Roman G Efremov

..This may be achieved after relative domain motions of the 'closure' type observed in molecular dynamics simulations. The results provide a framework for analysis of disease mutations and for future mutagenesis studies...

..The approximations and shortcomings of the models, along with their perspectives in design of new membrane active drugs, are discussed...

..From these results it is concluded that the membrane potential stabilizes the transmembrane orientation of a signal sequence, explaining the membrane potential dependence of preprotein translocation...

..Accomplished with our previous simulations of membrane alpha-helices, the computational method may be used to study partitioning of proteins with diverse folds into lipid bilayers...

..The computational approach permits efficient prediction of TM helical oligomers based solely on the sequences of interacting peptides...

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..The conclusion was reached that these factors are among the most important for the specific destabilization of a bilayer, which is followed by membrane fusion...

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..Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed...

..Perspectives of rational alteration of virus-binding activity of CCR5 are discussed...

..The modeling results agree well with experimental data and provide a strategy to delineate fusogenic regions in amino acid sequences of viral proteins...

..The latter effect is much more pronounced in anionic bilayers and might be related to the initial stage of peptide-induced destabilization of lipid bilayers...

..This makes the EphA1 receptor unique among the Eph family, implying its possible physiological role as an "extracellular pH sensor," and can have relevant physiological implications...

..A possible role of membrane lipid rafts in relation to Eph transmembrane domain oligomerization and Eph signal transduction was also discussed...

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..ErbB2 transmembrane segments associate in a right-handed alpha-helical bundle through the N-terminal tandem GG4-like motif Thr652-X3-Ser656-X3-Gly660, providing an explanation for the pathogenic power of some oncogenic mutations...

..This feature together with the diverse binding affinities of the sites to a wide variety of anionic targets on the membrane surface appears to be functionally meaningful and may adjust CT action against different types of cells...

..The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane...

..This, in turn, may be related to pH-dependent proapoptotic activity of BNIP3, which is triggering on by acidosis appearing under hypoxic conditions...

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..Implications of the observed effects to molecular events on initial stages of membrane destabilization induced by fusion peptides are discussed...

..Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles...

..nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...

..Results of MD simulations of Ltc2a in model membranes were used to develop a number of its analogs with predefined activity...

..The performance of this ligand-specific scoring function was considerably better than that of a standard scoring function used in the docking algorithm...

..These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism...

..These results clearly demonstrate that the P-type cytotoxins interact with membranes stronger than those of the S-type, although the mode of the membrane insertion is similar for both the types...

..Limitations and shortcomings of the methods, along with their perspectives in design of new membrane active agents, are discussed...

..A possible biological implication of the findings in relation to triggering necrosis-like cell death by BNip3 is discussed...

..We therefore assume that the "membrane score" method will be helpful in optimization of in silico models of TM domains in proteins, especially those in GPCRs...

..We assume that the developed "membrane score" method will be helpful in optimizing computer models of TM domains of MPs, especially G-protein coupled receptors...

..Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent...

..A proof of concept is gained through engineering specific mutations that resulted in elimination of the hemolytic activity of AMPs (latarcins) while leaving the beneficial antimicrobial effect intact...

..Altogether, computational methods provide efficient basis for rational design of MAPs with predefined properties and a spectrum of biological activities...

..This can lead to thickening of the membrane interface in zwitterionic as compared to negatively charged bilayers...

..The English version of the paper: Russian Journal of Bioorganic Chemistry, 2003, vol. 29, no. 6; see also http://www.maik.ru...

..8) with experimental data...

..The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins...

..The results are discussed in a context of voltage-driven peptaibol insertion into membrane...

..The proposed method was then tested on the results of docking obtained for an additional 70 complexes. In both cases the success rate was 5-8% better compared to the standard functions implemented in popular docking software...

..The present review summarizes experimental and computational data on the spatial organization of CTs and their dynamics in various environments (aqueous solution, membranous milieus)...

..Lateral microheterogeneities in fluid lipid bilayers seem to be among the most important factors determining the nature of the membrane-water interface in a cell...

..The model allowed the identification of atomic groups in 2,2'-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI...

..The models permit rationalization of experimental data, including those that were not used in model building. The perspectives opened by the constructed models and by the optimization procedure in the design of new drugs are discussed...

..Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation...

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..The other of predicted mutations were not studied experimentally yet. Several new mutations of barnase and barstar are also proposed to enhance the hydrophobic interactions on their binding interface...

..The developed "membrane scoring function" will be of use for optimization of TM domain packing in theoretical models of MPs, first of all G-protein coupled receptors...

..The approach we suggested may be useful in studying not only other latarcins but also a wider class of membrane-active peptides...

..Together, the results directly demonstrate the phenotypic diversity of WD mutations within the N-domain and indicate that the nucleotide-binding properties of the P(1)-ATPases are distinct from those of the P(2)-ATPases...

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..We conclude that His-1069 is responsible for proper orientation of ATP in the catalytic site of WNDP prior to ATP hydrolysis...

..In addition, we speculate on how copper binding may regulate the activity and intracellular distribution of WNDP, and what role the human copper chaperone Atox1 may play in these processes...