Papers by Nikolay Balabaev
The Journal of Chemical Physics, 2005
molecules have been performed on the isothermal-isobaric ensemble at 1 atm and 303 K. ͑The notati... more molecules have been performed on the isothermal-isobaric ensemble at 1 atm and 303 K. ͑The notation n : dpcis specifies the lipid tails: n refers to the total number of carbon atoms in the chain, d is the number of the methylene-interrupted double bonds, p denotes the number of carbons between the chain terminal CH 3 group and the nearest double bond, and cis refers to the conformation around the double bonds.͒ The characteristics of the free volume in these systems have been analyzed by means of a generalized version of the Voronoi-Delaunay method ͓M. G. Alinchenko et al., J. Phys. Chem. B 108, 19056 ͑2004͔͒. As a reference system, the hydrated bilayer of the saturated 14:0/14:0 PC molecules ͑dimyristoylphosphatidylcholine͒ has also been analyzed. It has been found that the profiles of the fraction of the free volume across the membrane exhibit a rather complex pattern. This fine structure of the free volume fraction profiles can be interpreted by dividing the membrane into three separate major zones ͑i.e., zones of the aqueous, polar, and apolar parts of the membrane͒ and defining five subzones within these zones according to the average position of various atomic groups in the membrane. The fraction of the free volume in the middle of the membrane is found to increase with increasing unsaturation of the sn-2 chain of the lipid molecule. This is due to the fact that with increasing number of methylene-interrupted double bonds the lipid tails become more flexible, and hence they do not extend to the middle of the membrane. It is found that there are no broad enough preformed channels in the bilayers through which small penetrants, such as water molecules, can readily go through; however, the existing channels can largely facilitate the permeation of these molecules.
Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ peptide in β-layers During Molecular Dynamics Simulations
Methods in molecular biology, 2022
Our task was to determine the most stable packing of peptides in β-layers to construct an oligome... more Our task was to determine the most stable packing of peptides in β-layers to construct an oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the amino acid sequences IVRGVVVAID, VDSWNVLVAG (VESWNVLVAG), KLVFFAEDVG, and IIGLMVGGVV were built. These sequences correspond to the amyloidogenic regions of ribosomal S1 protein from E. coli, protein glucantransferase Bgl2p from the yeast cell wall, and Aβ peptide. First, the amyloidogenic regions were predicted theoretically, and then were confirmed experimentally. Four β-layers with different orientation of the peptides in the layers and the layers relative to each other were constructed. To determine the most stable packing of β-strands, the molecular dynamic (MD) simulations in explicit water were carried out. Two charge states (pH3 and pH5) for each β-layer were considered. The fraction of the secondary structure was a measure of stability for β-layers. β-Layers, in which β-strands are antiparalle...
Open Access Multiple Unfolding Intermediates Obtained by Molecular Dynamic Simulations under Stretching for Immunoglobulin-Binding Domain of Protein
Abstract: We have studied the mechanical properties of the immunoglobulin-binding domain of prote... more Abstract: We have studied the mechanical properties of the immunoglobulin-binding domain of protein G at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process can occur either in a single step or through intermediate states. Analysis of the trajectories from the molecular dynamic simulations showed that the mechanical unfolding of the immunoglobulin-binding domain of protein G is triggered by the separation of the terminal β-strands and the order in which the secondary-structure elements break is practically the same in two- and multi-state events and at the different extension velocities studied. It is seen from our analysis of 24 trajectories that the theoretical pathway of mechanical unfolding for the immunoglobulin-binding domain of protein G does not coincide with that proposed in denaturant studies in the absence of force.
