Biophysical ChemistryThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

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New insights into DNA-binding behavior of Wilms tumor protein (WT1)--a dual study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - November 5, 2009 Category: Chemistry Authors: Nurmemmedov E, Yengo RK, Uysal H, Karlsson R, Thunnissen MM Tags: Biophys Chem Source Type: journals

New insights into DNA-binding behavior of Wilms Tumor Protein (WT1) - A dual study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - October 28, 2009 Category: Chemistry Authors: Nurmemmedov E, Yengo RK, Uysal H, Karlsson R, Thunnissen MM Tags: Biophys Chem Source Type: journals

Analysis of light-induced transmembrane ion gradients and membrane potential in Photosystem I proteoliposomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - October 6, 2009 Category: Chemistry Authors: Pennisi CP, Greenbaum E, Yoshida K Tags: Biophys Chem Source Type: journals

Controlled Gating of Lysenin Pores.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - October 5, 2009 Category: Chemistry Authors: Fologea D, Krueger E, Lee R, Naglak M, Mazur Y, Henry R, Salamo G Tags: Biophys Chem Source Type: journals

Conformation and thermostability of oligonucleotide d(GGTTGGTGTGGTTGG) containing thiophosphoryl internucleotide bonds at different positions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 lo...
Source: Biophysical Chemistry - October 1, 2009 Category: Chemistry Authors: Zaitseva M, Kaluzhny D, Shchyolkina A, Borisova O, Smirnov I, Pozmogova G Tags: Biophys Chem Source Type: journals

How hyaluronan-protein complexes modulate the hyaluronidase activity: The model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 o...
Source: Biophysical Chemistry - September 30, 2009 Category: Chemistry Authors: Vincent JC, Lenormand H Tags: Biophys Chem Source Type: journals

A new kinetic model for biochemical oscillations: Graph-theoretical analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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] (S...
Source: Biophysical Chemistry - September 29, 2009 Category: Chemistry Authors: Goldstein BN, Aksirov AM, Zakrjevskaya DT Tags: Biophys Chem Source Type: journals

Porphyrins affect the self-assembly of tubulin in solution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 tripho...
Source: Biophysical Chemistry - September 28, 2009 Category: Chemistry Authors: Valdez R, Johnson EM, Belcher JA, Fuini JF, Brancaleon L Tags: Biophys Chem Source Type: journals

The stability of triplex DNA is affected by the stability of the underlying duplex.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - September 24, 2009 Category: Chemistry Authors: Rusling DA, Rachwal PA, Brown T, Fox KR Tags: Biophys Chem Source Type: journals

Potential of mean force of the hepatitis C virus core protein-monoclonal 19D9D6 antibody interaction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 simulati...
Source: Biophysical Chemistry - September 21, 2009 Category: Chemistry Authors: Wang YT, Su ZY, Chen CL Tags: Biophys Chem Source Type: journals

DNA-templated photo-induced silver nanowires: Fabrication and use in detection of relative humidity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biophysical Chemistry - September 20, 2009 Category: Chemistry Authors: Lu J, Yang L, Xie A, Shen Y Tags: Biophys Chem Source Type: journals

Membrane-induced peptide structural changes monitored by infrared and circular dichroism spectroscopy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 t...
Source: Biophysical Chemistry - September 11, 2009 Category: Chemistry Authors: Laird DJ, Mulvihill MM, Whiles Lillig JA Tags: Biophys Chem Source Type: journals

Thermally induced structural changes of intrinsically disordered small heat shock protein Hsp22.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 H...
Source: Biophysical Chemistry - September 11, 2009 Category: Chemistry Authors: Kazakov AS, Markov DI, Gusev NB, Levitsky DI Tags: Biophys Chem Source Type: journals

Direct allowance for the effects of thermodynamic nonideality in the quantitative characterization of protein self-association by osmometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - September 10, 2009 Category: Chemistry Authors: Wills PR, Winzor DJ Tags: Biophys Chem Source Type: journals

Internal noise-driven circadian oscillator in Drosophila.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - September 5, 2009 Category: Chemistry Authors: Li Q, Li H Tags: Biophys Chem Source Type: journals

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - August 31, 2009 Category: Chemistry Authors: Fleming RM, Thiele I, Nasheuer HP Tags: Biophys Chem Source Type: journals

Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 simul...
Source: Biophysical Chemistry - August 31, 2009 Category: Chemistry Authors: Tan YH, Chen YM, Ye X, Lu Q, Tretyachenko-Ladokhina V, Yang W, Senear DF, Luo R Tags: Biophys Chem Source Type: journals

How does each substituent functional group of oseltamivir lose its activity against virulent H5N1 influenza mutants?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - August 21, 2009 Category: Chemistry Authors: Rungrotmongkol T, Udommaneethanakit T, Malaisree M, Nunthaboot N, Intharathep P, Sompornpisut P, Hannongbua S Tags: Biophys Chem Source Type: journals

On photoabsorption of the neutral form of the green fluorescent protein chromophore.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 [Pub...
Source: Biophysical Chemistry - August 13, 2009 Category: Chemistry Authors: Topol I, Collins J, Polyakov I, Grigorenko B, Nemukhin A Tags: Biophys Chem Source Type: journals

Complex formation between calmodulin and a peptide from the intracellular loop of the gap junction protein connexin43: Molecular conformation and energetics of binding.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biophysical Chemistry - August 6, 2009 Category: Chemistry Authors: Myllykoski M, Kuczera K, Kursula P Tags: Biophys Chem Source Type: journals

Evidence of alpha fluctuations in myoglobin's denaturation in the high temperature region: Average relaxation time from an Adam-Gibbs perspective.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 hydrati...
Source: Biophysical Chemistry - August 2, 2009 Category: Chemistry Authors: Olivares-Quiroz L, Garcia-Colin LS Tags: Biophys Chem Source Type: journals

Erythrocytic ATP release in the presence of modified cell-free hemoglobin.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 publis...
Source: Biophysical Chemistry - August 2, 2009 Category: Chemistry Authors: Cole RH, Malavalli A, Vandegriff KD Tags: Biophys Chem Source Type: journals

The role of chloride transport in the control of the membrane potential in skeletal muscle--theory and experiment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. I...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Gallaher J, Bier M, Siegenbeek van Heukelom J Tags: Biophys Chem Source Type: journals

Characterization of cooperative effects in linear alpha-glycylglycine clusters.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. Fu...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Bahrami A, Esrafili MD, Hadipour NL Tags: Biophys Chem Source Type: journals

Mathematical model of a network of interaction between p53 and Bcl-2 during genotoxic-induced apoptosis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 a...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Dogu Y, Díaz J Tags: Biophys Chem Source Type: journals

Molecular dynamics simulation study of valyl-tRNA synthetase with its pre- and post-transfer editing substrates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-tra...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Bharatham N, Bharatham K, Lee Y, Woo Lee K Tags: Biophys Chem Source Type: journals

Intrinsic noise in post-transcriptional gene regulation by small non-coding RNA.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 theoretical...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Jia Y, Liu W, Li A, Yang L, Zhan X Tags: Biophys Chem Source Type: journals

The binding mode of porphyrins with cation side arms to (TG4T)4 G-quadruplex: spectroscopic evidence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, an...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Wei C, Wang L, Jia G, Zhou J, Han G, Li C Tags: Biophys Chem Source Type: journals

A thermodynamic analysis of the binding interaction between polysorbate 20 and 80 with human serum albumins and immunoglobulins: a contribution to understand colloidal protein stabilisation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Garidel P, Hoffmann C, Blume A Tags: Biophys Chem Source Type: journals

Similarity studies of DNA sequences based on a new 2D graphical representation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Huang G, Liao B, Li Y, Yu Y Tags: Biophys Chem Source Type: journals

Phase transition induced fission in lipid vesicles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 w...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Leirer C, Wunderlich B, Myles VM, Schneider MF Tags: Biophys Chem Source Type: journals

A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Liu J, Brazier-Hicks M, Edwards R Tags: Biophys Chem Source Type: journals

Signal amplification in biological and electrical engineering systems: universal role of cascades.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Grubelnik V, Dugonik B, Osebik D, Marhl M Tags: Biophys Chem Source Type: journals

