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. Sat, 20 Mar 2010 15:57:40 +0100 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 http://www.medworm.com/index.php?rid=2909675&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%3D19837504%26dopt%3DAbstract Authors: Goldstein BN, Aksirov AM, Zakrjevskaya DT A graphical analysis demonstrates the ability of slow substrate activation and certain types of cooperativity between the two enzyme active sites to generate sustained oscillations. The analysis allows us to estimate kinetic parameter values for which oscillations exist. The scheme analyzed can explain the cyclical changes in functioning of various motor enzymes. Moreover, this scheme does not generate bistability for any parameter values. The graphical analysis presented is simple and visually clarifies the regulatory role of the details in the kinetic schemes. PMID: 19837504 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2909675 Tue, 29 Sep 2009 23:00:00 +0100 2909675 http://www.medworm.com/index.php?rid=2887223&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%3D19819610%26dopt%3DAbstract Authors: Valdez R, Johnson EM, Belcher JA, Fuini JF, Brancaleon L Self-assembly of tubulin heterodimers in solution has been studied in the past to predict the effects that ligands and/or conformational changes have on the formation of tubulin filaments. Self-assembly of tubulin in solution has produced formations similar to cellular microtubules (MTs). The present study reports on the effects that two porphyrins (protoporphyrin IX, PPIX and tetrakis(4-sulfonatophenyl)porphyrin, TPPS) produce on the self-assembly of tubulin alpha,beta-heterodimers in buffer solution. The study shows that, when incubated simultaneously with MT-stabilizing ligands (i.e., paclitaxel and guanosine triphosphate, GTP), porphyrins do not affect the ability of tubulin to form MT. However, if paclitaxel and GTP... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2887223 Mon, 28 Sep 2009 23:00:00 +0100 2887223 http://www.medworm.com/index.php?rid=2887222&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%3D19819611%26dopt%3DAbstract Authors: Rusling DA, Rachwal PA, Brown T, Fox KR We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C(+).GC and T.AT triplets) at pH 5.0 the T(m) is more than 10 degrees C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the T(m) is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular d... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2887222 Thu, 24 Sep 2009 23:00:00 +0100 2887222 http://www.medworm.com/index.php?rid=2887224&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%3D19819062%26dopt%3DAbstract Authors: Wang YT, Su ZY, Chen CL Antigen-antibody interactions are critical for understanding antigen-antibody associations in immunology. To shed further light on this question, we studied a dissociation of the 19D9D6-HCV core protein antibody complex structure. However, forced separations in single molecule experiments are difficult, and therefore molecular simulation techniques were applied in our study. The stretching, that is, the distance between the center of mass of the HCV core protein and the 19D9D6 antibody, has been studied using the potential of mean force calculations based on molecular dynamics and the explicit water model. Our simulations indicate that the 7 residues Gly70, Gly72, Gly134, Gly158, Glu219, Gln221 and Tyr314, the interaction region (antibody), and the 14 i... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2887224 Mon, 21 Sep 2009 23:00:00 +0100 2887224 http://www.medworm.com/index.php?rid=2881483&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%3D19815332%26dopt%3DAbstract Authors: Lu J, Yang L, Xie A, Shen Y A very simple and novel approach of fabricating Ag-DNA network is herein reported. The Ag-DNA network can be formed from reduction of silver ion absorbed on DNA template by sunlight. Mesh size of the Ag-DNA network and the diameter of the Ag-DNA nanowire can be controlled by adjusting the concentration of DNA and irradiation time, respectively. Furthermore, the Ag-DNA network placed onto comb-like gold electrodes can be utilized as a sensor for humidity, which presents a good response to the detection of relative humidity (RH). PMID: 19815332 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2881483 Sun, 20 Sep 2009 23:00:00 +0100 2881483 http://www.medworm.com/index.php?rid=2847050&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%3D19783088%26dopt%3DAbstract Authors: Laird DJ, Mulvihill MM, Whiles Lillig JA As more peptide secondary structures deduced by infrared spectroscopy (IR) have been reported in the literature, there have been overlaps in assignments of elements of secondary structure to carbonyl vibrational frequencies. We have investigated this phenomenon with regards to the use of IR for monitoring membrane-induced structural changes using conformationally diverse peptides. These IR studies, complemented by circular dichroism (CD) experiments, revealed that peptide-solvent interactions can mask membrane-induced conformational changes monitored by IR. A structural transition from random coil to alpha-helix upon the binding of mastoparan X to a membrane was clearly observed by CD but obscured in the amide I region of the IR spectru... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2847050 Fri, 11 Sep 2009 23:00:00 +0100 2847050 http://www.medworm.com/index.php?rid=2847049&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%3D19783089%26dopt%3DAbstract Authors: Kazakov AS, Markov DI, Gusev NB, Levitsky DI We applied different methods (differential scanning calorimetry, circular dichroism, Fourier transform infrared spectroscopy, and intrinsic fluorescence) to investigate the thermal-induced changes in the structure of small heat shock protein Hsp22. It has been shown that this protein undergoes thermal-induced unfolding that occurs within a very broad temperature range (from 27 degrees C to 80 degrees C and above), and this is accompanied by complete disappearance of alpha-helices, significant decrease in beta-sheets content, and by pronounced changes in the intrinsic fluorescence. The results confirm predictions that Hsp22 belongs to the family of intrinsically disordered proteins (IDP) with certain parts of its molecule (presumably... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2847049 Fri, 11 Sep 2009 23:00:00 +0100 2847049 http://www.medworm.com/index.php?rid=2847051&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%3D19782460%26dopt%3DAbstract Authors: Wills PR, Winzor DJ A procedure is described for the direct analysis of osmotic pressure data for reversibly dimerizing proteins that makes allowance for effects of thermodynamic nonideality on the statistical-mechanical basis of the potential-of-mean-force between molecules. Detailed consideration is also given to calculation of the magnitudes of the required virial coefficients. After illustration of the approach with analysis of simulated osmotic pressure data, the method is used to obtain dimerization constants from published osmotic pressure data for soybean proteinase inhibitor, hemoglobin and alpha-chymotrypsin. PMID: 19782460 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2847051 Thu, 10 Sep 2009 23:00:00 +0100 2847051 http://www.medworm.com/index.php?rid=2847052&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%3D19781844%26dopt%3DAbstract Authors: Li Q, Li H An internal noise-driven oscillator was studied in a two-variable Drosophila model, where both positive feedback and negative feedback are crucial to the circadian oscillations. It is shown that internal noise could sustain reliable oscillations for the parameter which produces a stable steady state in the deterministic system. The noise-sustained oscillations are interpreted by using phase plane analysis. The period of such oscillations fluctuates slightly around the period of deterministic oscillations and the coherence of oscillations becomes the best at an optimal internal noise intensity, indicating the occurrence of intrinsic coherence resonance. In addition, in the oscillatory region, the coherence of noisy circadian oscillations is suppressed by the internal... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2847052 Sat, 05 Sep 2009 23:00:00 +0100 2847052 http://www.medworm.com/index.php?rid=2847048&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%3D19783351%26dopt%3DAbstract Authors: Fleming RM, Thiele I, Nasheuer HP Constraint-based modeling is an approach for quantitative prediction of net reaction flux in genome-scale biochemical networks. In vivo, the second law of thermodynamics requires that net macroscopic flux be forward, when the transformed reaction Gibbs energy is negative. We calculate the latter by using (i) group contribution estimates of metabolite species Gibbs energy, combined with (ii) experimentally measured equilibrium constants. In an application to a genome-scale stoichiometric model of Escherichia coli metabolism, iAF1260, we demonstrate that quantitative prediction of reaction directionality is increased in scope and accuracy by integration of both data sources, transformed appropriately to in vivo pH, temperature and ionic strength... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2847048 Mon, 31 Aug 2009 23:00:00 +0100 2847048 http://www.medworm.com/index.php?rid=2797259&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%3D19748724%26dopt%3DAbstract Authors: Tan YH, Chen YM, Ye X, Lu Q, Tretyachenko-Ladokhina V, Yang W, Senear DF, Luo R We have utilized both molecular dynamics simulations and solution biophysical measurements to investigate the rescue mechanism of mutation N235K, which plays a key role in the recently identified global suppressor motif of K235/Y239/R240 in the human p53 DNA-binding domain (DBD). Previous genetic analysis indicates that N235K alone rescues five out of six destabilized cancer mutants. However, the solution biophysical measurement shows that N235K generates only a slight increase to the stability of DBD, implying a rescue mechanism that is not a simple additive contribution to thermodynamic stability. Our molecular simulations show that the N235K substitution generates two non-native salt bridges wit... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2797259 Mon, 31 Aug 2009 23:00:00 +0100 2797259 http://www.medworm.com/index.php?rid=2775094&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%3D19733000%26dopt%3DAbstract Authors: Rungrotmongkol T, Udommaneethanakit T, Malaisree M, Nunthaboot N, Intharathep P, Sompornpisut P, Hannongbua S To reveal the source of oseltamivir-resistance in influenza (A/H5N1) mutants, the drug-target interactions at each functional group were investigated using MD/LIE simulations. Oseltamivir in the H274Y mutation primarily loses the electrostatic and the vdW interaction energies at the -NH(3)(+) and -OCHEt(2) moieties corresponding to the weakened hydrogen-bonds and changed distances to N1 residues. Differentially, the N294S mutation showed small changes of binding energies and intermolecular interactions. Interestingly, the presence of different conformations of E276 positioned between the -OCHEt(2) group and the mutated residue is likely to play an important role in ose... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2775094 Fri, 21 Aug 2009 23:00:00 +0100 2775094 http://www.medworm.com/index.php?rid=2758853&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%3D19720446%26dopt%3DAbstract We present results of theoretical studies of the photoabsorption band corresponding to the vertical electronic transition S(0)-S(1) between first two singlet states of the model chromophore from the green fluorescent protein (GFP) in its neutral form. Predictions of quantum chemical approaches including ab initio and semi-empirical approximations are compared for the model systems which mimic the GFP chromophore in different environments. We provide evidences that the protein matrix in GFP accounts for a fairly large shift of about 40 nm in the S(0)-S(1) absorption band as compared to the gas phase. PMID: 19720446 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2758853 Thu, 13 Aug 2009 23:00:00 +0100 2758853 http://www.medworm.com/index.php?rid=2751925&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%3D19716642%26dopt%3DAbstract In this study, we used a synthetic peptide from this domain to reveal the conformation of the calmodulin-peptide complex by small angle X-ray scattering. Upon peptide binding, calmodulin lost its dumbbell shape, adopting a more globular conformation. We also studied the energetics of the interaction using calorimetry and computational methods. All our data indicate that calmodulin binds to the peptide from cx43 in the classical 'collapsed' conformation. PMID: 19716642 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2751925 Thu, 06 Aug 2009 23:00:00 +0100 2751925 http://www.medworm.com/index.php?rid=2745761&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%3D19713030%26dopt%3DAbstract Authors: Olivares-Quiroz L, Garcia-Colin LS In this work, we derive an analytical expression for the relaxation time tau as a function of temperature T for myoglobin protein (Mb, PDB:1MBN) in the high temperature limit (T>T(g)=200K). The method is based on a modified version of the Adam-Gibbs theory (AG theory) for the glass transition in supercooled liquids and an implementation of differential geometry techniques. This modified version of the AG theory takes into account that the entropic component in protein's denaturation has two major sources: a configurational contribution DeltaS(c) due to the unfolding of the highly ordered native state N and a hydration contribution DeltaS(hyd) arising from the exposure of non-polar residues to direct contact with solvent polar molecules. Ou... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2745761 Sun, 02 Aug 2009 23:00:00 +0100 2745761 http://www.medworm.com/index.php?rid=2741962&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%3D19709800%26dopt%3DAbstract In this study, the saturation of RBC suspensions was lowered by additions of deoxygenated hemoglobin-based oxygen carrier (HBOC) and then assayed for extracellular ATP. When an acellular human Hb intramolecularly cross-linked between alpha subunits (alphaalphaHb, p50=33 mmHg) was added to the red cell suspension, ATP production was significantly less than that in the presence of a lower p50 HBOC (Hb cross-linked between beta subunits, betabetaHb, p50=8 mmHg). These results provide a potential mechanism for the O(2) affinity of HBOCs to interfere with a vasodilatory signal. PMID: 19709800 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2741962 Sun, 02 Aug 2009 23:00:00 +0100 2741962 http://www.medworm.com/index.php?rid=2546532&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%3D19361905%26dopt%3DAbstract We present a model for the control of the transmembrane potential of mammalian skeletal muscle cell. The model involves active and passive transport of Na(+), K(+), and Cl(-). As we check the model against experimental measurements on murine skeletal muscle cells, we find that the model can account for the observed bistability of the transmembrane potential at low extracellular potassium concentration. The effect of bumetanide, a blocker of the Na,K,2Cl-cotransporter, is measured and modeled. A hyperosmotic medium is known to stimulate the Na,K,2Cl-cotransporter and we also measure and model the effects of such a medium. Increased chloride transport has two effects on the interval along the extracellular potassium concentration axis where the system is bistable: the interval is shifted tow... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546532 Sun, 28 Jun 2009 03:47:53 +0100 2546532 http://www.medworm.com/index.php?rid=2546530&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%3D19383568%26dopt%3DAbstract Authors: Bahrami A, Esrafili MD, Hadipour NL The aspects of N-H...O=CNH, N-H...O=CO and C-H...O=CNH interactions are analyzed by applying ab initio and DFT methods as well as Bader theory. We investigated geometry, binding energies, (17)O, (15)N chemical shift tensors, and Atoms in Molecules (AIM) properties of alpha-glycylglycine (alpha-glygly) clusters, via MP2, B3LYP and PW91(XC) methods. Dimer stabilization energies and equilibrium geometries are studied in various levels of theory. MP2 and DFT calculations reveal that for alpha-glygly clusters, stability of N-H...O and C-H...O hydrogen bonds are enhanced significantly as a result of cooperativity effects. Furthermore, a covalent nature is also detected for some hydrogen bondings. The n-dependent trend of (17)O and (15)N chemical s... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546530 Sun, 28 Jun 2009 03:47:49 +0100 2546530 http://www.medworm.com/index.php?rid=2546529&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%3D19395147%26dopt%3DAbstract Authors: Dogu Y, Díaz J Ionizing radiation like UV light, gamma and X rays, can produce genotoxic damage in fibroblast cells. This injury can be reverted by activation of specific nuclear molecules. However, intense genotoxic damage induces the activation of the p53 dependent apoptotic pathway. Activated nuclear p53 has the role of a transcription factor that switches on the transcription of the Puma protein, which once released into the cytoplasm leads to the activation of a network of chemical processes that produces cell death. This network is built up with the chemical interaction between pro-apoptotic p53, Puma and Bax proteins and the anti-apoptotic Bcl2 and Bcl-x(L) proteins. In this work we present a mathematical model of this modular network under different regimes of Pum... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546529 Sun, 28 Jun 2009 03:47:47 +0100 2546529 http://www.medworm.com/index.php?rid=2546528&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%3D19398261%26dopt%3DAbstract This study also intends to compare and contrast the pre-transfer editing with post-transfer editing of ValRS. Interestingly, the MD simulation results revealed that non-cognate substrates (Thr-AMP/Thr-A76) bind more strongly than the cognate substrates (Val-AMP/Val-A76) in both pre- and post-transfer editing respectively. The editing site mutations (Lys270Ala and Asp279Ala) severely affected the binding ability of pre-transfer substrate (Thr-AMP) by different ways. Even though pre- and post-transfer substrates bind to the same site, specific differences were observed which has led us to believe the existence of the pre-transfer editing process in ValRS. PMID: 19398261 [PubMed - in process] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546528 Sun, 28 Jun 2009 03:47:45 +0100 2546528 http://www.medworm.com/index.php?rid=2546527&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%3D19403234%26dopt%3DAbstract Authors: Jia Y, Liu W, Li A, Yang L, Zhan X Small non-coding RNA (sRNA) plays very important role in the post transcriptional regulation in various organisms. In complex regulatory networks, highly significant relative fluctuations in RNAs copy numbers can not be neglected due to very small copy number of individual RNA molecules. Here we consider two simple regulation schemes, where one is single target gene regulated by a sRNA and the other is two target mRNAs (mRNA(R) and mRNA(T)) regulated by one sRNA. The Fano factor (a measure of the relative size of the internal fluctuations) formulae of RNA molecules in the post transcriptional regulation are theoretically derived by using of the Langevin theory. For single target gene regulated by a sRNA, it is shown that the intrinsic noise o... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546527 Sun, 28 Jun 2009 03:47:43 +0100 2546527 http://www.medworm.com/index.php?rid=2546526&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%3D19411133%26dopt%3DAbstract Authors: Wei C, Wang L, Jia G, Zhou J, Han G, Li C Interactions of 5,10,15,20-Tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4) and 5,10,15,20-Tetrakis(N-propylpyridinium-4-yl)-21H,23H-porphyrin (TPrPyP4) with the parallel four-stranded (TG(4)T)4 G-quadruplex DNA in 100 mM K(+)-containing buffer were studied using circular dichroism (CD) spectroscopy, visible absorption titration, and steady and time-resolved fluorescence spectroscopies. The results show that the binding stoichiometric ratios of both TMPyP4 and TPrPyP4 to (TG(4)T)4 are 3:1. Two types of independent and nonequivalent binding sites with the higher and lower binding affinities are confirmed, and the stronger and weaker binding constants are 9.44x10(7) and 6.94x10(5) M(-1) for (TG(4)T)4-TMPyP4 complex, 7.86x10(7... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546526 Sun, 28 Jun 2009 03:47:41 +0100 2546526 http://www.medworm.com/index.php?rid=2546525&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%3D19427732%26dopt%3DAbstract Authors: Garidel P, Hoffmann C, Blume A The development of liquid therapeutic protein drugs imposes the presence of specific stabilisation agents to prevent protein degradation in order to reach shelf-lives of at least 2 years for drugs stored at 2-8 degrees C. Non-ionic detergents are used to avoid protein adsorption and the formation of protein aggregates. Depending on the protein and excipient (detergent) used the stabilisation effect is quite different and cannot be predicted up to now. One reason for this is the inadequate understanding of the principles that govern the stabilisation of proteins in the presence of detergents. One stabilisation mechanism discussed implicates a direct binding of detergent molecules to the hydrophobic surface area(s) of the protein in order to minimi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546525 Sun, 28 Jun 2009 03:47:39 +0100 2546525 http://www.medworm.com/index.php?rid=2546524&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%3D19428172%26dopt%3DAbstract Authors: Huang G, Liao B, Li Y, Yu Y We denoted the four nucleotides, A, T, G and C, as four two-component vectors, and illustrated a nucleotide sequence as a curve in the 2D space by concatenating the vectors representing the nucleotides in the sequence. We studied the similarities among multiple nucleotide sequences by comparing their corresponding curves, with the beta-globin genes from 7 species as an example. PMID: 19428172 [PubMed - in process] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546524 Sun, 28 Jun 2009 03:47:37 +0100 2546524 http://www.medworm.com/index.php?rid=2546523&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%3D19442430%26dopt%3DAbstract Authors: Leirer C, Wunderlich B, Myles VM, Schneider MF In this work we demonstrate how the first order phase transition in giant unilamellar vesicles (GUVs) can function as a trigger for membrane fission. When driven through their gel-fluid phase transition GUVs exhibit budding or pearl formation. These buds remain connected to the mother vesicle presumably by a small neck. Cooling these vesicles from the fluid phase (T>T(m)) through the phase transition into the gel state (T<T(m)), leads to complete rupture and fission of the neck, while the mother vesicle remains intact. Pearling tubes which formed upon heating break-up and decay into multiple individual vesicles which then diffuse freely. Finally we demonstrate that mimicking the intracellular bulk viscosity by increasing the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546523 Sun, 28 Jun 2009 03:47:35 +0100 2546523 http://www.medworm.com/index.php?rid=2546522&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%3D19442431%26dopt%3DAbstract Authors: Liu J, Brazier-Hicks M, Edwards R Glutathione transferases (GSTs) catalyse the detoxification of a range of xenobiotics, including crop protection agents in plants. Recent studies in cultures of the model plant Arabidopsis thaliana have shown that the herbicide safener fenclorim (4,6-dichloro-2-phenylpyrimidine) is conjugated by GSTs acting in the cytosol which are induced in response to this chemical treatment. The primary glutathione conjugates are then hydrolyzed to S-(4-chloro-2-phenylpyrimidin-6-yl)-cysteine, which after accumulating transiently in the cells and medium is then metabolized by a series of competing lyases and transferases, including GSTs, to a series of polar derivatives. This system therefore represents an example of an inducible metabolic pathway, where G... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546522 Sun, 28 Jun 2009 03:47:33 +0100 2546522 http://www.medworm.com/index.php?rid=2546521&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%3D19447541%26dopt%3DAbstract Authors: Grubelnik V, Dugonik B, Osebik D, Marhl M In this paper we compare the cascade mechanisms of signal amplification in biological and electrical engineering systems, and show that they share the capacity to considerably amplify signals, and respond to signal changes both quickly and completely, which effectively preserves the form of the input signal. For biological systems, these characteristics are crucial for efficient and reliable cellular signaling. We show that this highly-efficient biological mechanism of signal amplification that has naturally evolved is mathematically fully equivalent with some man-developed amplifiers, which indicates parallels between biological evolution and successful technology development. PMID: 19447541 [PubMed - in process] (Source: Biophysi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546521 Sun, 28 Jun 2009 03:47:31 +0100 2546521 http://www.medworm.com/index.php?rid=2546520&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%3D19457605%26dopt%3DAbstract Authors: Gruszecki WI, Luchowski R, Gagoś M, Arczewska M, Sarkar P, Hereć M, Myśliwa-Kurdziel B, Strzałka K, Gryczynski I, Gryczynski Z Amphotericin B (AmB) is a life-saving polyene antibiotic used to treat deep-seated mycotic infections. Both the mode of therapeutic action as well as toxic side effects are directly dependent on molecular organization of the drug. Binding of AmB to lipid monolayers formed with dipalmitoylphosphatidylcholine, pure and containing 40 mol% cholesterol or ergosterol, the sterols of human and fungi respectively, has been examined by means of Fluorescence Lifetime Imaging Microscopy. AmB emits fluorescence with the characteristic lifetimes dependent on actual molecular organization: tau(M2) < or = 10 ps and tau(M1) = 0.35 ns in the ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546520 Sun, 28 Jun 2009 03:47:29 +0100 2546520 http://www.medworm.com/index.php?rid=2546519&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%3D19481330%26dopt%3DAbstract Authors: Cong W, Liu Q, Liang Q, Wang Y, Luo G Differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy and quantum calculation based on molecular modeling were applied to investigate the interaction between pirarubicin (THP), an anthracycline antibiotic frequently used in chemotherapy, and zwitterionic distearoylphosphatidylcholine (DSPC) or anionic distearoylphosphatidylglycerol (DSPG). DSC and FTIR studies suggested that DSPG bilayers were less perturbed by THP than those of DSPC, and this might be due to the strong interactions between NH(3)(+) of THP and the phosphate (PO(2)(-)) group in the polar head of DSPG, which limit the further access of THP into its bilayers. Quantum calculation results based on molecular modeling could further confirm the DS... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546519 Sun, 28 Jun 2009 03:47:27 +0100 2546519 http://www.medworm.com/index.php?rid=2546517&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%3D19482408%26dopt%3DAbstract Authors: Routh P, Mukherjee P, Dawn A, Nandi AK Biomolecular hybrids of a conducting polymer [poly(o-methoxy aniline) (POMA)] and RNA are prepared at the three different compositions by mixing aqueous solutions of diethyl, 2-hydroxy ethyl, ammonium salt of RNA (type IX from Torula Yeast) and POMA (ES, emeraldine salt; doping level [Cl]/[N]=0.52). A slow increase of pH up to 30 h of aging occurs in the mixture till it levels up. The TEM micrographs indicate a fibrillar network structure in all the hybrid compositions (POMA: RNA=1:3, 1:1, 3:1, by weight). In the complexes three types of supramolecular interactions, viz. (i) electrostatic, (ii) H-bonding and (iii) pi-pi interactions, are evident from the FTIR spectroscopy. The CD spectra indicate a small distortion of A-RNA conformation t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546517 Sun, 28 Jun 2009 03:47:25 +0100 2546517 http://www.medworm.com/index.php?rid=2546515&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%3D19482409%26dopt%3DAbstract Authors: Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of backbone (15)N provides an additional evaluation criteria. As a final test we check the binding modes against available structure-activity-relationships. We find that the most likely bind... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546515 Sun, 28 Jun 2009 03:47:22 +0100 2546515 http://www.medworm.com/index.php?rid=2546513&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%3D19487068%26dopt%3DAbstract Authors: Audie J Here we summarize recent work on the continued development of our fast and simple empirical equation for predicting and structurally rationalizing protein-protein and protein-peptide binding affinities. Our empirical expression consists of six regression-weighted physical descriptors and derives from two key simplifying assumptions: (1) the assumption of rigid-body association and (2) the assumption that all contributions not explicitly considered in the equation make a net contribution to binding of approximately 0 kcal. Within the strict framework of rigid-body association, we tested relative binding affinity predictions using our empirical equation against the corresponding experimental binding free energy data for 197 interface alanine mutants. Our methodology prod... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546513 Sun, 28 Jun 2009 03:47:20 +0100 2546513 http://www.medworm.com/index.php?rid=2546511&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%3D19491057%26dopt%3DAbstract Authors: Koukiekolo R, Jakubek ZJ, Cheng J, Sagan SM, Pezacki JP Eukaryotes have evolved complex cellular responses to double-stranded RNA. One response that is highly conserved across many species is the RNA silencing pathway. Tombusviruses have evolved a mechanism to evade the RNA silencing pathway that involves a small protein, p19, that acts as a suppressor of RNA silencing. This protein binds specifically to small-interfering RNAs (siRNAs) with nanomolar affinity in a sequence-independent manner and with size selectivity. PMID: 19491057 [PubMed - in process] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546511 Sun, 28 Jun 2009 03:47:17 +0100 2546511 http://www.medworm.com/index.php?rid=2546509&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%3D19493608%26dopt%3DAbstract Authors: Kaluzhny D, Shchyolkina A, Livshits M, Lysov Y, Borisova O Human genome is shown to be enriched with (GT)(n) stretches of lengths from 8 to 20 dinucleotides. Low temperature (T< or =10 degrees C) conformations of d(GT)(n) oligonucleotides (n=7, 8, 12, 16, 20) were studied by means of circular dichroism (CD), thermal melting, ethidium bromide (EtBr) probing and single nucleotide substitutions. Rotational relaxation times for EtBr:d(GT)(n) complexes confirmed a monomolecular state of the oligonucleotides. CD spectra indicated involvement of all guanines of d(GT)(8) and d(GT)(16) in G-quartets, while dT(GT)(7), d(GT)(12) and d(GT)(20) were shown to be only partially ordered. The schemes of the d(GT)(8) and d(GT)(16) folds are suggested. PMID: 19493608 [PubMed - in process]... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546509 Sun, 28 Jun 2009 03:47:15 +0100 2546509 http://www.medworm.com/index.php?rid=2546505&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%3D19501951%26dopt%3DAbstract Authors: Amatore C, Arbault S, Bonifas I, Guille M Around 30% of exocytosis events recorded by amperometry at carbon fiber microelectrodes exhibit a pre-spike feature (PSF) termed a "foot". This wave is associated with the release of the neurotransmitters via a transitory fusion pore, whilst the large, main exocytotic spike is due to complete release. The amperometric data reported herein were obtained using bovine chromaffin cells stimulated with either potassium or barium ions, two commonly-employed elicitors of exocytosis. Identical trends are observed with both activators: (i) they induce the same ratio (close to 30%) of events with a foot in the population of amperometric spikes, and (ii) spikes with a foot can be divided into two primary categories, depending on the temporal vari... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546505 Sun, 28 Jun 2009 03:47:10 +0100 2546505 http://www.medworm.com/index.php?rid=2546504&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%3D19539421%26dopt%3DAbstract Authors: Drochioiu G, Manea M, Dragusanu M, Murariu M, Dragan ES, Petre BA, Mezo G, Przybylski M The stoichiometries and the affinity toward simple and paired metal ions of synthetic amyloid-beta(1-40) peptide (Abeta1-40) were investigated by electrospray ion trap mass spectrometry (ESI-MS), circular dichroism (CD), and atomic force microscopy (AFM). The results lead to the working hypothesis that pH-dependent metal binding to Abeta1-40 may induce conformational changes, which affect the affinity toward other metals. A significant copper and zinc binding to Abeta1-40 peptide at pH 5.5 was found, whereas nickel ions commonly bind to each molecule of beta-amyloid peptide. Some complexes of Abeta1-40 with more than one nickel ion were identified by ESI-MS. In addition, nickel ions proved ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546504 Mon, 15 Jun 2009 23:00:00 +0100 2546504 http://www.medworm.com/index.php?rid=2546502&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%3D19545938%26dopt%3DAbstract Authors: Varhač R, Tomášková N, Fabián M, Sedlák E Effect of anions of the Hofmeister series (thiocyanate, perchlorate, iodide, bromide, nitrate, chloride, sulfate, and phosphate) on local and global stability and flexibility of horse heart ferricytochrome c (cyt c) has been studied. Global stability of cyt c was determined by iso/thermal denaturations monitored by change in ellipticity in the far-UV region and its local stability was determined from absorbance changes in the Soret region. Particularly, relative stability/flexibility of the Met80-heme iron bond has been assessed by analysis of binding of cyanide into the heme iron. Both global and local stabilities of cyt c exhibited monotonous increase induced by a change of anion from chaotropic to kos... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546502 Fri, 05 Jun 2009 23:00:00 +0100 2546502 http://www.medworm.com/index.php?rid=2546531&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%3D19380189%26dopt%3DAbstract Authors: Le Ny AL, Lee CT Direct observation of the mechanism and dynamics of photo-initiated DNA compaction and re-expansion using a light-responsive cationic surfactant has been achieved with fluorescence microscopy. The surfactant undergoes a reversible photoisomerization upon exposure to visible (trans isomer, relatively hydrophobic) or UV (cis isomer, relatively hydrophilic) light. Thus, surfactant binding to DNA and the DNA condensation that result can both be initiated and controlled with light illumination. The inherent kinetics of DNA conformational changes, directly visualized following the in situ light "trigger" of surfactant photoisomerization, are found to occur at rates of approximately 9 microm/s or 240 kbp/s, at or near rates that can be achieved in natural processes. ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546531 Sun, 31 May 2009 23:00:00 +0100 2546531 http://www.medworm.com/index.php?rid=2546507&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%3D19501449%26dopt%3DAbstract In this study, we use Saturation Transfer Difference (STD) NMR spectroscopy to acquire an atom-specific map of the interactions between soluble and aggregated Transthyretin peptide (TTR(105-115)) in early- and late-stage amyloidogenesis. Atomic Force Microscopy (AFM) was used to monitor the transition of early-stage samples, containing protofilaments, to late-stage samples composed of fully-mature fibrils. Progressive aggregation was accompanied by an increase in the correlation time tau(c) of soluble TTR(105-115) as indicated by (1)H NMR line broadening, but no significant change in the (1)H chemical shifts. The STD profile of backbone amide protons is in good agreement with an earlier computational study predicting hydrogen bonding propensity for each residue in small TTR(105-115) aggreg... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2546507 Thu, 21 May 2009 23:00:00 +0100 2546507 http://www.medworm.com/index.php?rid=2210182&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%3D19231807%26dopt%3DAbstract Authors: Rungrotmongkol T, Malaisree M, Udommaneethanakit T, Hannongbua S PMID: 19231807 [PubMed - in process] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210182 Tue, 24 Feb 2009 21:02:28 +0100 2210182 http://www.medworm.com/index.php?rid=2210181&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%3D19231808%26dopt%3DAbstract Authors: Mitrasinovic PM PMID: 19231808 [PubMed - in process] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210181 Tue, 24 Feb 2009 21:02:25 +0100 2210181 http://www.medworm.com/index.php?rid=2210178&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%3D19232814%26dopt%3DAbstract Authors: Perc M We show that the spatial synchronization of noise-induced excitations on scale-free networks, mediated through nonlinear chemical coupling, depends vitally on the intensity of additive noise and the coupling strength. In particular, a twofold optimization is needed for achieving maximal spatial synchrony, thus indicating the existence of an optimal noise intensity as well as an optimal coupling strength. On the other hand, the traditional linear coupling via gap junctions, while still requiring a fine-tuning of the noise intensity, does not postulate the existence of an optimal coupling strength since the synchronization increases monotonously with the increasing coupling strength. Presented results reveal inherent differences in optimal spatial synchronization evoked b... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210178 Fri, 06 Feb 2009 05:00:00 +0100 2210178 http://www.medworm.com/index.php?rid=2210177&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%3D19233539%26dopt%3DAbstract Authors: Baran M, Borowski E, Mazerski J The work presented is a part of our continual study on the behavior of the polyene macrolide antibiotic amphotericin B (AmB) complexes with sterols on the molecular level. In contrast to the previously researched AmB-ergosterol binary complex, the AmB-ergosterol-AmB aggregates simulated of 2:1 stoichiometry retain significantly higher stability and relatively rigid, "sandwich" geometry. Van der Waals forces with a considerable share of the electrostatic interactions are responsible for such behavior. System of the intermolecular hydrogen bonds also seems to be of notable importance for the complex's structure preservation. The most energetically favored geometries match fairly close the geometric criteria and the network of interactions postulat... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210177 Wed, 04 Feb 2009 05:00:00 +0100 2210177 http://www.medworm.com/index.php?rid=2210176&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%3D19233540%26dopt%3DAbstract Authors: Goldstein BN A graph-theoretic approach is shown to simplify the analysis of transient enzyme kinetics. The coefficients of the characteristic polynomial for kinetic equations are obtained by graphical construction of directed trees and sub-trees in the kinetic scheme. An example of kinetic schemes, providing a simple time-dependent analytical solution, is demonstrated. This example describes a substrate-inhibited enzymatic reaction and interprets the pH-dependent inhibition of the lactate dehydrogenase. It is shown that rapid equilibrium in some parts of the kinetic scheme can simplify the analysis. The enzyme pre-incubation with a product is shown to be characterized by the non-monotonous transient kinetics. This phenomenon is useful to estimate correctly the kinetic paramet... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210176 Wed, 04 Feb 2009 05:00:00 +0100 2210176 http://www.medworm.com/index.php?rid=2210179&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%3D19232813%26dopt%3DAbstract Authors: Castelletto V, Hamley IW There has been great interest recently in peptide amphiphiles and block copolymers containing biomimetic peptide sequences due to applications in bionanotechnology. We investigate the self-assembly of the peptide-PEG amphiphile FFFF-PEG5000 containing the hydrophobic sequence of four phenylalanine residues conjugated to PEG of molar mass 5000. This serves as a simple model peptide amphiphile. At very low concentration, association of hydrophobic aromatic phenylalanine residues occurs, as revealed by circular dichroism and UV/vis fluorescence experiments. A critical aggregation concentration associated with the formation of hydrophobic domains is determined through pyrene fluorescence assays. At higher concentration, defined beta-sheets develop as revea... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210179 Tue, 03 Feb 2009 05:00:00 +0100 2210179 http://www.medworm.com/index.php?rid=2210180&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%3D19232456%26dopt%3DAbstract Authors: Pérez-López S, Nieto-Suárez M, Mestres C, Alsina MA, Haro I, Vila-Romeu N The GB virus C/hepatitis G virus (GBV C/HGV) is a Flaviviridae member that despite its non pathogenicity, has become of great interest given that it could inhibit the replication of the human immunodeficiency virus (HIV). Therefore, a better knowledge of the virus peptides involved in the cellular membrane fusion mechanism has become our aim. The selected peptide, named E2(347-363), corresponds to the GBV-C/HGV E2 protein and has been synthesized in order to study its interaction with in vitro membrane models. Two phospholipids, varying the charge and the unsaturations of the hydrocarbon chain have been chosen: 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dioleoyl-sn-glycero-... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2210180 Fri, 30 Jan 2009 05:00:00 +0100 2210180 http://www.medworm.com/index.php?rid=2172683&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%3D19200635%26dopt%3DAbstract Authors: Anderson JS, Hernández G, Lemaster DM Electrostatic interactions at the protein surface yield over a billion-fold range of amide hydrogen exchange rates. This range is equivalent to the maximal degree of attenuation in exchange rates that have been shown to occur for amides buried within the protein interior. Continuum dielectric analysis of Ala-Ala, Ala-Gly, Gly-Ala and trans-Pro-Ala peptide conformer acidities predicts that the relative orientation of the two neighboring peptide groups can account for a million-fold variation in hydroxide-catalyzed hydrogen exchange rates. As in previous protein studies, an internal dielectric value of 3 was found to be applicable to simple model peptides, presumably reflecting the short lifetime of the peptide anion intermediate. Despi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2172683 Sat, 24 Jan 2009 05:00:00 +0100 2172683 http://www.medworm.com/index.php?rid=2149557&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%3D19178992%26dopt%3DAbstract Authors: Tatoli S, Zazza C, Sanna N, Palma A, Aschi M Molecular dynamics simulations on hydrogen peroxide complex with wild-type (WT) and Arg38Leu mutated (R38L) Horseradish Peroxidase (HRP) were carried out over nanoseconds timescale in water solution at 300 K. Comparison of the results provides interesting insights about the role of highly conserved Arg38 and His42 residues in the chemical features of HRP, underlying its biological activity which initiates with Compound0 (Cpd0). In the WT-HRP enzyme current molecular dynamics simulations show, for the first time, that Arg38 residue: i) prevents the entrance of water inside the reaction cavity, hence providing a hydrophobic reactive scenario, ii) it maintains the distance between His42 and heme-H(2)O(2) complex suitable for the occurr... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2149557 Thu, 15 Jan 2009 05:00:00 +0100 2149557 http://www.medworm.com/index.php?rid=2147487&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%3D19176270%26dopt%3DAbstract Authors: Kawakubo T, Okada O, Minami T Muscle contraction is caused by directed movement of myosin heads along actin filaments. This movement is triggered by ATP hydrolysis, which occurs within the motor domain of myosin. The mechanism for this intramolecular process remains unknown owing to a lack of ways to observe the detailed motions of each atom in the myosin molecule. We carried out 10-ns all-atom molecular dynamics simulations to investigate the types of dynamic conformational changes produced in the motor domain by the energy released from ATP hydrolysis. The results revealed that the thermal fluctuations modulated by perturbation of ATP hydrolysis are biased in one direction that is relevant to directed movement of the myosin head along the actin filament. PMID: 19176270 [... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2147487 Tue, 13 Jan 2009 05:00:00 +0100 2147487 http://www.medworm.com/index.php?rid=2137414&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%3D19168275%26dopt%3DAbstract Authors: Nozad AG, Meftah S, Ghasemi MH, Kiyani RA, Aghazadeh M A systematic computational study is carried out to investigate hydrogen bond (HB) interactions in the real crystalline structures of l-Cysteine at 30 and 298 K by density functional theory (DFT) calculations of electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (monomer) and nine-molecule (cluster) models of l-Cysteine are created by available crystal coordinates at both temperatures and the EFG tensors are calculated for both models to indicate the effect of HB interactions on the tensors. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G and cc-pVTZ basis sets are converted to those experimentally measurable nuclear quadrupole resonance (NQR) ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2137414 Wed, 07 Jan 2009 05:00:00 +0100 2137414 http://www.medworm.com/index.php?rid=2131243&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%3D19162392%26dopt%3DAbstract Authors: Vetrova EV, Kudryasheva NS, Cheng KH The interaction of quinone with luciferase from Photobacterium leiognathi was studied based on the fluorescence decay measurements of the endogenous flavin bound to the enzyme. Homologous 1,4-quinones, 1,4-benzoquinone, methyl-1,4-benzoquinone, 2-methyl-5-isopropyl-1,4-benzoquine and 1,4-naphthoquinone, were investigated. In the absence of quinone, the fluorescence intensity and anisotropy decays of the endogenous flavin exhibited two intensity decay lifetimes (~1 and 5 ns) and two anisotropy decay lifetimes (~0.2 and 20 ns), suggesting a heterogeneous quenching and a rotational mobility microenvironment of the active site of the luciferase, respectively. In the presence of quinone, the intensity decay heterogeneity was largely maintained, ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2131243 Wed, 07 Jan 2009 05:00:00 +0100 2131243 http://www.medworm.com/index.php?rid=2131245&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%3D19162390%26dopt%3DAbstract Authors: Hald B, Madsen MF, Danø S, Quistorff B, Sørensen PG The changes in the partial pressures of oxygen and carbon dioxide (P(O(2)) and P(CO(2))) during blood circulation alter erythrocyte metabolism, hereby causing flux changes between oxygenated and deoxygenated blood. In the study we have modeled this effect by extending the comprehensive kinetic model by Mulquiney and Kuchel [P.J. Mulquiney, and P.W. Kuchel. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement, Biochem. J. 1999, 342, 581-596.] with a kinetic model of hemoglobin oxy-/deoxygenation transition based on an oxygen dissociation model developed by Dash and Bassingthwaighte [R. Dash, and J. Bassingthwaighte. Blood H... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2131245 Wed, 31 Dec 2008 05:00:00 +0100 2131245 http://www.medworm.com/index.php?rid=2131244&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%3D19162391%26dopt%3DAbstract Authors: Sen A, Nielsen PE The effects of incorporation of the modified nucleobases, 2,6-diaminopurine (D) (substituting for adenine) and 7-chloro-1,8-naphthyridin-2-(1H)-one (bicyclic thymine, bT) (substituting for thymine), that stabilize PNA.DNA duplex formation by increasing hydrogen bonding and/or base pair stacking interactions have been studied by thermal denaturation in terms of thermodynamics. Although the stabilizing effect of the bT base (in contrast to that of D base) is abolished upon addition of dimethyl formamide, thereby indicating that the stabilization is predominantly due to hydrophobic stacking forces, duplex stabilization was found to be enthalpic for both nucleobases. Increased stabilization (although not fully linearly) was observed with increasing numbers of mod... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2131244 Wed, 31 Dec 2008 05:00:00 +0100 2131244 http://www.medworm.com/index.php?rid=2128769&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%3D19157682%26dopt%3DAbstract This report presents the following evidence that diclofenac interacts with red cell membranes: a) X-ray diffraction and fluorescence spectroscopy of phospholipid bilayers showed that diclofenac interacted with a class of lipids found in the outer moiety of the erythrocyte membrane; b) in isolated unsealed human erythrocyte membranes (IUM) the drug induced a disordering effect on the acyl chains of the membrane lipid bilayer; c) in scanning electron microscopy (SEM) studies on human erythrocytes it was observed that the drug induced changes different from the normal biconcave morphology of most red blood cells. This is the first time in which structural effects of diclofenac on the human erythrocyte membrane have been described. PMID: 19157682 [PubMed - as supplied by publisher] (Source... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2128769 Wed, 31 Dec 2008 05:00:00 +0100 2128769 http://www.medworm.com/index.php?rid=2125213&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%3D19155119%26dopt%3DAbstract Authors: Eronina TB, Chebotareva NA, Bazhina SG, Makeeva VF, Kleymenov SY, Kurganov BI It has been shown that the relatively low concentrations of proline (0.1 M) have a slight accelerating effect on thermal aggregation of glycogen phosphorylase b (Phb) from rabbit skeletal muscle registered by the accumulaton of the aggregated protein. The suppression of Phb aggregation at high proline concentrations is mainly due to the protective action of proline on the stage of unfolding of the Phb molecule. The enhancement of Phb stability in the presence of the high concentrations of proline was demonstrated by the data on differential scanning calorimetry, analytical ultracentrifugation and thermoinactivation kinetics. The construction of the protein aggregate size versus time plots allowed the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2125213 Wed, 31 Dec 2008 05:00:00 +0100 2125213 http://www.medworm.com/index.php?rid=2125214&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%3D19155118%26dopt%3DAbstract Authors: Pecher P, Arnold U The significant contribution of disulfide bonds to the conformational stability of proteins is generally considered to result from an entropic destabilization of the unfolded state causing a faster escape of the molecules to the native state. However, the introduction of extra disulfide bonds into proteins as a general approach to protein stabilization yields rather inconsistent results. By modeling studies, we selected positions to introduce additional disulfide bonds into ribonuclease A at regions that had proven to be crucial for the initiation of the folding or unfolding process, respectively. However, only two out of the six variants proved to be more stable than unmodified ribonuclease A. The comparison of the thermodynamic and kinetic data disclosed a... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2125214 Tue, 30 Dec 2008 05:00:00 +0100 2125214 http://www.medworm.com/index.php?rid=2104362&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%3D19138815%26dopt%3DAbstract Authors: Anarbaev RO, Rogozina AL, Lavrik OI Water is essential for the stability and functions of proteins and DNA. Reverse micelles are simple model systems where the structure and dynamics of water are controlled. We have estimated the size of complex reverse micelles by light scattering technique and examined the local microenvironment using fluorescein as molecular probe. The micelle size and water polarity inside reverse micelles depend on water volume fraction. We have investigated the different hydration and confinement effects on activity, processivity, and stability of mammalian DNA polymerase beta in reverse micelles. The enzyme displays high processivity on primed single-stranded M13mp19 DNA with maximal activity at 10% of water content. The processivity and activity of DNA... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2104362 Thu, 25 Dec 2008 05:00:00 +0100 2104362 http://www.medworm.com/index.php?rid=2089861&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%3D19126445%26dopt%3DAbstract Authors: Widomska J, Kostecka-Gugała A, Latowski D, Gruszecki WI, Strzałka K Carotenoid geometry is a factor that determines their solubility and orientation in the lipid membrane as well as antioxidant capacities and bioavailability. The effects of the cis-isomers of carotenoids (zeaxanthin and beta-carotene) on the thermotropic properties of lipid membranes formed with dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) were investigated by means of differential scanning calorimetry. The results were compared with the effects caused by the all-trans-isomer. Both the trans and cis isomers of zeaxanthin shifted the main phase transition temperature to lower values and decreased the cooperativity of the phase transition. The effect of all-trans ze... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2089861 Wed, 24 Dec 2008 05:00:00 +0100 2089861 http://www.medworm.com/index.php?rid=2083886&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%3D19121888%26dopt%3DAbstract Authors: Despa F Insulin regulates the energy homeostasis of the human body. This is synthesized in the endoplasmic reticulum (ER) of pancreatic beta cells from proinsulin. Chronic hyperglycemia increases considerably the proinsulin secretion, overcrowding the ER. Recent experimental evidence demonstrates that such states favor the proinsulin denaturation. The biophysical mechanism of this cellular dysfunction remains largely unknown. We use basic molecular principles and numerical simulations of time-dependent crowding conditions in the ER to show that crowding effects enhance the propensity of proinsulin molecules to (mis)fold in compressed, nonnative structures. Present results suggest: i) misfolding events and toxic accumulations increase dramatically if the proinsulin load exceeds... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2083886 Wed, 24 Dec 2008 05:00:00 +0100 2083886 http://www.medworm.com/index.php?rid=2073721&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%3D19117661%26dopt%3DAbstract This study suggests singular approach of tuning bioinspired morphologies via natural principles of interaction and affinity. We envisage that such hemispherical capsules provide an expeditious entry into interesting soft structures which may be harnessed for potential applications. PMID: 19117661 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2073721 Sat, 13 Dec 2008 05:00:00 +0100 2073721 http://www.medworm.com/index.php?rid=2060757&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%3D19101067%26dopt%3DAbstract Authors: Miao TF, Liao SY, Qian L, Zheng KC, Ji LN Studies on the electronic structures and trend in DNA-binding affinities of a series of Co(capital SHA, Cyrillic) complexes have been carried out, using the density functional theory (DFT) at the B3LYP/LanL2DZ level. The optimized geometric structures of these Co(capital SHA, Cyrillic) complexes in aqueous solution are more close to experimental data than those in vacuo. The electronic structures of these Co(capital SHA, Cyrillic) complexes were analyzed on the basis of their geometric structures optimized in aqueous solution, and the trend in the DNA-binding constants (K(b)) was reasonably explained. In addition, the electronic absorption spectra of these complexes were calculated and simulated in aqueous solution using the time depen... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2060757 Sun, 07 Dec 2008 05:00:00 +0100 2060757 http://www.medworm.com/index.php?rid=2046553&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%3D19073357%26dopt%3DAbstract Authors: Miñones J, Pais S, Miñones J, Conde O, Dynarowicz-Łątka P This paper is aimed at investigating sterol/phospholipid interactions in the exact proportion that occurs in fungi/mammalian cells. We have performed a thorough analysis of surface pressure (pi)-area (A) isotherms with the Langmuir monolayer technique, complemented with Brewster angle microscopy (BAM) images. The following mixtures were analysed: cholesterol (Chol)-dipalmitoyl phosphatidylcholine (DPPC), Chol-dioleoyl phosphatidylcholine (DOPC), ergosterol (Erg)-DPPC, and Erg-DOPC. For each system, two different concentrations of the sterols were used, 13 and 30%, corresponding to the range of concentration found in various natural membranes. The obtained results show the existence of attractive in... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2046553 Wed, 03 Dec 2008 05:00:00 +0100 2046553 http://www.medworm.com/index.php?rid=2046552&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%3D19073358%26dopt%3DAbstract Authors: Cieślik-Boczula K, Koll A The influence of 3-pentadecylphenol (PDP) on the structure and physicochemical properties of the lipid bilayers of DPPC liposomes was studied using ATR-IR and (31)P NMR methods. On the basis of analysis of the bands assigned to the CH(2) stretching, CH(2) scissoring, CO stretching, and PO(2)(-) stretching vibrations it was revealed that PDP influences both the hydrophobic and hydrophilic parts of the DPPC liposome bilayer. Analysis of the (31)P NMR line-shape indicated a lamellar to non-lamellar phase transition in PDP-doped DPPC dispersions. It was shown that PDP/DPPC isotropic aggregates have similar nuCO and nu(as)PO(2)(-) band positions and lower gauche populations in the hydrophobic chain region compared with the DPPC bilayer in the liquid-... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2046552 Wed, 03 Dec 2008 05:00:00 +0100 2046552 http://www.medworm.com/index.php?rid=2046554&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%3D19070416%26dopt%3DAbstract Authors: Guo J, Cai W, Du B, Qian M, Sun Z PMID: 19070416 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2046554 Thu, 27 Nov 2008 05:00:00 +0100 2046554 http://www.medworm.com/index.php?rid=2017397&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%3D19056157%26dopt%3DAbstract Authors: Szklarczyk O, Zuberek J, Antosiewicz JM The electrostatic free energy of binding of two analogues of the 5'-mRNA cap, differing in size and electric charge, to the wild type and mutated eukaryotic initiation factor eIF4E was computed using the finite difference solutions to the Poisson-Boltzmann equation. Two definitions of the solute-solvent dielectric boundary were used: van der Waals model, solvent exclusion (SE) model. The computed electrostatic energies were supplemented by estimations of the non polar and entropic contributions. A comparison with experimental data for the investigated systems was done. It appears that the SE model with additional contribution fits experimental findings better than the van der Waals model does. PMID: 19056157 [PubMed - as supplied by ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=2017397 Mon, 17 Nov 2008 05:00:00 +0100 2017397 http://www.medworm.com/index.php?rid=1998819&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%3D19038487%26dopt%3DAbstract In this study we discuss stacking interactions in cytosine dimer in conformations appearing in B-DNA crystals. The variational-perturbational scheme was applied for decomposition of the intermolecular interaction energy at the MP2 level of theory. The significant influence of the mutual orientation of cytosine monomers was observed not only on the total intermolecular interaction energy but also on its components: Different components of intermolecular interaction energy depend in different manner on parameters describing mutual orientation of cytosine monomers. PMID: 19038487 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1998819 Thu, 13 Nov 2008 05:00:00 +0100 1998819 http://www.medworm.com/index.php?rid=1990445&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%3D19028005%26dopt%3DAbstract Authors: Nozad AG, Najafi H, Meftah S, Aghazadeh M A systematic computational study was carried out to characterize the hydrogen bond, HB, interactions of sulfabenzamide crystal structure by DFT calculations of electric field gradient, EFG, tensors at the sites of (14)N, (17)O, and (2)H nuclei. The computations were performed with the B3LYP and B3PW91 DFT methods and 6-311+G and 6-311++G standard basis sets using the Gaussian 98 package. To perform the calculations, a hydrogen-bonded heptameric cluster of sulfabenzamide was created by X-ray coordinates where the hydrogen atom positions were optimized and the EFG tensors were calculated for the target molecule. Additional optimization and EFG calculations were also performed for crystalline monomer and an isolated gas-phase sulfabenzami... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1990445 Mon, 10 Nov 2008 05:00:00 +0100 1990445 http://www.medworm.com/index.php?rid=1980461&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%3D19019530%26dopt%3DAbstract Authors: Romani AP, Ito AS Adrenocorticotropin (ACTH) and alpha-melanocyte stimulating hormone (alpha-MSH) are peptides which present many physiological effects related to pigmentation, motor and sexual behavior, learning and memory, analgesia, anti-inflammatory and antipyretic processes. The 13 amino acid residues of alpha-MSH are the same initial sequence of ACTH and due to the presence of a tryptophan residue in position 9 of the peptide chain, fluorescence techniques could be used to investigate the conformational properties of the hormones in different environments and the mechanisms of interaction with biomimetic systems like sodium dodecyl sulphate (SDS) micelles, sodium dodecyl sulphate-poly(ethylene oxide) (SDS-PEO) aggregates and neutral polymeric micelles. In buffer solution... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1980461 Thu, 06 Nov 2008 05:00:00 +0100 1980461 http://www.medworm.com/index.php?rid=1945144&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%3D18990481%26dopt%3DAbstract Authors: Hsieh CP The fluctuation theorem gives a mathematical expression to quantify the probability of observing events violating the second law of thermodynamics in a small system over a short period of time. The theorem predicts the ratio of forward (entropy-producing) runs to the backward (entropy-consuming) runs for a nanometer-sized molecular machine in a nonequilibrium system. However, few experimental verifications of the theorem have been carried out. In this paper, I show that the Ussing flux ratio, the ratio of outward to inward unidirectional ion fluxes across a membrane channel, can be derived from the fluctuation theorem if we consider the ion channel and the contacting solutions as a small nonequilibrium system. The entropy change due to ion electrodiffusion is expresse... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1945144 Sat, 01 Nov 2008 04:00:00 +0100 1945144 http://www.medworm.com/index.php?rid=1945143&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%3D18990482%26dopt%3DAbstract Authors: Gosak M Calcium ions are an important second messenger in living cells. Calcium signals in form of waves serve as a means of intercellular communication and thus represent a vibrant subject for experimental and theoretical investigations. Here we study the role of cellular variability on the occurrence of Ca(2+) wave propagation in a net of diffusively coupled cells. Dynamics of individual cells is simulated by a mathematical model for Ca(2+) oscillations. Structural diversity of cells is introduced via variations of the bifurcation parameters, which signify cell sensitivity for external stimulation. Remarkably, for sufficient values of variability Ca(2+) waves emerge, which are mostly ordered for intermediate variability strength. We analyze the spatial profile via the autoco... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1945143 Sat, 25 Oct 2008 04:00:00 +0100 1945143 http://www.medworm.com/index.php?rid=1924386&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%3D18963381%26dopt%3DAbstract Authors: Börjesson K, Sandin P, Wilhelmsson LM The fluorescent cytosine analog tC(O) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(O), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tC(O) is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transiti... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1924386 Sat, 11 Oct 2008 04:00:00 +0100 1924386 http://www.medworm.com/index.php?rid=1914452&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%3D18951690%26dopt%3DAbstract Authors: Yadav SC, Jagannadham MV, Kundu S, Jagannadham MV Milin, a potent molluscicide from the latex of Euphorbia milii, holds promise in medicinal biochemistry. Electrophoresis, size exclusion chromatography, mass spectrometry and other biochemical characteristics identify milin as a homodimeric, plant subtilisin-like serine protease, the first of its kind. The subunits of milin are differentially glycosylated affecting dimer association, solubility and proteolytic activity. The dimeric dissociation is SDS-insensitive and strongly temperature dependent but does not appear to be linked by disulfide bridges. N-terminal sequence of acid hydrolyzed peptide fragments shows no homology to known serine protease. Peptide mass fingerprinting and de novo sequencing of the tryptic fragments al... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1914452 Wed, 08 Oct 2008 04:00:00 +0100 1914452 http://www.medworm.com/index.php?rid=1894739&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%3D18938024%26dopt%3DAbstract Authors: Delfino I, Cannistraro S The hybrid system obtained by conjugating the protein azurin, which is a very stable and well-described protein showing a unique interplay among its electron transfer and optical properties, with 20-nm sized gold nanoparticles has been investigated. Binding of azurin molecules to gold nanoparticle surface results in the red shift of the nanoparticle resonance plasmon band and in the quenching of the azurin single tryptophan fluorescence signal. These findings together with the estimate of the hydrodynamic radius of the composite, obtained by means of Dynamic Light Scattering, are consistent with the formation of a monolayer of protein molecules, with preserved natural folding, on nanoparticle surface. The fluorescence quenching of azurin bound molecule... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1894739 Tue, 30 Sep 2008 04:00:00 +0100 1894739 http://www.medworm.com/index.php?rid=1879733&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%3D18851894%26dopt%3DAbstract Authors: Gyurova AY, Zhivkov AM The interface electric polarizability of bacteria (charge dependent (ChD) and Maxwell-Wagner (MW) polarizabilities) gives information about their electric charge, determined by the structure and functional state. It is well known that the polarizability could be changed significantly by adding some substances to the suspension, and can be measured using an electro-optical (EO) method. There are some literature data, according to which the adding of ethanol decreases the electric polarizability of the cells. However the reason for the change in this parameter is not clear, as well as which component (ChD and/or MW) of polarizability has the main contribution. Generally the present work shows that the effect of ethanol is connected to the change of the int... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1879733 Tue, 30 Sep 2008 04:00:00 +0100 1879733 http://www.medworm.com/index.php?rid=1865359&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%3D18842331%26dopt%3DAbstract Authors: Zhao X, Shang Y, Hu J, Liu H, Hu Y The interaction between DNA and cationic gemini surfactant trimethylene-1, 3-bis (dodecyldimethylammonium bromide) (12-3-12) has been investigated by the measurements of fluorescence, surface tension, UV spectrum and circular dichroism (CD). Micelle-like structure of 12-3-12 induced by DNA appears at critical aggregation concentration (CAC), which is much lower than critical micelle concentration (CMC) of 12-3-12 in DNA-free solution. CAC is independent of DNA concentration, but the CMC of the mixed solutions of DNA and 12-3-12(CMC(mix)) increases with the increasing of DNA concentration. The surface tensions of the mixed system are higher than that of the pure surfactant solution, much different from the so-called synergistic lowering of the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1865359 Tue, 23 Sep 2008 04:00:00 +0100 1865359 http://www.medworm.com/index.php?rid=1859355&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%3D18835080%26dopt%3DAbstract In this report, peptides derived from the C-terminal of p21 that cover the binding domain of calmodulin were used to investigate the association of p21 with calmodulin. We found p21(141-164) interaction with Ca(2+)-saturated dansyl-labelled calmodulin caused a significant increase in dansyl fluorescence intensity and a blue shift of the maximum emission from 510 to 475 nm. The Trp fluorescence intensities of mutated p21(141-164) peptides (F150W, Y151W and F159W) increased upon binding to Ca(2+)-saturated calmodulin and fluorescence maxima were blue shifted from 350 nm to 330 nm. The results suggested p21(141-164) is most likely buried in the hydrophobic binding tunnel of calmodulin. Both dansyl and Trp fluorescence titrations generated dissociation constants around 0.1 muM and a stoichiome... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1859355 Sat, 20 Sep 2008 04:00:00 +0100 1859355 http://www.medworm.com/index.php?rid=1859354&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%3D18835508%26dopt%3DAbstract Authors: Poddar NK, Ansari ZA, Singh RK, Moosavi-Movahedi AA, Ahmad F Thermal denaturation curves of ribonuclease-A were measured by monitoring changes in the far-UV circular dichroism (CD) spectra in the presence of different concentrations of six sugars (glucose, fructose, galactose, sucrose, raffinose and stachyose) and mixture of monosaccharide constituents of each oligosaccharide at various pH values in the range of 6.0-2.0. These measurements gave values of T(m) (midpoint of denaturation), DeltaH(m) (enthalpy change at T(m)), DeltaC(p) (constant-pressure heat capacity change) under a given solvent condition. Using these values of DeltaH(m), T(m) and DeltaC(p) in appropriate thermodynamic relations, thermodynamic parameters at 25 degrees C, namely, DeltaG(D)(o) (Gibbs energy chang... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1859354 Sat, 20 Sep 2008 04:00:00 +0100 1859354 http://www.medworm.com/index.php?rid=1859356&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%3D18834656%26dopt%3DAbstract Authors: Ramprakash J, Schwarz FP The thermodynamics of RNA polymerase (RNAP) binding to a 108 base pair (bp) synthetic promoter with consensus sequences at the -35 and -10 bp binding regions upstream from the transcription start point were determined using isothermal titration calorimetry (ITC). The binding constant at 25 degrees C is 2.37+/-0.18x10(7) M(-1), which is reduced to 0.17+/-0.06x10(7) M(-1) with mutations in the -10 bp region but remained the same with mutations in the -35 binding region. The binding reactions were enthalpically-driven with exothermic binding enthalpies ranging from -57+/-6 kJ mol(-1) at 15 degrees C to -271+/-20 kJ mol(-1) at 35 degrees C yielding a large binding heat capacity change of -10.7+/-1.9 kJ mol(-1) K(-1), indicating a conformational change upon... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1859356 Thu, 18 Sep 2008 04:00:00 +0100 1859356 http://www.medworm.com/index.php?rid=1850888&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%3D18829149%26dopt%3DAbstract Comment on: Construction of simplified models to simulate estrogenic disruptions by esters of 4-hydroxybenzoic acid (parabens). Patricia Guadarrama, Serguei Fomine, Roberto Salcedo, Ana Martínez. Biophys. Chem. 137 (2008) 1-6. doi:10.1016/j.bpc2008.06.001. Biophys Chem. 2008 Sep 16; Authors: Godfrey D PMID: 18829149 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1850888 Tue, 16 Sep 2008 04:00:00 +0100 1850888 http://www.medworm.com/index.php?rid=1844527&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%3D18823691%26dopt%3DAbstract Authors: Faísca PF, Gomes CM In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and a gross, generic feature of the native geometry, namely, the relative number of local and non-local native contacts. The results from our study, which is based on Monte Carlo simulations of simple lattice proteins, show that folding to a structure that is rich in local contacts is considerably more plastic than folding to a native geometry characterized by having a very large number of long-range contacts (i.e., contacts between amino acids that are separated by more than 12 units of backbone distance). The smaller f... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1844527 Sun, 14 Sep 2008 04:00:00 +0100 1844527 http://www.medworm.com/index.php?rid=1844526&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%3D18824290%26dopt%3DAbstract Authors: Guadarrama P, Fomine S, Salcedo R, Martínez A PMID: 18824290 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1844526 Sun, 14 Sep 2008 04:00:00 +0100 1844526 http://www.medworm.com/index.php?rid=1840847&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%3D18819743%26dopt%3DAbstract Authors: Surujpaul PP, Gutiérrez-Wing C, Ocampo-García B, de M Ramírez F, Arteaga de Murphy C, Pedraza-López M, Camacho-López MA, Ferro-Flores G A multifunctional system of gold nanoparticles (AuNP) capped by the [Tyr(3)]Octreotide (TOC) peptide was prepared and characterized by transmission electron microscopy (TEM) and UV-Vis, infrared and fluorescence spectroscopy. AuNP and AuNP-TOC fluorescence emission spectra were obtained both in solution and in murine AR42J-tumor tissues. Results suggest that AuNP were functionalized with TOC through interactions with the N-terminal amine of the phenylalanine, the amide groups and possibly with the indole group of the tryptophan residue. The fluorescence analyses in tissue revealed a recognition of the AuNP-TOC conjugat... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1840847 Sun, 14 Sep 2008 04:00:00 +0100 1840847 http://www.medworm.com/index.php?rid=1840846&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%3D18819744%26dopt%3DAbstract Authors: Moyon NS, Singh TS, Mitra S A systematic study on the spectroscopy and photophysical properties of widely used analgesic and anti-pyretic drug acetaminophen (NAPAP) was presented using steady state and time-resolved fluorescence spectroscopy. The results in homogeneous solvents were compared with those in bio-mimicking environments of cyclodextrin and micellar cavities. Extensive theoretical calculations using time dependent density functional theory (TDDFT) were also done to substantiate the spectral assignment as well as to compare the structure and stability of possible hydrogen bonded conformations of NAPAP in aqueous medium. Facile proton dissociation occurs due to extensive charge redistribution in the excited state. The variation in fluorescence yield and the life time ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1840846 Fri, 12 Sep 2008 04:00:00 +0100 1840846 http://www.medworm.com/index.php?rid=1833064&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%3D18814949%26dopt%3DAbstract Authors: Oancea D, Stuparu A, Nita M, Puiu M, Raducan A An isoconversional method is proposed in order to calculate the kinetic parameters of enzyme inactivation. The method provides an efficient and low-cost procedure to describe both operational and thermal inactivation. Unlike the ordinary kinetic assays performed at constant enzyme concentration and at various substrate concentrations, the isoconversional method requires several extended kinetic curves for constant initial substrate concentration and different enzyme concentrations. The procedure was tested and validated using simulated data obtained for several kinetic models frequently discussed in the literature. After the validation, the isoconversional method was used for the investigation of the thermoinactivation of urease d... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1833064 Thu, 11 Sep 2008 04:00:00 +0100 1833064 http://www.medworm.com/index.php?rid=1833066&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%3D18814946%26dopt%3DAbstract Authors: Subach F, Kirsanova O, Liquier J, Gromova ES The X-ray structure for the type IIE EcoRII restriction endonuclease has been resolved [X.E. Zhou, Y. Wang, M. Reuter, M. Mucke, D.H. Kruger, E.J. Meehan and L. Chen. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J. Mol. Biol. 335 (2004) 307-319.], but the structure of the R.EcoRII-DNA complex is still unknown. The aim of this article was to examine the structure of the pre-reactive R.EcoRII-DNA complex in solution by fluorescence spectroscopy. The structure for the R.EcoRII-DNA complex was resolved by determining the fluorescence resonance energy transfer (FRET) between two fluorescent dyes, covalently attached near the EcoRII recognition sites, t... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1833066 Wed, 10 Sep 2008 04:00:00 +0100 1833066 http://www.medworm.com/index.php?rid=1833065&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%3D18814948%26dopt%3DAbstract Authors: Rahaman H, Khan KA, Hassan I, Wahid M, Singh SB, Singh TP, Moosavi-Movahedi AA, Ahmad F We have determined the sequence of mitochondrial cytochrome c (cyt-c) from the goat heart, and it was found to have a unique amino acid sequence among all amino acid sequences of cyt-c reported till date. Its sequence alignment with the bovine cytochrome c (b-cyt-c) led us to conclude that the goat cytochrome c (g-cyt-c) differs in amino acid sequence from b-cyt-c at only one position, i.e., Pro44(bovine) --> Ala44(goat). It has been observed that guanidinium chloride (GdmCl) induces a two-state transition between the native (N) and denatured (D) states of g-cyt-c. This conclusion is reached from the coincidence of GdmCl-induced transition curves monitored by measurements of absorbance a... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1833065 Thu, 04 Sep 2008 04:00:00 +0100 1833065 http://www.medworm.com/index.php?rid=1825322&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%3D18804320%26dopt%3DAbstract Authors: Tada K, Saito K, Goto M, Tamai N, Matsuki H, Kaneshina S We investigated the thermotropic and barotropic bilayer phase behavior of 1-myristoyl-2-oleoyl-sn-glycero-3-phosphocholine (MOPC) and 1-oleoyl-2-myristoyl-sn-glycero-3-phosphocholine (OMPC) by means of the differential scanning calorimetry (DSC) and high-pressure light-transmittance technique. Water could be used as a solvent for measurements at high pressures because of the elevation of the transition temperatures above 0 degrees C by pressurization, whereas aqueous 50 wt.% ethylene glycol solution was used mainly for those at low pressures. Only one phase transition was observed in the DSC thermogram of the MOPC bilayer membrane as an endothermic peak, and also observed at high pressures as an abrupt change of the ligh... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1825322 Wed, 03 Sep 2008 04:00:00 +0100 1825322 http://www.medworm.com/index.php?rid=1811239&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%3D18801607%26dopt%3DAbstract Authors: Kratochvílová I, Král K, Bunček M, Víšková A, Nešpůrek S, Kochalska A, Todorciuc T, Weiter M, Schneider B The conductivity of DNA covalently bonded to a gold surface was studied by means of the STM technique. Various single- and double-stranded 32-nucleotide-long DNA sequences were measured under ambient conditions so as to provide a better understanding of the complex process of charge-carrier transport in natural as well as chemically modified DNA molecules. The investigations focused on the role of several features of DNA structure, namely the role of the negative charge at the backbone phosphate group and the related complex effects of counterions, and of the stacking interactions between the bases in Watson-Crick and other ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1811239 Thu, 28 Aug 2008 04:00:00 +0100 1811239 http://www.medworm.com/index.php?rid=1802582&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%3D18793820%26dopt%3DAbstract Authors: Avila CL, de Arcuri BF, Gonzalez-Nilo F, De Las Rivas J, Chehín R, Morero R Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is considered a classical glycolytic protein that can promote the fusion of phospholipid vesicles and can also play a vital role on in vivo fusogenic events. However, it is not clear how this redox enzyme, which lack conserved structural or sequence motifs related to membrane fusion, catalyze this process. In order to detect if this ability is present in other NAD(P)H dehydrogenases with available structure, spectroscopic studies were performed to evaluate the capability of alcohol dehydrogenase (ADH), glutamic dehydrogenase (GDH) and sorbitol dehydrogenase (SDH) to bind, aggregate, destabilize and fuse vesicles. Based on finite difference Poisson-B... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1802582 Sat, 23 Aug 2008 04:00:00 +0100 1802582 http://www.medworm.com/index.php?rid=1779081&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%3D18775599%26dopt%3DAbstract Authors: Xu W, Mu Y Replica-exchange molecular dynamics simulations with hybrid Hamiltonian in explicit solvent were performed to study the folding of a designed 20-residue miniprotein, Trpcage, from a fully extended structure. During the simulations several folding/unfolding events happened. In the folded states the majority of experimentally observed NMR NOE restraints are satisfied. The folded structures have root mean squared deviation of 2.0 A with respect to the NMR structures considering all heavy atoms. The free-energy surface constructed by the hybrid Hamiltonian simulations is similar to the one built by a standard replica-exchange simulation which started from the native structure. Consistent with previous experimental observation, a pre-existing hydrophobic collapse in the ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1779081 Wed, 13 Aug 2008 04:00:00 +0100 1779081 http://www.medworm.com/index.php?rid=1745876&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%3D18725174%26dopt%3DAbstract Authors: Nakakido M, Tanaka Y, Mitsuhori M, Kudou M, Ejima D, Arakawa T, Tsumoto K Arginine hydrochloride has been used to suppress protein aggregation during refolding and in various other applications. We investigated the structure of hen egg-white lysozyme (HEL) and solvent molecules in arginine hydrochloride solution by X-ray crystallography. Neither the backbone nor side-chain structure of HEL was altered by the presence of arginine hydrochloride. In addition, no stably bound arginine molecules were observed. The number of hydration water molecules, however, changed with the arginine hydrochloride concentration. We suggest that arginine hydrochloride suppresses protein aggregation by altering the hydration structure and the transient binding of arginine molecules that could not be... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1745876 Sat, 09 Aug 2008 04:00:00 +0100 1745876 http://www.medworm.com/index.php?rid=1729310&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%3D18718697%26dopt%3DAbstract Authors: Gagoś M, Gruszecki WI Amphotericin B (AmB) is a life-saving antibiotic, used to treat deep-seated mycotic infections. Both the therapeutic and toxic side effects of AmB are directly dependent on its molecular organization. Organization of AmB was studied in monocomponent monomolecular layers formed at the argon-water interface, by means of polarized and non-polarized electronic absorption spectroscopy and analyzed in terms of the exciton splitting theory. The results provide direct indication that AmB forms spontaneously dimers that can be assembled into molecular structures characterized by homogeneous orientational distribution in the monolayer, interpreted as cylindrical pores. The structures are not stable at surface pressures higher than 20 mN/m and therefore dimers... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1729310 Thu, 07 Aug 2008 04:00:00 +0100 1729310 http://www.medworm.com/index.php?rid=1708811&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%3D18703268%26dopt%3DAbstract Authors: Kinsley N, Sayed Y, Mosebi S, Armstrong RN, Dirr HW Molecular docking and ANS-displacement experiments indicated that 8-anilinonaphthalene sulfonate (ANS) binds the hydrophobic site (H-site) in the active site of dimeric class Mu rGST M1-1. The naphthalene moiety provides most of the van der Waals contacts at the ANS-binding interface while the anilino group is able to sample different rotamers. The energetics of ANS binding were studied by isothermal titration calorimetry (ITC) over the temperature range of 5-30 degrees C. Binding is both enthalpically and entropically driven and displays a stoichiometry of one ANS molecule per subunit (or H-site). ANS binding is linked to the uptake of 0.5 protons at pH 6.5. Enthalpy of binding depends linearly upon temperature yielding a De... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1708811 Tue, 05 Aug 2008 04:00:00 +0100 1708811 http://www.medworm.com/index.php?rid=1708810&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%3D18703269%26dopt%3DAbstract Authors: Tripathi P, Hofmann H, Kayastha AM, Ulbrich-Hofmann R alpha-Amylase from mung beans (Vigna radiata) being one of the few plant alpha-amylases purified so far was studied with respect to its conformational stability by CD and fluorescence spectroscopy. The enzyme was shown to bind 3-4 Ca(2+) ions, which all are important for its activity. In contrast to other alpha-amylases no inhibition was observed at high Ca(2+) concentrations (100 mM). Depletion of calcium decreased the transition temperature from 87 to 48 degrees C. Kinetic stopped-flow fluorescence measurements allowed detecting two unfolding phases at >6 M GdmCl, whereas only one phase was observed at <5 M GdmCl. These results suggest that the first (reversible) step of unfolding is slower than the second (irrevers... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1708810 Wed, 30 Jul 2008 04:00:00 +0100 1708810 http://www.medworm.com/index.php?rid=1682845&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%3D18676081%26dopt%3DAbstract Authors: Garcia W, Figueira AC, de Oliveira Neto M, de Guzzi CA, Buzzá HH, Portugal RV, Calgaro MR, Polikarpov I Human nerve growth factor-induced B (NGFI-B) is a member of the NR4A subfamily of orphan nuclear receptors (NRs). Lacking identified ligands, orphan NRs show particular co-regulator proteins binding properties, different from other NRs, and they might have a non-classical quaternary organization. A body of evidence suggests that NRs recognition of and binding to ligands, DNA, homo- and heterodimerization partners and co-regulator proteins involve significant conformational changes of the NR ligand-binding domains (LBDs). To shed light on largely unknown biophysical properties of NGFI-B, here we studied structural organization and unfolding properties of NGFI-B ligand (l... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1682845 Fri, 18 Jul 2008 04:00:00 +0100 1682845 http://www.medworm.com/index.php?rid=1657108&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%3D18653272%26dopt%3DAbstract Authors: Marquis BJ, Haynes CL In this work, carbon-fiber microelectrode amperometry (CFMA) is employed to probe changes in the biophysical mechanism of exocytosis under varied cell culture conditions. Degranulation and serotonin exocytosis from mouse peritoneal mast cells (MPMCs) were measured both without and with co-cultured Swiss-albino 3t3 fibroblasts using CFMA. After 24 h in culture, there are distinct differences in the exocytotic characteristics of MPMCs cultured with and without fibroblast support cells, as detected by CFMA, including an increased number of secreted serotonin molecules, number of granule fusion events, secretion rate, and granule membrane tension. Beyond 48 h in culture, MPMCs cultured alone cannot be analyzed using CFMA due to decreased viability and membran... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1657108 Wed, 09 Jul 2008 04:00:00 +0100 1657108 http://www.medworm.com/index.php?rid=1630875&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%3D18625543%26dopt%3DAbstract Authors: Rocha S, Thünemann AF, Pereira MD, Coelho M, Möhwald H, Brezesinski G Peptide aggregation in amyloid fibrils is implicated in the pathogenesis of several diseases such as Alzheimer's disease. There is a strong correlation between amyloid fibril formation and a decrease in conformational stability of the native state. Amyloid-beta peptide (Abeta), the aggregating peptide in Alzheimer's disease, is natively unfolded. The deposits found in Alzheimer's disease are composed of Abeta fibrillar aggregates rich in beta-sheet structure. The influence of fluorinated complexes on the secondary structure and fibrillogenesis of Abeta peptide was studied by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). CD spectra show that complexes of polyamphol... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1630875 Fri, 27 Jun 2008 04:00:00 +0100 1630875 http://www.medworm.com/index.php?rid=1615827&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%3D18617319%26dopt%3DAbstract In this study we present a new function of NSAIDs belonging to the oxicam group, as membrane fusogenic agents. Small Unilamellar Vesicles (SUVs) formed by the phospholipid, dimyristoylphosphatidylcholine (DMPC), were used as model membranes. Fluorescence assays using terbium/dipicolinic acid (Tb/DPA) were used to monitor content mixing and corresponding leakage in presence of the drugs. Transmission Electron Microscope (TEM) was also used to image fusion bodies in drug treated vesicles as compared to the untreated ones. The results show that the three oxicam NSAIDs viz. Meloxicam, Piroxicam and Tenoxicam can induce fusion of DMPC vesicles and lead the fusion process to completion at a very low drug to lipid ratio (D/L) of 0.045. The oxicam drugs exhibit differential fusogenic behavior as r... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1615827 Sat, 21 Jun 2008 04:00:00 +0100 1615827 http://www.medworm.com/index.php?rid=1602862&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%3D18603348%26dopt%3DAbstract Authors: Merlino A, Sica F, Mazzarella L, Zagari A, Vergara A Model biopolymers are powerful tools to guide the interpretation of physical properties in complex systems. (Pro-Pro-Gly)(10), (PPG)(10), is a collagen-model peptide, whose structure is known at high resolution. Herein, Raman microscopy data of (PPG)(10) powders and single crystals are reported. The spectra interpretation leads to an accurate assignment of three well-resolved amide bands corresponding to the three peptide bonds (PP, PG and GP) present in the (PPG)(10) structure. These data together with the availability of torsional angles phi and psi derived from the high-resolution crystal structure, provide the opportunity to test the validity of theoretical equations for the calculation of non-canonical amide III bands a... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1602862 Sat, 21 Jun 2008 04:00:00 +0100 1602862 http://www.medworm.com/index.php?rid=1581852&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%3D18599180%26dopt%3DAbstract Authors: Wei C, Han G, Jia G, Zhou J, Li C Interactions of 5,10,15,20-Tetrakis(N-propylpyridinium-4-yl)-21H,23H-porphyrin (TPrPyP4) with dimer hairpin (G(4)T(4)G(4))2 and parallel four-stranded (TG(4)T)4 G-quadruplex DNAs in Na(+)-containing buffer were studied. The results show that two TPrPyP4 molecules bind to both G-quadruplexes by a noncooperative and nonequivalent binding mode, and there are one high affinity site and one low affinity site, the respective binding constants are 8.06x10(8) and 1.13x10(6) M(-1) for (G(4)T(4)G(4))2-TPrPyP4, 8.04x10(7) and 9.08x10(5)M(-1) for (TG(4)T)4-TPrPyP4. TPrPyP4 presents two lifetimes of about 5.8 and 12.0 ns in the complexes of G-quadruplexes-TPrPyP4. The primary results suggest that two TPrPyP4 molecules bind to both G-quadruplexes by termina... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1581852 Wed, 18 Jun 2008 04:00:00 +0100 1581852 http://www.medworm.com/index.php?rid=1560574&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%3D18586378%26dopt%3DAbstract Authors: Chugh J, Sharma S, Kumar D, Misra JR, Hosur RV The GTPase effector domain (GED) of dynamin forms large soluble oligomers in vitro, while its mutant - I697A - lacks this property at low concentrations. With a view to understand the intrinsic structural characteristics of the polypeptide chain, the global unfolding characteristics of GED wild type (WT) and I697A were compared using biophysical techniques. Quantitative analysis of the CD and fluorescence denaturation profiles revealed that unfolding occurred by a two-state process and the mutant was less stable than the WT. Even in the denatured state, the mutation caused chemical shift perturbations and significant differences were observed in the (15)N transverse relaxation rates (R(2)), not only at the mutation site but all ar... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1560574 Tue, 17 Jun 2008 04:00:00 +0100 1560574 http://www.medworm.com/index.php?rid=1560575&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%3D18584938%26dopt%3DAbstract This study provides deeper insights into the possibility of developing viable drug-resistant mutants. PMID: 18584938 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1560575 Sat, 14 Jun 2008 04:00:00 +0100 1560575 http://www.medworm.com/index.php?rid=1551218&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%3D18583018%26dopt%3DAbstract Authors: Yao S, Babon JJ, Norton RS Molecular rotational correlation times are of interest for many studies carried out in solution, including characterization of biomolecular structure and interactions. Here we have evaluated the estimates of protein effective rotational correlation times from their translational self-diffusion coefficients measured by pulsed-field gradient NMR against correlation times determined from both collective and residue-specific (15)N relaxation analyses and those derived from 3D structure-based hydrodynamic calculations. The results show that, provided the protein diffusive behavior is coherent with the Debye-Stokes-Einstein model, translational diffusion coefficients provide rapid estimates with reasonable accuracy of their effective rotational correlation... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1551218 Sat, 14 Jun 2008 04:00:00 +0100 1551218 http://www.medworm.com/index.php?rid=1525862&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%3D18556112%26dopt%3DAbstract Authors: Kyrychenko A, Waluk J The distribution of 1H-pyrrolo[3,2-h]quinoline (PQ), 11H-dipyrido[2,3-a]carbazole (PC) and 7-azaindole (7AI) at a water/membrane interface has been investigated by molecular dynamics (MD) simulations. The MD study focused on favorable binding sites of the azaaromatic probes across a dipalmitoylphosphatidylcholine (DPPC) bilayer. Our simulations show that PQ and PC are preferably accommodated at the hydrocarbon core of the bilayer below the glycerol moiety. In addition, it is found that the hydrophobic aromatic parts of the probes are located inside a more ordered region of DPPC, consisting of hydrophobic lipid chains. In contrast to PQ and PC, 7AI is characterized by a broad distribution between a DPPC interface and water, so that the three preferable bin... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1525862 Fri, 13 Jun 2008 04:00:00 +0100 1525862 http://www.medworm.com/index.php?rid=1525863&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%3D18555583%26dopt%3DAbstract Authors: Schlatterer JC, Greenbaum NL Metal ions play a crucial role in the conformation and splicing activity of Group II introns. Results from 2-aminopurine fluorescence and solution NMR studies suggest that metal ion binding within the branch site region of native D6 of the Group II intron is specific for alkaline earth metal ions and involves inner sphere coordination. Although Mg(2+) and Ca(2+) still bind to a mutant stem loop sequence from which the internal loop had been deleted, ion binding to the mutant RNA results in decreased, rather than increased, exposure of the branch site residue to solvent. These data further support the role of the internal loop in defining branch site conformation of the Group II intron. The specific bound Mg(2+) may play a bivalent role: facilitates... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1525863 Sat, 24 May 2008 04:00:00 +0100 1525863 http://www.medworm.com/index.php?rid=1508027&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%3D18538917%26dopt%3DAbstract Authors: Yin G, Li Y, Li J, Li J, Du W, Wei Q, Fang W Solution (1)H NMR spectroscopy has been carried out to investigate the molecular and electronic structures of the active site in H64Q/V68F double mutant mouse neuroglobin in the cyanomet form. Two heme orientations resulting from a 180 degrees rotation about the alpha-gamma-meso axis were observed with a population ratio about 1:1, and the clearly distinguished B isomer was used to perform the study. Based on the analysis of the dipolar shifts and paramagnetic relaxation constants, the distal Gln(64)(E7) side chain is obtained to adopt an orientation that may produce hydrogen bond between the N(epsilon)H(1) and the Fe-bound cyanide. The side chain of Phe(68)(E11) is oriented out of the heme pocket just like that in triple mutant of ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1508027 Mon, 19 May 2008 04:00:00 +0100 1508027 http://www.medworm.com/index.php?rid=1499801&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%3D18534738%26dopt%3DAbstract Authors: Crea F, De Stefano C, Porcino N, Sammartano S The interaction between protonated branched poly(ethylenimine) [BPEI] and phytate (1,2,3,4,5,6 hexakis (di-hydrogen phosphate) myo-inositol) [Phy] was studied potentiometrically. The measurements were carried out at t=25 degrees C and at low ionic strength values, without addition of supporting electrolyte, to avoid interferences with other anions and cations. In order to simplify the data treatment, BPEI was considered as a simple tetramine. Different species Phy(BPEI)H(j), with j=6,7,8, and Phy(BPEI)(2)H(7) were found, having quite high stability. The ability of phytate to sequester BPEI was quantified by considering the parameter pL(50), namely the concentration (-log [Phy](tot)) necessary to bind 50% of polyammonium cation (as ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1499801 Sat, 17 May 2008 04:00:00 +0100 1499801 http://www.medworm.com/index.php?rid=1477768&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%3D18508186%26dopt%3DAbstract This study has provided two very important observations. AQ has been found to support electron transfer in different categories of media, acetonitrile/water on one hand and SDS micelles on other. While in our earlier work 2-methyl 1,4-naphthoquinone was found to undergo a switchover in reactivity (J. Am. Chem. Soc. 126 (2004) 10589-10593). Again A and dA are found to behave differently on account of an extra sugar unit, which not only affects the rate of reaction but the reaction pathway has been found to be modified too. PMID: 18508186 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1477768 Mon, 05 May 2008 04:00:00 +0100 1477768 http://www.medworm.com/index.php?rid=1469529&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%3D18501496%26dopt%3DAbstract Authors: Deepa P, Kolandaivel P, Senthilkumar K The antitumor activity of a drug is associated with its molecular properties as well as its interactions with target molecules. The molecular structures of usual, mismatch base pairs and their drug (Hydroxyurea and 5-Fluorouracil) interacting complexes were studied using density functional theory methods. The two and three-body interaction energies have been used to analyze the influence of a drug on the stability of base pairs. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The Atoms in Molecules theory and Natural Bond Orbital analysis have been performed to study the hydrogen bonds in the drug interacting complexes. PMID: 18501496 [PubMed - as supplied by publish... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1469529 Tue, 29 Apr 2008 04:00:00 +0100 1469529 http://www.medworm.com/index.php?rid=1439398&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%3D18472207%26dopt%3DAbstract Authors: Veettil S, Budisa N, Jung G The photostability of the widely used autofluorescent proteins EGFP and EYFP and their fluorinated counterparts were compared by means of fluorescence correlation spectroscopy. We analyzed the reduction of the apparent diffusional time in analogy to fluorescence quenching in which the 'photon concentration' is treated as the quencher concentration. The quantum yields of photobleaching Phi(bl) of EYFP (6.1x10(-)(5)) and EGFP (8.2x10(-)(5)) are in agreement with the previously published values. Among the investigated mutants, EYFP has the highest photostability and there is an enhanced photobleaching in (2-F) Tyr-EYFP. It turns out that the chromophore fluorination has no significant influence on the photostability. PMID: 18472207 [PubMed - as sup... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1439398 Wed, 23 Apr 2008 04:00:00 +0100 1439398 http://www.medworm.com/index.php?rid=1439399&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%3D18472206%26dopt%3DAbstract Authors: Gagoś M, Hereć M, Arczewska M, Czernel G, Dalla Serra M, Gruszecki WI Amphotericin B (AmB) is a polyene antibiotic used to treat deep-seated mycoses. Both the therapeutic action and the toxic side effects of this drug are dependent on its molecular organization. AmB appears as a zwitterion at neutral pH owing to NH(3)(+) and COO(-) groups. The results obtained with electronic absorption, fluorescence, resonance light scattering and infrared absorption spectroscopic analyses show that in the aqueous medium at pH above 10 AmB appears in the monomeric form owing to the negative net electric charge of the molecule. On the contrary, anomalously high aggregation level has been observed at pH below 2, despite the positive net electric charge. The effect is interpreted in ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1439399 Tue, 22 Apr 2008 04:00:00 +0100 1439399 http://www.medworm.com/index.php?rid=1432298&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%3D18462861%26dopt%3DAbstract Authors: Wang Y, Li Q Dynamical behaviors of unidirectionally, linearly coupled as well as isolated calcium subsystems are investigated by taking into account the internal noise resulting from finite system size and thus small numbers of interacting molecules. For an isolated calcium system, the internal noise can induce stochastic oscillations for a steady state close to the Hopf-bifurcation point, and the regularity of those stochastic oscillations depends resonantly on the system size, exhibiting system-size resonance. For the coupled system consisting of two subsystems, the system-size resonance effect observed in the subsystem subject to coupling is significantly amplified due to the nontrivial effects of coupling. PMID: 18462861 [PubMed - as supplied by publisher] (Source: Bi... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1432298 Fri, 18 Apr 2008 04:00:00 +0100 1432298 http://www.medworm.com/index.php?rid=1422959&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%3D18456386%26dopt%3DAbstract Authors: Zhang Y Kinesin is a stepping motor that successively produces forward and backward 8-nm steps along microtubules. Under physiological conditions, the steps powering kinesin's motility are biased in one direction and drive various biological motile processes. So far, the physical mechanism underlying the unidirectional bias of the kinesin is not fully understood. Recently, Martin Bier have provided a stepper model [Martin Bier, 2003, Processive motor protein as an overdamped Brownian stepper, Phys. Rev. Lett. 91, 148104], in which the stepping cycle of kinesin includes two distinguished phases: (i) a power stroke phase and (ii) a ratcheted diffusion phase which is characterized as a "random diffusional search". At saturating ATP level, this model can fit the experimental resul... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1422959 Fri, 11 Apr 2008 04:00:00 +0100 1422959 http://www.medworm.com/index.php?rid=1406800&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%3D18440694%26dopt%3DAbstract Authors: Golub NV, Markossian KA, Kasilovich NV, Sholukh MV, Orlov VN, Kurganov BI A comparative study of thermal denaturation and inactivation of aspartate aminotransferase from pig heart mitochondria (mAAT) has been carried out (10 mM Na phosphate buffer, pH 7.5). Analysis of the data on differential scanning calorimetry shows that thermal denaturation of mAAT follows the kinetics of irreversible reaction of the first order. The kinetics of thermal inactivation of mAAT follows the exponential law. It has been shown that the inactivation rate constant (k(in)) is higher than the denaturation rate constant (k(den)). The k(in)/k(den) ratio decreases from 28.8+/-0.1 to 1.30+/-0.09 as the temperature increases from 57.5 to 77 degrees C. The kinetic model explaining the discrepancy between ... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1406800 Thu, 10 Apr 2008 04:00:00 +0100 1406800 http://www.medworm.com/index.php?rid=1406801&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%3D18440120%26dopt%3DAbstract Authors: Chen XB, Niu LS, Shi HJ A numerical simulation of the phase separation in binary lipid membrane under the effect of stationary shear flow is performed. We numerically solved the modified two-dimensional time-dependent Ginzburg-Landau (TDGL) equations with an external velocity term, employing the CDS (i.e., Cell Dynamical System) technique. In the present simulation, stationary shear flows with different shear rates are taken into account. The evolution process of the phase separation is illustrated macroscopically via the snapshot figures and simulated scattering patterns at several typical moments. For each case, the growth exponents of the characteristic domain sizes in both directions parallel and perpendicular to the flow are studied, and the domain area as well. Also, the... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1406801 Tue, 08 Apr 2008 04:00:00 +0100 1406801 http://www.medworm.com/index.php?rid=1399085&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%3D18433978%26dopt%3DAbstract Authors: Bágeľová J, Fedunová D, Gažová Z, Fabian M, Antalík M Influence of ionic (NaCl) and non-ionic (sorbitol) additives on structural transitions of cytochrome c was investigated by circular dichroism, optical and EPR spectroscopy. Transformations of cytochrome c, induced by the acidification of solution and temperature perturbation, were monitored in the heme pocket together with changes in the secondary structure. NaCl and sorbitol exhibited antagonistic effect on the acid-induced transition of the protein. Sorbitol enhanced the stability of native conformation while NaCl destabilized this state. The midpoints of acid-induced transitions in the axial coordination of heme as well as in the secondary structure occurred nearly at the same pH valu... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1399085 Fri, 04 Apr 2008 04:00:00 +0100 1399085 http://www.medworm.com/index.php?rid=1279377&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%3D18304723%26dopt%3DAbstract Authors: Zhao P, Xu LC, Huang JW, Zheng KC, Liu J, Yu HC, Ji LN A novel cationic porphyrin-anthraquinone (Por-AQ) hybrid has been synthesized and characterized. Using the combination of absorption titration, fluorescence spectra, circular dichroism (CD) as well as viscosity measurements, the binding properties of the hybrid to calf thymus (CT) DNA have been investigated compared with its parent porphyrin. The experimental results show that at low [Por]/[DNA] ratios, the parent porphyrin binds to DNA in an intercalative mode while the hybrid binds in a combined mode of outside binding (for porphyrin moiety) and partial intercalation (for anthraquinone). Ethidium bromide (EB) competition experiment determined the binding affinity constants (K(app)) of the compounds for CT DNA. Theoretica... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1279377 Wed, 05 Mar 2008 09:00:55 +0100 1279377 http://www.medworm.com/index.php?rid=1279376&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%3D18304724%26dopt%3DAbstract Authors: Choi JY, Lee JM, Lee H, Jung MJ, Kim SK, Kim JM The binding mode of Delta- and Lambda-[Ru(1,10-phenanthroline)(2)dipyrido[3,2-a:2',3'-c]phenazine](2+) ([Ru(phen)(2)DPPZ](2+)) to DNA in the presence of 4',6-diamidino-2-phenylindole (DAPI) at a low and high [DAPI]/[DNA base] ratio (0.02 and 0.20, respectively) was investigated using electric absorption and circular dichroism spectroscopy. The spectral properties of both the Delta- and Lambda-[Ru(phen)(2)DPPZ](2+) were not altered in the presence of DAPI disregarding the [DAPI]/[DNA] ratio, suggesting that the presence of DAPI in the minor groove of DNA does not affect the binding mode of the [Ru(phen)(2)DPPZ](2+) complex to DNA. The transferring excited energy of DAPI to both Delta- and Lambda-[Ru(phen)(2)DPPZ](2+) occurs throug... Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1279376 Wed, 05 Mar 2008 09:00:52 +0100 1279376 http://www.medworm.com/index.php?rid=1258017&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%3D18295961%26dopt%3DAbstract This study therefore extends the existence of helix-rich equilibrium and transient intermediates of predominantly beta-sheet proteins to alkaline buffer conditions. PMID: 18295961 [PubMed - as supplied by publisher] (Source: Biophysical Chemistry) Biophysical Chemistry journals http://www.medworm.com/rss/comments.php?id=1258017 Wed, 13 Feb 2008 05:00:00 +0100 1258017