Molecular Dynamics of Oligopeptides. I. The Use of Long Trajectories and High Temperatures to Determine the Statistical Weight of Conformational Subst Ates
Biophysics, 1997
Computer Research and Modeling
В настоящей работе исследуется механическая стабильность белка клеточной адгезии, кадгерина, мето... more В настоящей работе исследуется механическая стабильность белка клеточной адгезии, кадгерина, методом молекулярной динамики с использованием явной модели растворителя. Было проведено моделирование разворачивания белка за концы с постоянной скоростью для апоформы белка и при наличии в ней ионов разных типов (Ca 2+ , Mg 2+ , Na + , K +). Было выполнено по 8 независимых вычислительных экспериментов для каждой формы белка и показано, что одновалентные ионы меньше стабилизируют структуру, чем двухвалентные при механическом разворачивании молекулы кадгерина за концы. Модельная система из двух аминокислот и иона металла между ними в опытах по растяжению демонстрирует свойства аналогичные поведению кадгерина: cистемы с ионами калия и натрия обладают меньшей механической стабильностью на внешнее силовое воздействие в сравнении с системами с кальцием и магнием.
Computer Research and Modeling
Механическое разворачивание под действием внешних сил двух похожих по пространственной структуре,... more Механическое разворачивание под действием внешних сил двух похожих по пространственной структуре, но отличающихся по аминокислотной последовательности иммуноглобулинсвязывающих доменов белков L и G исследуется методом молекулярной динамики с использованием явной модели растворителя. Рассчитаны механические характеристики этих белков. Показано, что на пути механического разворачивания обоих белков появляются промежуточные состояния. Проведенные расчеты выявили три существенно различающихся пути механического разворачивания белков L и G. Ключевые слова: молекулярная динамика, механическое разворачивание, контакты между элементами вторичной структуры
Успехи математических наук, 2017
Computer modelling of structure and dynamics of C-50 n-paraffin crystal, hexagonal phase of C-50 crystal and ethylene/propylene statistical copolymers
Macromolecular Symposia, 1999
ABSTRACT
The effect of a solid wall on polymer chain behavior under shear flow
The Journal of Chemical Physics, 1998
Molecular dynamics computer simulations are used to investigate the properties of isolated bead–r... more Molecular dynamics computer simulations are used to investigate the properties of isolated bead–rod chains with excluded volume effects under a simple shear flow. With the help of the collisional dynamics technique, the simulations are performed with both the chains end grafted to an impenetrable wall and the isolated free-space chains immersed in a solvent. The comparison of these chains shows up the effect of the wall presence. We have calculated both the microscopic properties (such as end-to-end distance of polymer chain, the deformation ratio) and the macroscopic rheological properties of the model polymer solution (such as shear viscosity, first normal stress difference). A comparative analysis of the chains dynamics shows that the response of the grafted chains to simple shear flow is much different from that of the free chains. It was demonstrated that the grafting of polymer chains also gives rise to the distinctive rheological properties of the polymer solutions. For example, the effective viscosity of the grafted chains is an order of magnitude higher then the viscosity of the free chains.
Polymers
We studied the conformational behavior of silicon-containing dendrimers during their adsorption o... more We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for th...
Polymers
A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the f... more A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the fourth to the seventh generations belonging to the siloxane and carbosilane families, differing in spacer length, core functionality, and the type of chemical bonds, has been performed via atomic molecular dynamics simulations. The average radial and angular positions of all Si branching atoms of various topological layers within the dendrimer interior, as well as their variations, have been calculated, and the distributions of the relaxation times of their radial and angular motions have been found. It has been shown that the dendrons of all the dendrimers elongate from the center and decrease in a solid angle with an increasing generation number. The characteristic relaxation times of both angular and radial motions of Si atoms are of the order of a few nanoseconds, and they increase with an increasing generation number and decrease with temperature, with the angular relaxation times be...
Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17
Journal of structural biology, 2018
Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicell... more Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1 Å·ps) and constant forces (700 and 900 pN) using molecular dynamics (MD) simulations at T = 300 K. 114 independent MD simulations were performed and their analysis has been done. Despite structural similarity of these domains we have found that R15 is less mechanically stable than R16, which is less stable than R17. This result is in agreement with the thermal unfolding rates. Moreover, we have observed the relationship between mechanical stability, flexibility of the domains and the number of aromatic residues involved in aromatic clusters.