Molecular organization of antifungal antibiotic amphotericin B in lipid monolayers studied by means of Fluorescence Lifetime Imaging Microscopy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Gruszecki WI, Luchowski R, Gagoś M, Arczewska M, Sarkar P, Hereć M, Myśliwa-Kurdziel B, Strzałka K, Gryczynski I, Gryczynski Z Tags: Biophys Chem Source Type: journals

Investigation on the interactions between pirarubicin and phospholipids.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 fu...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Cong W, Liu Q, Liang Q, Wang Y, Luo G Tags: Biophys Chem Source Type: journals

Self assembly of poly(o-methoxy aniline) with RNA and RNA/DNA hybrids: physical properties and conformational change of poly(o-methoxy aniline).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-p...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Routh P, Mukherjee P, Dawn A, Nandi AK Tags: Biophys Chem Source Type: journals

The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M Tags: Biophys Chem Source Type: journals

Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 predict...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Audie J Tags: Biophys Chem Source Type: journals

Studies of a viral suppressor of RNA silencing p19-CFP fusion protein: a FRET-based probe for sensing double-stranded fluorophore tagged small RNAs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Koukiekolo R, Jakubek ZJ, Cheng J, Sagan SM, Pezacki JP Tags: Biophys Chem Source Type: journals

A novel intramolecular G-quartet-containing fold of single-stranded d(GT)(8) and d(GT)(16) oligonucleotides.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. T...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Kaluzhny D, Shchyolkina A, Livshits M, Lysov Y, Borisova O Tags: Biophys Chem Source Type: journals

Quantitative investigations of amperometric spike feet suggest different controlling factors of the fusion pore in exocytosis at chromaffin cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ampe...
Source: Biophysical Chemistry - June 28, 2009 Category: Chemistry Authors: Amatore C, Arbault S, Bonifas I, Guille M Tags: Biophys Chem Source Type: journals

Interaction of beta-amyloid(1-40) peptide with pairs of metal ions: An electrospray ion trap mass spectrometric model study.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 o...
Source: Biophysical Chemistry - June 15, 2009 Category: Chemistry Authors: Drochioiu G, Manea M, Dragusanu M, Murariu M, Dragan ES, Petre BA, Mezo G, Przybylski M Tags: Biophys Chem Source Type: journals

Kinetics of cyanide binding as a probe of local stability/flexibility of cytochrome c.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - June 5, 2009 Category: Chemistry Authors: Varhač R, Tomášková N, Fabián M, Sedlák E Tags: Biophys Chem Source Type: journals

Conformation and dynamics of DNA molecules during photoreversible condensation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 photoi...
Source: Biophysical Chemistry - May 31, 2009 Category: Chemistry Authors: Le Ny AL, Lee CT Tags: Biophys Chem Source Type: journals

Binding interactions in early- and late-stage amyloid aggregates of TTR((105-115)).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 profi...
Source: Biophysical Chemistry - May 21, 2009 Category: Chemistry Authors: Liang Y, Jasbi SZ, Haftchenary S, Morin S, Wilson DJ Tags: Biophys Chem Source Type: journals

Comment on "Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV)".Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19231807 [PubMed - in process] (Source: Biophysical Chemistry)
Source: Biophysical Chemistry - February 24, 2009 Category: Chemistry Authors: Rungrotmongkol T, Malaisree M, Udommaneethanakit T, Hannongbua S Tags: Biophys Chem Source Type: journals

Reply to Comment on "Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV)".Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19231808 [PubMed - in process] (Source: Biophysical Chemistry)
Source: Biophysical Chemistry - February 24, 2009 Category: Chemistry Authors: Mitrasinovic PM Tags: Biophys Chem Source Type: journals

Optimal spatial synchronization on scale-free networks via noisy chemical synapses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 synchronizati...
Source: Biophysical Chemistry - February 6, 2009 Category: Chemistry Authors: Perc M Tags: Biophys Chem Source Type: journals

Molecular modeling of amphotericin B-ergosterol primary complex in water II.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 preservat...
Source: Biophysical Chemistry - February 4, 2009 Category: Chemistry Authors: Baran M, Borowski E, Mazerski J Tags: Biophys Chem Source Type: journals

Transient enzyme kinetics: Graph-theoretic approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biophysical Chemistry - February 4, 2009 Category: Chemistry Authors: Goldstein BN Tags: Biophys Chem Source Type: journals