284 Sat, 20 Mar 2010 00:00:00 +0100 3480284 http://www.medworm.com/index.php?rid=3480283&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20392558%26dopt%3DAbstract Authors: Vindigni A, Marino F, Gileadi O RecQ helicases are a ubiquitous family of DNA unwinding enzymes required to preserve genome integrity, thus preventing premature aging and cancer formation. The five human representatives of this family play non-redundant roles in the suppression of genome instability using a combination of enzymatic activities that specifically characterize each member of the family. These enzymes are in fact not only able to catalyze the transient opening of DNA duplexes, as any other conventional helicase, but can also promote annealing of complementary strands, branch migration of Holliday junctions and, in some cases, excision of ssDNA tails. Remarkably, the balance between these different activities seems to be regulated by protein oligomerization. This re... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3480283 Sat, 20 Mar 2010 00:00:00 +0100 3480283 http://www.medworm.com/index.php?rid=3464387&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20381231%26dopt%3DAbstract Rubredoxin mutant A51C unfolding dynamics: A Förster Resonance Energy Transfer study. Biophys Chem. 2010 Mar 16; Authors: Santos A, Duarte AG, Fedorov A, Martinho JM, Moura I The unfolding dynamics of the rubredoxin mutant A51C (RdA51C) from Desulfovibrio vulgaris (DvRd) was studied on the temperature range from 25 degrees C to 90 degrees C and by incubation at 90 degrees C. By Förster Resonance Energy Transfer (FRET) the donor (D; Trp37) to acceptor (A; 1,5-IAEDANS) distance distribution was probed at several temperatures between 25 degrees C and 90 degrees C, and incubation times at 90 degrees C. From 25 degrees C to 50 degrees C the half-width distributions values (hw) are small and the presence of a discrete D-A distance was considered. At temperatures higher than... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3464387 Tue, 16 Mar 2010 00:00:00 +0100 3464387 http://www.medworm.com/index.php?rid=3456785&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20378240%26dopt%3DAbstract Authors: Maloletkina OI, Markossian KA, Belousova LV, Kleimenov SY, Orlov VN, Makeeva VF, Kurganov BI Effect of 2-hydroxypropyl-beta-cyclodextrin (HP-beta-CD) on thermal aggregation of creatine kinase from rabbit skeletal muscle (RMCK) at 48 degrees C has been studied using dynamic light scattering. An increase in the duration of the lag period on the kinetic curves of aggregation, registered as an increment of the light scattering intensity in time, has been observed in the presence of HP-beta-CD. It has been shown that the initial parts of the dependences of the hydrodynamic radius (R(h)) of the protein aggregates on time follow the exponential law. The reciprocal value of parameter t(2R) (t(2R) is the time interval over which the R(h) value is doubled) was used to characterize the r... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3456785 Tue, 16 Mar 2010 00:00:00 +0100 3456785 http://www.medworm.com/index.php?rid=3433526&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20356666%26dopt%3DAbstract Authors: Debnath D, Nielsen KL, Otzen DE Although the beta-barrel membrane protein OmpA can be produced in a biologically active form in E. coli from co-expressed fragments, the fragments have not been demonstrated to associate in vitro. We have produced 3 complementary fragment pairs of OmpA which can associate to form a folded complex according to the SDS band-shift assay. We are able to convert 25-35% of the fragment populations to non-covalent but SDS-stable complexes. The periplasmic chaperone Skp effectively prevented this association. Two separately expressed and purified overlapping fragments of OmpA can form a protease-resistant complex that undergoes the characteristic band-shift upon heating. Our work demonstrates that although membrane insertion and folding of beta-barrel m... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3433526 Tue, 16 Mar 2010 00:00:00 +0100 3433526 http://www.medworm.com/index.php?rid=3425836&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20350777%26dopt%3DAbstract Authors: Jang KJ, Yeo GY, Cho TS, Eom GH, Kim C, Kim SK [M(Hdpa)(2)(NO(3))(n)](x+) (M=Zn(II), Cd(II), Cu(II) and Ni(II), n=1,2, and x=0, 1) complexes were synthesized, and their activity as catalysts for DNA cleavage reactions were investigated using electrophoresis and linear dichroism technique (LD). All four metal complexes effectively cleaved pBR322 super-coiled DNA. The electrophoresis analysis showed that the [Zn(Hdpa)(2)(NO(3))](+) and [Cd(Hdpa)(2)(NO(3)) (2)] complexes most effectively cleaved the super-coiled DNA, whereas the [Ni(Hdpa)(2)(NO(3))](+) complex was least effective. The magnitude of LD in the DNA absorption region reflects the flexibility and length of DNA when the conditions for measurement are properly adjusted. The double stranded DNA cleavage increases the flex... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3425836 Tue, 16 Mar 2010 00:00:00 +0100 3425836 http://www.medworm.com/index.php?rid=3416679&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20346569%26dopt%3DAbstract Authors: Lee S, Heerklotz H, Chalikian TV Protein denaturation events are generally associated with a change in the state of ionization of abnormally titrating groups and, therefore, are coupled with changes in buffer ionization/neutralization equilibria. Consequently, buffer ionization should influence the measured change in volume accompanying protein denaturation. Changes in volume accompanying protein denaturation reflect the differential packing and hydration of polypeptide chains in their native and denatured conformations while also describing the pressure stability of proteins. A characteristic feature of conformational transitions of globular proteins is a near zero change in volume that is comparable in magnitude with the volume of ionization of biologically relevant buffers.... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3416679 Fri, 12 Mar 2010 00:00:00 +0100 3416679 http://www.medworm.com/index.php?rid=3416677&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20346571%26dopt%3DAbstract Authors: Ascenzi P, Fasano M Human serum albumin (HSA), the most prominent protein in plasma, binds different classes of ligands at multiple sites. The globular domain structural organization of monomeric HSA is at the root of its allosteric properties which are reminiscent of those of multimeric proteins. Here, both functional and structural aspects of the allosteric modulation of heme and drug (e.g., warfarin and ibuprofen) binding to HSA and of the drug-dependent reactivity of HSA-heme are reviewed. PMID: 20346571 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3416677 Sat, 06 Mar 2010 00:00:00 +0100 3416677 http://www.medworm.com/index.php?rid=3416678&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20346570%26dopt%3DAbstract Authors: Vetcher AA, McEwen AE, Abujarour R, Hanke A, Levene SD Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly v... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3416678 Wed, 03 Mar 2010 00:00:00 +0100 3416678 http://www.medworm.com/index.php?rid=3399451&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20303644%26dopt%3DAbstract Authors: Radu I, Budyak IL, Hoomann T, Kim YJ, Engelhard M, Labahn J, Büldt G, Heberle J, Schlesinger R Sensory rhodopsin I (SRI) from Halobacterium salinarum mediates both positive and negative phototaxis in a light-dependent manner. SRI photoactivation elicits extensive structural changes which are transmitted to the cognate transducer (HtrI). The atomic structure of the SRI-HtrI complex has not been solved yet and, therefore, details on the interaction which define the binding site between receptor and transducer are missing. The related complex SRII-HtrII from Natronobacterium pharaonis exhibits a hydrogen bond between the receptor Y199 and transducer N54. This bond has been suggested to mediate signal relay in the SRII-HtrII system. Our previous results on the SRI-HtrI comple... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3399451 Tue, 02 Mar 2010 00:00:00 +0100 3399451 http://www.medworm.com/index.php?rid=3379610&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20231052%26dopt%3DAbstract In this study absorbance, fluorescence, circular dichroic spectroscopy, viscosity, thermal melting and calorimetric techniques were employed to understand the binding of the phenothiazinium dye, thionine, with deoxyribonucleic acids of varying base composition. Strong hypochromic and bathochromic effects and quenching of fluorescence were observed that showed strong binding of thionine to the DNAs. The binding parameters evaluated from Scatchard analysis through McGhee-von Hippel analysis showed that the binding was non-cooperative and affinities of the order of 10(5)M(-)(1). The results of ferrocyanide fluorescence quenching studies and viscosity experiments, taken together suggested the intercalation of thionine while thermal melting, differential scanning calorimetry and circular dichro... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3379610 Mon, 01 Mar 2010 00:00:00 +0100 3379610 http://www.medworm.com/index.php?rid=3379612&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20227164%26dopt%3DAbstract Authors: Kral T, Leblond J, Hof M, Scherman D, Herscovici J, Mignet N Lipopolythioureas (LPT) are original non cationic systems representing an alternative to cationic lipids. Their high transfection efficiency prompted us to investigate further their biophysical properties, and in particular how thiourea lipids interact with DNA. The interaction of lipopolythiourea with DNA was investigated by fluorescence correlation microscopy (FCS). Influence of the lipid length and nature of the thiourea head on the thiourea/DNA interaction were studied. FCS revealed a strong interaction between lipopolythiourea and DNA, occurring at 1 equivalent of a thiourea lipid by a DNA phosphate group, and leading to a condensed plasmid state. From previous in vitro experiments, we could conclude that the li... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3379612 Thu, 25 Feb 2010 00:00:00 +0100 3379612 http://www.medworm.com/index.php?rid=3379611&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20227815%26dopt%3DAbstract Authors: Brasen JC, Barington T, Olsen LF We have investigated the regulation of the oscillatory generation of H(2)O(2) and oscillations in shape and size in neutrophils in suspension. The oscillations are independent of cell density and hence do not represent a collective phenomena. Furthermore, the oscillations are independent of the external glucose concentration and the oscillations in H(2)O(2) production are 180 degrees out of phase with the oscillations in NAD(P)H. Cytochalasin B blocked the oscillations in shape and size whereas it increased the period of the oscillations in H(2)O(2) production. 1- and 2-butanol also blocked the oscillations in shape and size, but only 1-butanol inhibited the oscillations in H(2)O(2) production. We conjecture that the oscillations are likely to ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3379611 Thu, 25 Feb 2010 00:00:00 +0100 3379611 http://www.medworm.com/index.php?rid=3361210&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20219280%26dopt%3DAbstract Authors: Lorenz B, Keller R, Sunnick E, Geil B, Janshoff A A versatile model system to study membrane-membrane interactions in great detail is introduced. Based on colloidal probe microscopy with membrane covered spherical probes attached to tip-less cantilevers the interaction forces and adhesion energies are quantified down to single molecule resolution. Two opposing membranes equipped with ligands on one side and receptors on the other side were brought in contact at a defined load and pulled apart at constant velocity. Ni-NTA functionalized lipids served as receptors on the probe, while lipopeptides displaying short His-tags (CGGH(6) or CGWH(6)) were incorporated in the planar supporting membrane on a silicon substrate. The rather intricate force distance curves were scrutinized in... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3361210 Wed, 17 Feb 2010 00:00:00 +0100 3361210 http://www.medworm.com/index.php?rid=3346992&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20202738%26dopt%3DAbstract Authors: Wei C, Wang J, Zhang M The binding mode and stoichiometry of the cationic porphyrin TMPyP4 to G-quadruplex structure are still controversial to date, mainly due to the intricate polymorphism of G-rich sequences in the different conditions of solution. Here in the presence of the molecular crowding agent PEG, the binding interaction of TMPyP4 and another porphyrin derivative TPrPyP4 with four-stranded parallel (G(4)T(4)G(4))4 G-quadruplex was studied systematically using circular dichroism, visible absorption titration, and steady-state and time-resolved fluorescence spectroscopies. The results show that each (G(4)T(4)G(4))4 molecule is able to bind four TMPyP4 or TPrPyP4 molecules. Two types of independent and nonequivalent binding sites with the higher and lower binding affin... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3346992 Tue, 16 Feb 2010 00:00:00 +0100 3346992 http://www.medworm.com/index.php?rid=3346991&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20206434%26dopt%3DAbstract Authors: Behn D, Bosk S, Hoffmeister H, Janshoff A, Witzgall R, Steinem C The pkd1 and pkd2 genes encode for the proteins polycystin-1 (PC1) and polycystin-2 (PC2). These genes are mutated in patients diagnosed with autosomal dominant polycystic kidney disease. PC1 and PC2 interact via their C-terminal, cytosolic regions, which is an essential step in the regulation of cell proliferation and differentiation. Here, we developed an assay that allowed us to quantitatively monitor the interaction of the C-terminal region of PC1 (cPC1) with that of PC2 (cPC2) to be able to answer the question of how Ca(2+) influences the PC1/PC2 complex formation. By means of the quartz crystal microbalance (QCM) technique, we were able to determine binding affinities and kinetic constants of the cPC1/cPC2 ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3346991 Thu, 11 Feb 2010 00:00:00 +0100 3346991 http://www.medworm.com/index.php?rid=3346990&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20206435%26dopt%3DAbstract In conclusion, our study gives for the first time evidence that ectoines have an effect on lipid membranes increasing the hydration of the surface and thus increasing the mobility of the lipid head groups and