Data in brief, 2016
The amyloidogenic peptide VDSWNVLVAG from Bgl2p-glucantransferase of Saccharomyces cerevisiae cel... more The amyloidogenic peptide VDSWNVLVAG from Bgl2p-glucantransferase of Saccharomyces cerevisiae cell wall and its modifying analog VESWNVLVAG were taken for the construction of four types of bilayers which differ by orientation of the peptides in the layers and of the layers relative to each other. These bilayers were used as starting models for the molecular dynamics (MD) at three charge states (neutral, pH3, and pH5). The changes of the fraction of secondary structure during 1 ns simulations were received for 96 MD trajectories. The data article contains the necessary information for the construction of models of β-strands organization in the oligomer structure. These results were used in the associated research article "Structural model of amyloid fibrils for amyloidogenic peptide from Bgl2p-glucantransferase of S. cerevisiae cell wall and its modifying analog. New morphology of amyloid fibrils" (Selivanova et al., 2016) [1].
Self-consistent solutions in the continuous model of F centers and the problem of relaxed excited states
Opt Spectrosc, 1983
Russian Journal of Physical Chemistry B, 2014
X ray serial nanocrystallography is a new technique for determining the three dimensional struc t... more X ray serial nanocrystallography is a new technique for determining the three dimensional struc ture of biological macromolecules from data on the diffraction of ultrashort pulses generated by X ray free electron lasers. The maximum achievable resolution for a set of experimental data as a function of the sample sizes and parameters of the equipment is estimated based on simulations of the diffraction process with allow ance for changes in the electronic structure of the atoms of the sample under the influence of X rays. Esti mates show that nanocrystallography greatly enhances the possibilities of X ray analysis, reducing the requirements for the minimum permitted size of the crystals and enabling to explore poorly crystallizable molecular objects, such as many membrane proteins and complexes of macromolecules.
On micro pattern of plastic deformation in polyethylene crystal
Doklady Akademii nauk / [Rossiĭskaia akademii nauk]
Russian Journal of Physical Chemistry B, 2014
A brief overview of the design of femtosecond X ray free electron lasers (XFEL), characteristics ... more A brief overview of the design of femtosecond X ray free electron lasers (XFEL), characteristics of the emitted X ray pulses, and potentialities of XFEL are presented. A concise analysis of the problems in modeling X ray scattering patterns produced by ultraintense radiation sources is given.
Computer simulation of intramolecular mobility of dendrimers
Journal of Molecular Liquids, 1999
Structure and intramolecular mobility of a carbosilane dendrimer of the 5th generation has been a... more Structure and intramolecular mobility of a carbosilane dendrimer of the 5th generation has been analysed in a wide temperature range by molecular dynamics. It is shown that in a “poor” solvent, the frequency of conformational transitions, frot, is independent on the conformer position in the macromolecule with the exception of chain end fragments. For the latter, the frequency was 2–3
Acta Crystallographica Section D Biological Crystallography, 2015
The calculation of diffracted intensities from an atomic model is a routine step in the course of... more The calculation of diffracted intensities from an atomic model is a routine step in the course of structure solution, and its efficiency may be crucial for the feasibility of the study. An intense X-ray free-electron laser (XFEL) pulse can change the electron configurations of atoms during its action. This results in time-dependence of the diffracted intensities and complicates their calculation. An algorithm is suggested that enables this calculation with a computational cost comparable to that for the time-independent case. The intensity is calculated as a sum of the `effective' intensity and a finite series of `correcting' intensities. These intensities are calculated in the conventional way but with modified atomic scattering factors that are specially derived for a particular XFEL experiment. The total number of members of the series does not exceed the number of chemically different elements present in the object under study. This number is small for biological molecul...
Acta Crystallographica Section D Biological Crystallography, 2015
Author(s) of this paper may load this reprint on their own web site or institutional repository p... more Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr.
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Papers by Nikolay Balabaev