Biomedical subjects

K V Shaĭtan

Publications and source records attributed to K V Shaĭtan.

At least 19 recordsLinked to original sources

PubMed1989

[The effect of time-relaxation spectral width on temperature dependences of parameters of Mossbauer spectra of biopolymers].

A new model for description of dynamic properties of macromolecule, especially globular proteins, is proposed. The model proposes the existence of time-relaxation spectra determining the time characteristics of biomacromolecule dynamics. The time dependence of mean-square deviation of atom from the initial state and spectra of Rayleigh scattering of Mossbauer radiation (RSNR) have been calculated. The temperature dependence of model spectra properties has been investigated. It has been shown that with the increase of time-relaxation spectra range of macromolecules the square under RSNR spectra with temperature growth decreases more quietly. It has been concluded that the idea concerning the time-relaxation spectra existence doesn't explain the sharp decrease of square of protein experimental spectra.

Biopolymers↗

PubMedDate not supplied

[Molecular dynamics of oligopeptides. 3. Maps of levels of free energy of modified dipeptides and dynamic correlation in amino acid residues].

A method of free energy maps for studying the dynamic correlations of fluctuations in molecules with conformational mobility is proposed. An agreement between the structure of the free energy level map and the type of the corresponding cross-correlation function (in the presence and absence of the correlation of fluctuations in conformational freedom degree in modified dipeptides) was established.

Amino Acids↗

PubMedDate not supplied

[Dynamic properties, electronic structure and functional activity of radioprotectors].

The methods of molecular dynamics and quantum chemistry were used to study the correlation between the functional activity of radioprotectors and their dynamic properties and atomic charges. It is shown that electrostatic interactions determine the correlation between the dynamics and functional activity of radioprotectors. The effects of conformation dynamics of aminothiols on the functions of radioprotectors is discussed.

Electrons↗

PubMedDate not supplied

[Statistical distribution of dipeptides in protein structures and dynamic characteristics of some protein fragments].

Statistical distributions of the occurrence of dipeptide fragments in proteins were studied. Various algorithms of ordering of files of frequency distribution were used. A correlation of occurrence of pairs of amino acid residues in various classes of proteins was established. The problem of the dynamic compatibility of amino acid residues in protein structures is discussed. The dynamic properties of frequently and seldom occurring dimers of amino acids are compared.

Amino Acid Sequence↗

PubMedDate not supplied

[About the effect of the amplitude of fluctuations on the coefficient of rubbing of the brownian oscillator in aqueous media].

The methods of molecular dynamics and correlation functions of coordinates were applied to investigate molecular oscillations in water solution at a variation of the amplitude of fluctuations. It was established, that the amplitude of fluctuation exceeds the threshold value (in water of the order of 0.3-0.45 A), of the force of friction sharply increases, and the vibration mode changes to the mode of limited diffusion. The consistency of the results with the theory of Mössbauer effect and the model of Brownian oscillator for conformational mobility in biopolymers is discussed.

Animals↗

PubMedDate not supplied

[Evaluation of effect of the peptide structure on energetics of reduction-oxidation reactions of proteins containing Fe4S4 clusters in computer experiments].

The methods of molecular dynamics were used to study the influence of peptide matrix and conformational relaxation on the thermal effects of redox reactions of two proteins containing Fe4S4 clusters with sharply differing redox potential values. It was shown that the depth of immersion of the Fe4S4 cluster in the protein globule affects the parameters of chemical equilibrium. It was found that the peptide matrix makes a determining contribution to the compensation of the Coulomb repulsion energy in Fe4S4 clusters.

Bacterial Proteins↗

PubMedDate not supplied

[Molecular dynamics of oligopeptides. 4. Dynamic characteristics of frequently and rarely occurring dipeptide fragments of proteins].

The existence of differences in the dynamic organization of frequently and the rarely occurring dipeptide fragments in globular and membrane proteins was shown. The dynamic isomorphism and the collective degrees of freedom in these fragments were analyzed. A topological classification of the maps of the levels of free energy for pairs of dihedral angles of the main chain and side residues was carried out.

Algorithms↗

PubMedDate not supplied

[Molecular dynamics of bending fluctuations in the protein secondary structures].

A comparative study of the dynamics of protein secondary structure elements by the example of alpha-helices of myoglobin, barnase, polylysine, and polyglycine and beta-layers of barnase and GFP was carried out by the methods of molecular dynamics. The effective Young's moduli of both free secondary structure elements and those built in the protein globule were determined. A heterogeneity of the elastic properties of the secondary structure elements was found. The melting of myoglobin alpha-helix in a virtual viscous medium was studied.

Bacterial Proteins↗

PubMedDate not supplied

[Dynamic attractor for the Berendsen thermostat an the slow dynamics of biomacromolecules].

It was shown that the nonlinear relaxation of a model system confined to the Berendsen's thermostat is determined by an attractor regime. The latter does not correspond generally to the true thermodynamic state of the system. Therefore, the use of the Berendsen's thermostat for molecular dynamics simulations, even in the case of large protein molecules at trajectory lengths of more than 10 ns, can lead to wrong conclusions. Our results agree with the concept of slow dynamics for macroscopic systems considered within the framework of the topological approach to stochastic dynamics.

Biopolymers↗

PubMedDate not supplied

[Effect of disulfide bonds on lysozyme dynamics].