fluidizing the lipid layer accordingly. This increased fluidity may be of advantage for cell membranes to withstand extreme conditions like temperature or osmotic pressure and might also accelerate cellular repair mechanisms. PMID: 20206435 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3346990 Thu, 11 Feb 2010 00:00:00 +0100 3346990 http://www.medworm.com/index.php?rid=3336015&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20199841%26dopt%3DAbstract Authors: Sanchez-Ruiz JM The relevance of protein stability for biological function and molecular evolution is widely recognized. Protein stability, however, comes in two flavours: thermodynamic stability, which is related to a low amount of unfolded and partially-unfolded states in equilibrium with the native, functional protein; kinetic stability, which is related to a high free-energy barrier "separating" the native state from the non-functional forms (unfolded states, irreversibly-denatured protein). Such barrier may guarantee that the biological function of the protein is maintained, at least during a physiologically relevant time-scale, even if the native state is not thermodynamically stable with respect to non-functional forms. Kinetic stabilization is likely required in many c... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3336015 Thu, 11 Feb 2010 00:00:00 +0100 3336015 http://www.medworm.com/index.php?rid=3327946&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20189291%26dopt%3DAbstract Authors: Bordallo HN, Boldyreva EV, Fischer J, Koza MM, Seydel T, Minkov VS, Drebushchak VA, Kyriakopoulos A The paper illustrates the benefit of combining several experimental techniques (incoherent elastic and inelastic neutron scattering, DSC, and X-ray diffraction) to study subtle dynamic transitions in a biologically important system, probing a broad time (frequency) range of the molecular motions in a wide temperature interval of 2-300K. As a case study the crystalline form (a monoclinic polymorph) of l-cysteine ((+)NH(3)-CH(CH(2)SH)-COO(-)) - an essential amino acid - has been selected. Crystals of amino acids are widely used to mimic important structural and dynamic features of peptides. The conformational lability of cysteine and the dynamics of the thiol-side chains are known... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3327946 Thu, 11 Feb 2010 00:00:00 +0100 3327946 http://www.medworm.com/index.php?rid=3327945&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20189292%26dopt%3DAbstract Authors: Marhl M, Gosak M, Perc M, Roux E Calcium signaling controls several essential physiological functions in different cell types. Hence, it is not surprising that different aspects of Ca(2+) dynamics are in the focus of in-depth and extensive investigations. Efforts concentrate on the development of proper theoretical models that would provide a unified description of Ca(2+) signaling. Remarkably, experimentally recorded Ca(2+) signals exhibit a rather large diversity, which can be observed irrespective of the cell type, measuring techniques, or the nature of the signal. Our goal in the present study therefore is to present a theoretical explanation for the variability observed in experiments, whereby we focus on caffeine-induced Ca(2+) responses in isolated airway myocytes. By e... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3327945 Thu, 11 Feb 2010 00:00:00 +0100 3327945 http://www.medworm.com/index.php?rid=3327944&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20189293%26dopt%3DAbstract We present a model for the electrostatic contribution to the nonideality of a two-component acidic-zwitterionic lipid membrane. Our model is based on the mean-field Poisson-Boltzmann approach; it includes a protonation/deprotonation equilibrium applicable to acidic lipids such as phosphatidic acid or phosphatidylglycerol. It also includes an electrostatic model for zwitterionic lipids such as phosphatidylcholine or phosphatidylethanolamine that accounts for the spatial separation of the two headgroup charges and the orientational freedom of the headgroup. Modeling the nonelectrostatic contribution to the free energy using the Bragg-Williams approximation of a binary lattice gas enables us to compute binodal lines that reflect the influence of membrane electrostatics on the nonideal mixing ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3327944 Sat, 06 Feb 2010 00:00:00 +0100 3327944 http://www.medworm.com/index.php?rid=3291273&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20167416%26dopt%3DAbstract Authors: Lape M, Elam C, Paula S Inhibitors of the transmembrane protein sarco/endoplasmic reticulum calcium ATPase (SERCA) are invaluable tools for the study of the enzyme's physiological functions and they have been recognized as a promising new class of anticancer agents. For the discovery of novel enzyme inhibitors, small molecule docking for virtual screens of large compound libraries has become increasingly important. Since the performance of various docking routines varies considerably, depending on the target and the chemical nature of the ligand, we critically evaluated the performance of four frequently used programs - GOLD, AutoDock, Surflex-Dock, and FRED - for the docking of SERCA inhibitors based on the structures of thapsigargin, di-tert-butylhydroquinone, and cyclopiazo... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3291273 Thu, 04 Feb 2010 00:00:00 +0100 3291273 http://www.medworm.com/index.php?rid=3284545&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156670%26dopt%3DAbstract Authors: Drescher S, Graf G, Hause G, Dobner B, Meister A Herein, we report the synthesis of two novel, amino-functionalized single-chain bolalipids and, based on those, a general synthetic approach for the insertion of various carboxylic acids into the bolalipid headgroups, e.g. alpha-lipoic acid for one-dimensional fixation of gold nanoparticles, sorbic acid for polymerization experiments, or lysine for the use in gene delivery systems. The temperature- and pH-dependent self-assembly of amino-functionalized bolalipids into nanofibers and micelles was investigated by differential scanning calorimetry (DSC), transmission electron microscopy (TEM) and dynamic light scattering (DLS). Rheological measurements were used to describe the macroscopic behavior of the formed temperature switcha... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3284545 Thu, 04 Feb 2010 00:00:00 +0100 3284545 http://www.medworm.com/index.php?rid=3276574&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153101%26dopt%3DAbstract Authors: Brandenburg K, Garidel P, Fukuoka S, Howe J, Koch MH, Gutsmann T, Andrä J An analysis of the interaction of the NK-lysin derived peptide NK-2 and of analogs thereof with bacterial lipopolysaccharide (LPS, endotoxin) was performed to determine the most important biophysical parameters for an effective LPS neutralization. We used microcalorimetry, FTIR spectroscopy, Zeta potential measurements, and small-angle X-ray scattering to analyze the peptide:LPS binding enthalpy, the accessible LPS surface charge, the fluidity of the LPS hydrocarbon chains, their phase transition enthalpy change, the aggregate structure of LPS, and how these parameters are modulated by the peptides. We conclude that (i) a high peptide:LPS binding affinity, which is facilitated by electrostatic and h... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3276574 Fri, 29 Jan 2010 00:00:00 +0100 3276574 http://www.medworm.com/index.php?rid=3276575&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153100%26dopt%3DAbstract In this study we explored the amyloidogenic propensity and conformational properties of hIAPP in the presence of negatively charged membrane (DOPC/DOPG phospholipid bilayers) surfaces upon addition of two recently designed potent hIAPP-derived inhibitors of hIAPP amyloidogenesis, the hexapeptide NF(N-Me)GA(N-Me)IL (NFGAIL-GI) and the 37-residue non-amyloidogenic hIAPP analog [(N-Me)G24, (N-Me)I26]-IAPP (IAPP-GI). For comparison, the effects of insulin, which is a natively occurring hIAPP aggregation inhibitor, rat IAPP (rIAPP), which is a natively non-amyloidogenic hIAPP analog, and the hIAPP amyloid core peptide hIAPP(22-27) or NFGAIL were also studied. The aim of our study was to test whether and how the above peptides which have been shown to completely block or suppress hIAPP amyloidog... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3276575 Thu, 28 Jan 2010 00:00:00 +0100 3276575 http://www.medworm.com/index.php?rid=3276576&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153099%26dopt%3DAbstract Authors: Yi M, Xia K, Zhan M An integrated mathematical model, which incorporates scaffold proteins into a mitogen-activated protein kinases cascade, is constructed. By employing Monte Carlo simulation, regulatory property of scaffold protein on signaling ability for the mitogen-activated protein kinases cascade is investigated theoretically. It is found that (i) scaffold binding increases signal amplification if dephosphorylation is slow and decreases amplification if dephosphorylation is rapid. Also, increasing the number of scaffold decreases amplification if dephosphorylation is slow. (ii) The scaffold number can control the timing of kinase activation so that the time flexibility of signaling is enhanced. (iii) It is observed that for slow dephosphorylation case, scaffolds decreas... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3276576 Mon, 25 Jan 2010 00:00:00 +0100 3276576 http://www.medworm.com/index.php?rid=3244573&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20122787%26dopt%3DAbstract Authors: Abu-Ghazalah RM, Irizar J, Helmy AS, Macgregor RB Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, ... associated strands. Some of the remarkable features of these structures are their extreme thermostability and resistance to chemical denaturants and nucleases. However, the nature of the molecular interactions that stabilize these structures remains unclear. Based on dimethyl sulfate (DMS) methylation results, our group previously proposed DNA frayed wires to be a unique set of nucleic-acid assemblies in which the N7 of guanine does not participate in the guanine-guanine inter... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3244573 Wed, 20 Jan 2010 00:00:00 +0100 3244573 http://www.medworm.com/index.php?rid=3236588&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20117876%26dopt%3DAbstract Authors: Galantini L, Leggio C, Konarev PV, Pavel NV Small angle X-ray scattering (SAXS) technique, supported by light scattering measurements and spectroscopic data (circular dichroism and fluorescence) allowed us to restore the 3D structure at low resolution of defatted human serum albumin (HSA) in interaction with ibuprofen. The data were carried out on a set of HSA solutions with urea concentrations between 0.00 and 9.00M. The Singular Value Decomposition method, applied to the complete SAXS data set allowed us to distinguish three different states in solution. In particular a native conformation N (at 0.00M urea), an intermediate I1 (at 6.05M urea) and an unfolded structure U (at 9.00M urea) were recognized. The low-resolution structures of these states were obtained by exploiting... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3236588 Mon, 18 Jan 2010 00:00:00 +0100 3236588 http://www.medworm.com/index.php?rid=3212669&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20096501%26dopt%3DAbstract Authors: Dürrschmidt P, Mansfeld J, Ulbrich-Hofmann R A very thermostable variant of the thermolysin-like protease from Bacillus stearothermophilus (G8C/N60C) was previously created by introduction of a disulfide bond into the cysteine-free pseudo-wild type variant (pWT) and thus fixing the unfolding region 56-69. In the present paper, we show that G8C/N60C and pWT can be reactivated from the completely unfolded states, accessible at >/=7.5M guanidine hydrochloride, and analyze the kinetics of folding, autoproteolytic degradation and aggregation. From changes in the fluorescence spectra with time of renaturation, it can be concluded that a folding intermediate with native-like structure, but which is still inactive and sensitive to autoproteolysis, is rapidly formed after renat... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3212669 Wed, 13 Jan 2010 00:00:00 +0100 3212669 http://www.medworm.com/index.php?rid=3212667&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20096989%26dopt%3DAbstract Authors: Yamamoto T, Sugawara M, Kikukawa T, Miyauchi S, Yamaguchi M, Tero A, Takagi S, Nakagaki T Transport across the cell membrane is crucial in drug delivery. However, the process is complicated because nucleoside derivatives that are commonly used as anti-viral drugs are transported through two different types of specific transporters: concentrative transporters and equilibrative transporters. Cross-disciplinary approaches involving both biological experiments and theoretical considerations are therefore necessary to study the transport of nucleoside analogues such as ribavirin. Here we constructed an experimental model system using the Xenopus laevis oocyte that expressed examples of both types of transporters: human concentrative nucleoside transporter 3 and human equilibrative ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3212667 Wed, 06 Jan 2010 00:00:00 +0100 3212667 http://www.medworm.com/index.php?rid=3212668&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20096988%26dopt%3DAbstract Authors: Tsoi M, Do TT, Tang V, Aguilera JA, Perry CC, Milligan JR We have examined the changes in physical properties of aqueous solutions of the plasmid pUC18 that take place on the addition of the cationic oligopeptide penta-arginine. An increase in sedimentation rate and static light scattering, and changes in the nucleic acid CD spectrum all suggest that this ligand acts to condense the plasmid. Dynamic light scattering suggests the hydrodynamic radii of the condensate particles are a few micrometers, ca. 50-fold larger than that of the monomeric plasmid. Condensation of the plasmid also produces a ca. 100-fold decrease in the strand break yield produced by gamma irradiation. This extensive protection against reactive intermediates in the bulk of the solution implies that condense... