17 Result(s)
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Article
G. A. Armeev
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Article
Refinement of Nucleosome Positions within Individual Genes Using Molecular Modeling Methods and MNase Sequencing Data
Chromatin organization plays an important role in regulating the genetic machinery of the cell. A nucleosome is a basic unit of chromatin packaging and harbors about 145 bp of DNA. The packaging of genetic mat...
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Memory Effect in Porous Polyethylene Films Preliminarily Deformed in the Medium of Supercritical CO2
The dynamics of recovery of the open porous structure in HDPE films, which are preliminarily uniaxially deformed in the medium of supercritical CO2 followed by shrinkage in the longitudinal direction, upon their ...
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Design of Nucleic Acid Biosensors Based on CRISPR/Cas Systems and Reporter Split Proteins
Highly sensitive, specific, rapid, and easy-to-use diagnostic methods for the detection of nucleic acids of pathogens are required for the diagnosis of many human, animal, and plant diseases and environmental ...
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The Effect of the Viscosity of the Medium on the Molecular Dynamics of the Formation of Secondary Structure of (AlaGly)25 and (AlaGly)75 Polypeptides
Folding of model polypeptide sequences consisting of 50 and 150 amino-acid residues with the alanine and glycine repeat was explored using Langevin dynamics techniques at different values of the viscosity of a...
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Investigation of the Effect of a Single-Stranded Break on the Mechanical Parameters of DNA by Molecular Dynamics Method
Early detection and repair of damaged DNA is important for cell functioning and survival. The recently proposed mechanism of intranucleosomal loop formation suggests the relaxation of DNA supercoiling accumula...
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The Effect of Oncomutations and Posttranslational Modifications of Histone H1 on Chromatosome Structure and Stability
The stability of chromatosome when introducing posttranslational modifications and mutations observed in the case of oncological diseases into the structure of the linker histone was studied using bioinformati...
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Construction and Analysis of Amino Acid Substitution Matrices for Optimal Alignment of Microbial Rhodopsin Sequences
Pairwise alignment of amino acid sequences is the basic tool of bioinformatics, which is widely used both independently and within numerous more complex methods. The effectiveness of this tool critically depen...
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Joint Effect of Histone H1 Amino Acid Sequence and DNA Nucleotide Sequence on the Structure of Chromatosomes: Analysis by Molecular Modeling Methods
A chromatosome consisting of a nucleosome core, linker DNA, and linker histone (LH) is an important structural element of chromatin and plays a role in replication and transcription regulation. There are two e...
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Investigation of histone-DNA binding energy as a function of DNA unwrap** from nucleosome using molecular modeling
The present study contributes to the understanding of DNA compaction in the cell nucleus at the nucleosomal level. The interaction between DNA and histones affects key processes of cell life, including replica...
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Conformational motion correlations in the formation of polypeptide secondary structure in a viscous medium
The Langevin dynamics method and statistical correlation analysis were used to study the α-helical structure folding dynamics of the (Ala)50, (AlaGly)25, and (AlaGly)75 polypeptides depending on the viscosity of ...
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On the possibility of determining the structure of proteins in experiments using X-ray free electron lasers in the nonstationary scattering mode
The problem of determining the structure of proteins by X-ray analysis using X-ray free electron lasers at pulse intensities several orders of magnitude higher than those achieved to date is considered. In thi...
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Characterization of lipodisc nanoparticles containing sensory rhodopsin II and its cognate transducer from Natronomonas pharaonis
We describe the preparation and properties of lipodisc nanoparticles–lipid membrane fragments with a diameter of about 10 nm, stabilized by amphiphilic synthetic polymer molecules. We used the lipodisc nanopar...
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Nucleosome structure relaxation during DNA unwrap**: Molecular dynamics simulation study
Effects of local relaxation of the nucleosome structure after DNA unwrap** from the histone octamer are considered in this paper. The influence of charge distribution in histones on the kinetics of DNA rewra...
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The dynamics of irreversible evaporation of a water–protein droplet and the problem of structural and dynamic experiments with single molecules
The effect of isothermal and adiabatic evaporation on the state of a water–protein droplet is discussed. The considered problem relates to the design of various approaches for structural and dynamic experiment...
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Modeling of the structure of protein–DNA complexes using the data from FRET and footprinting experiments
We discuss the question of constructing three-dimensional models of DNA in complex with proteins using computer modeling and indirect methods of studying the conformation of macromolecules. We consider the met...
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Molecular dynamics study of the ionic environment and electrical characteristics of nucleosomes
Foundations of nucleosome structure and formation have been investigated in the present work using the molecular modeling approach. Formation of compact nucleosomes by histone proteins and parts of DNA macromo...
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Conformational flexibility of nucleosomes: A molecular dynamics study
One of the major problems of molecular biology is studying the underlying principles of chromatin work. This problem is associated with understanding the processes of epigenetic regulation of gene expression, ...