The effect of destruction of disulfide bonds on the dynamics of proteins was studied by an example of lysozyme by the methods of molecular dynamics. In lysozyme, in the absence of disulfide bonds, the characteristic times of motions of secondary structure devices increased 3-7 times, whereas the amplitudes of fluctuations of secondary structure devices practically did not vary. In the absence of S-S-bonds, the volume of the molecule decreased approximately by 2%, primarily due to a "cleft" between the major and the small domains of lysozyme. Thus, disulfide bonds not only "glue" the secondary structure devices of the protein but also play a role of "rods", maintaining a certain free volume of the molecule necessary for the realization of its functions.

Amino Acid Sequence↗

PubMedDate not supplied

[Possible effects of the influence of dynamic disorder of biological systems on characteristics of intramolecular mobility, determined by Mossbauer spectroscopy].

A model for describing dynamic properties of proteins is proposed. The model involves the distribution over amplitudes and correlation times of intramolecular dynamics. It has been shown that distribution parameters and its temperature dependence have a great influence upon the values of experimental dynamic characteristics. Besides the discrepancy between the real and experimental temperature, dependence of characteristics on intramolecular dynamics can be observed.

Models, Chemical↗

PubMedDate not supplied

[Dynamics of electron-conformational transitions in proteins and physical mechanisms of biomacromolecule function].

The proteins can be considered as a microheterogeneous structured media possessing memory and feedback properties. The conformational energy surface depends on the chemical states of protein groups. Conformational motions are local diffusion with relaxation times much longer than vibrational relaxation times in condensed media. Owing to the hierarchy of relaxation times chemical reaction rates depend on conformation parametrically. Regulation of functional activity by conformational mobility is accomplished via transmission of information in the form of changes in the distribution functions of separate groups along the conformational substates. The interpretation of drastic effects on conformational mobility needs super-stochastic approaches. A possible mechanism of sharp conformational change are discussed in terms of the catastrophe theory.

Diffusion↗

PubMedDate not supplied

[The mechanism of action of pressure on intramolecular protein dynamics].

The physical mechanisms of pressure influence on the protein dynamics and parameters of Mossbauer spectra were investigated. The pressure effects measured for human serum albumin using Rayleigh Scattering of Mossbauer Radiation techniques were described using the model of local diffusion. Parameters of this model were determined by analysing the experimental data. As a result an estimation of approximate values for activation volumes was performed. It was shown that the obtained values are well consistent with the previous experimental results.

Humans↗

PubMedDate not supplied

[Relationship between structure and function of alpha-fetoprotein: conformational status and biological activity].

Alpha-fetoprotein (AFP) is the major mammalian fetal protein and the recognized tumor marker. This review summarizes data on structure and function of AFP with emphasis on human AFP, which is intensively investigated. During the last decade multiple functionally important sites of human AFP have been revealed or predicted by searching of similarity between primary structures of AFP and other proteins or their DNA sequences. A number of peptides derived from human AFP have been studied by different teams of investigators. These peptides were obtained by limited proteolysis of AFP or synthesized using solid phase chemistry. Study of biological (physiological) activities of these peptides allows determining biologically active sites of alpha-fetoprotein and constructing its structural and functional map. Biomodulating properties of these peptides make them a potential basis for design of drugs for different purposes including using in anticancer therapy. Conformational changes in AFP molecule have been intensively studied for the last few years and sufficient conformational mobility of AFP with the ability to form molten globule form (MGF) despite its stability in solution has been demonstrated. Native molecule of AFP may contain cryptic biologically active sites, which are not available for ligand binding. These sites become open and available for interaction after changes in conformation of AFP molecule. Study of conformational changes of AFP under different conditions allows understanding molecular mechanisms of its functioning. This review describes and analyses data obtained, mainly, during the last few years on study of conformational states of alpha-fetoprotein and relationship between conformational changes of AFP and its biological activity. Biochemical, biophysical and functional characterislics of some well-studied peptide fragments of AFP and their structural and functional mapping are presented.

Animals↗

PubMedDate not supplied

[Molecular dynamics of oligopeptides 6. A comparative study of poincare cross-section of monopeptide frames in media with different hydrophobicity].

A comparative study of the molecular dynamics of natural amino acid residues and their closest homologues and isomers was carried out. Molecular dynamics protocols not interfering with the principle of equidistribution of energy with respect to degrees of freedom were used. Poincare cross-sections, auto- and cross-correlation of complex exponential curves as a function of dihedrons were considered. The classification of dynamic properties of conformational degrees of freedom in the series of amino acid residues was carried out.

Amino Acids↗

PubMedDate not supplied

[The dynamic heterogeneity of the phospholipid bilayer and diffusion of molecules at the interface].

The method of steered molecular dynamics was developed to evaluate the kinetic parameters of the penetration of molecules through the interface. Heterogeneous microviscosity of a membrane was calculated by the example of a hydrated 1-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcholine bilayer. The influence of the chemical nature of the penetrant molecule on its penetration through the membrane was studied.

Diffusion↗

PubMedDate not supplied

[Evaluation of the contribution of various types of movement of protein globules into effects observed using the Rayleigh scattering of Mössbauer radiation or the Mössbauer absorption spectroscopy].

Conditions (regions of hydration degrees and temperatures) are considered at which effects observed in Rayleigh Scattering of Mössbauer Radiation and Mössbauer Absorption Spectroscopy can be attributed to changes in intramolecular mobility, rather than contribution of different types of motions of macromolecules as a whole.

Light↗

PubMedDate not supplied

[Study of protein dynamics using Mössbauer spectroscopy].

Last experimental results of the study of protein dynamics by Mössbauer absorption spectroscopy and Rayleigh scattering of Mössbauer radiation are reviewed. Dynamical properties of proteins following from the theoretical treatment of these data are described.

Humans↗