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3212668 Mon, 04 Jan 2010 00:00:00 +0100 3212668 http://www.medworm.com/index.php?rid=3200943&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20089348%26dopt%3DAbstract Authors: Margaron Y, Bostan L, Exposito JY, Malbouyres M, Trunfio-Sfarghiu AM, Berthier Y, Lethias C Tenascin-X is an extracellular matrix protein whose absence leads to an Ehlers-Danlos Syndrome in humans, mainly characterised by connective tissue defects including the disorganisation of fibrillar networks, a reduced collagen deposition, and modifications in the mechanical properties of dense tissues. Here we tested the effect of tenascin-X on in vitro collagen fibril formation. We observed that the main parameters of fibrillogenesis were unchanged, and that the diameter of fibrils was not significantly different when they were formed in the presence of tenascin-X. Interestingly, mechanical analysis of collagen gels showed an increased compressive resistance of the gels containing ten... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3200943 Mon, 04 Jan 2010 00:00:00 +0100 3200943 http://www.medworm.com/index.php?rid=3194494&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20083338%26dopt%3DAbstract This report presents evidence that naproxen interacts with red cell membranes as follows: a) in scanning electron microscopy (SEM) studies on human erythrocytes it has been observed that the drug induced shape changes, forming echinocytes at a concentration as low as 10microM; b) X-ray diffraction showed that naproxen strongly interacted with DMPC multilayers; in contrast, no perturbing effects on DMPE multilayers were detected; c) differential scanning calorimetry (DSC) data showed a decrease in the melting temperature (T(m)) of DMPC liposomes, which was attributed to a destabilization of the gel phase, effect that was less pronounced for DMPE. These experimental results were observed at concentrations lower than those reported for plasma after therapeutic administration. This is the firs... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3194494 Mon, 04 Jan 2010 00:00:00 +0100 3194494 http://www.medworm.com/index.php?rid=3164200&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20060206%26dopt%3DAbstract Authors: Oard SV, Enright FM, Li B Computational analysis of two membrane-permeabilizing peptides, barley alpha-hordothionin and wheat beta-purothionin, revealed that anions can trigger dynamic and structural changes in the thionin antiparallel double alpha-helix core. Analysis of the molecular dynamics simulations demonstrated that anions induced unfolding of the alpha2 and alpha1 helices at the carboxyl ends which are located on the opposite ends of the alpha-helix core. An internalized water molecule was observed inside the unfolded alpha2 C-end. Strong interactions of anions with the R30 regulating network or simultaneous interactions of anions with the phospholipid-binding site and the R30 hydrogen bonding network triggered unfolding of the alpha2 C-end. An increase of anion densi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3164200 Mon, 04 Jan 2010 00:00:00 +0100 3164200 http://www.medworm.com/index.php?rid=3122533&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20034725%26dopt%3DAbstract Authors: Suarez M, Tortosa P, Garcia-Mira MM, Rodríguez-Larrea D, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM, Jaramillo A Many enzymes possess, besides their native function, additional promiscuous activities. Proteins with several activities (multipurpose catalysts) may have a wide range of biotechnological and biomedical applications. Natural promiscuity, however, appears to be of limited scope in this context, because the latent (promiscuous) function is often related to the evolved one (sharing the active site and even the chemical mechanism) and its enhancement upon suitable mutations usually brings about a decrease in the native activity. Here we explore the use of computational protein design to overcome these limitations. The high-plasticity positions close to the orig... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=3122533 Tue, 22 Dec 2009 00:00:00 +0100 3122533 http://www.medworm.com/index.php?rid=2959819&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19853363%26dopt%3DAbstract Authors: Nurmemmedov E, Yengo RK, Uysal H, Karlsson R, Thunnissen MM Wilms Tumor suppressor protein (WT1) is a transcription factor that is involved in a variety of developmental functions during organ development. It is also implicated in the pathology of several different cancer forms. The protein contains four C(2)H(2)-type zinc fingers and it specifically binds GC-rich sequences in the promoter regions of its target genes, which are either up or down regulated. Two properties make WT1 a more unusual transcription factor - an unconventional amino acid composition for zinc finger 1, and the insertion of a tri-peptide KTS in some of the splice isoforms of WT1. Using six WT1 constructs in which zinc fingers are systematically deleted, a dual study based on a bacterial 1-hybrid system a... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2959819 Thu, 05 Nov 2009 06:20:05 +0100 2959819 http://www.medworm.com/index.php?rid=2935209&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19853363%26dopt%3DAbstract Authors: Nurmemmedov E, Yengo RK, Uysal H, Karlsson R, Thunnissen MM Wilms Tumor suppressor protein (WT1) is a transcription factor that is involved in a variety of developmental functions during organ development. It is also implicated in the pathology of several different cancer forms. The protein contains four C(2)H(2)-type zinc fingers and it specifically binds GC-rich sequences in the promoter regions of its target genes, which are either up or down regulated. Two properties make WT1 a more unusual transcription factor - an unconventional amino acid composition for zinc finger 1, and the insertion of a tri-peptide KTS in some of the splice isoforms of WT1. Using six WT1 constructs in which zinc fingers are systematically deleted, a dual study based on a bacterial 1-hybrid system a... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2935209 Wed, 28 Oct 2009 20:46:10 +0100 2935209 http://www.medworm.com/index.php?rid=2935207&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854559%26dopt%3DAbstract Authors: Pennisi CP, Greenbaum E, Yoshida K Photosystem I (PSI) complexes can support a light-driven electrochemical gradient for protons, which is the driving force for energy-conserving reactions across biological membranes. In this work, a computational model that enables a quantitative description of the light-induced proton gradients across the membrane of PSI proteoliposomes is presented. Using a set of electrodiffusion equations, a compartmental model of a vesicle suspended in aqueous medium was studied. The light-mediated proton movement was modeled as a single proton pumping step with backpressure of the electric potential. The model fits determinations of pH obtained from PSI proteoliposomes illuminated in the presence of mediators of cyclic electron transport. The model also... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2935207 Tue, 06 Oct 2009 00:00:00 +0100 2935207 http://www.medworm.com/index.php?rid=2935208&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854558%26dopt%3DAbstract Authors: Fologea D, Krueger E, Lee R, Naglak M, Mazur Y, Henry R, Salamo G Lysenin forms unitary large conductance pores in artificial bilayer membranes containing sphingomyelin. A population of lysenin pores inserted into such a bilayer membrane exhibited a dynamic negative conductance region, as predicted by a simple two-state model for voltage-gated channels. The recorded I-V curves demonstrated that lysenin pores inserted into the bilayer are uniformly oriented. Additionally, the transition between the two-states was affected by changes in the monovalent ion concentration and pH, pointing towards an electrostatic interaction governing the gating mechanism. PMID: 19854558 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2935208 Mon, 05 Oct 2009 00:00:00 +0100 2935208 http://www.medworm.com/index.php?rid=2923945&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19846249%26dopt%3DAbstract Authors: Zaitseva M, Kaluzhny D, Shchyolkina A, Borisova O, Smirnov I, Pozmogova G The thrombin-binding aptamer d(GGTTGGTGTGGTTGG) (TBA) is an efficient tool for the inhibition of thrombin function. We have studied conformations and thermodynamic stability of a number of modified TBA oligonucleotides containing thiophosphoryl substitution at different internucleotide sites. Using circular dichroism such modifications were found not to disrupt the antiparallel intramolecular quadruplex specific for TBA. Nevertheless, the presence of a single thiophosphoryl bond between two G-quartet planes led to a significant decrease in the quadruplex thermostability. On the contrary, modifications in each of the loop regions either stabilized an aptamer structure or did not reduce its stability. Acco... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2923945 Thu, 01 Oct 2009 00:00:00 +0100 2923945 http://www.medworm.com/index.php?rid=2909676&cid=s_34562_59_f&fid=34562&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19836126%26dopt%3DAbstract Authors: Vincent JC, Lenormand H Hyaluronan (HA) is the substrate of hyaluronidase (HAase). In addition, HA is able to form electrostatic complexes with many proteins, including HAase. Experiments have shown the strong inhibition of the HA hydrolysis catalyzed by HAase when performed at low HAase over HA concentration ratio and under low ionic strength conditions. Non-catalytic P proteins are able to compete with HAase to form electrostatic complexes with HA and thus to modulate HAase activity. We have modeled the HA-HAase-P system by considering the competition between the two complex equilibria HA-P and HA-HAase, the Michaelis-Menten type behavior of HAase, and the non-activity of the electrostatically complexed HAase. Simulations performed by introducing experimental data produce a ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2909676 Wed, 30 Sep 2009 23:00:00 +0100 2909676