G. A. Armeev

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 the medium. Friction forces that arise when the effective viscosity of the medium is similar to the viscosity of water were found to result in strong correlations between the backbone torsion angles. The polypeptides under study folded mainly to produce α-helical structures. A structure of two contacting α-helices that were approximately equal in length and had a loop between them was observed for a longer chain of 150 residues. A method to visualize the correlation matrix of the dihedral angles of a polypeptide chain was developed for analyzing the effects of the dynamic correlation of conformational degrees of freedom. The analysis of the dynamics of the correlation matrix showed that rotations involving angles of the same type (φ–φ and ψ–ψ) occur predominantly in one direction. Rotations invoving different angles (φ–ψ) occur predominantly in opposite directions, so that the total macromolecule does not rotate. A significant reduction in the effective viscosity of the medium disrupts the correlation and makes the rotations stochastic, thus distorting the formation of the regular (helical) structure. The effects of correlated conformational motions are consequences of viscous friction forces. This conclusion agrees with our previous results that outlined the principle of the minimum rate of energy dissipation and the equipartition of energy dissipation rate between conformational degrees of freedom.

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 methods of interpreting the experimental data obtained by indirect methods of studying the three-dimensional structure of biomolecules. We discuss some aspects of integrating such data into the process of constructing the molecular models of DNA–protein complexes based on the geometric characteristics of DNA. We propose an algorithm for estimating conformations of such complexes based on the information about the local flexibility of DNA and on the experimental data obtained by Forster resonance energy transfer (FRET) and hydroxyl footprinting. Finally, we use this algorithm to predict the hypothetical configuration of DNA in a nucleosome bound with histone H1.

Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning

Abstract Nucleosomes are the most abundant protein–DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical footprinting (HRF) of protein–DNA complexes is a chemical technique that probes nucleosome organization in solution with a high precision unattainable by other methods. In this work we propose an integrative modeling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments. Our method precisely identifies DNA positioning on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints. We performed high-resolution HRF for Saccharomyces cerevisiae centromeric nucleosome of unknown structure and characterized it using our integrative modeling approach. Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function.

Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles

We present here raw trajectories of molecular dynamics simulations for nucleosome with linker DNA strands as well as minimalistic nucleosome core particle model. The simulations were done in explicit solvent using CHARMM36 force field. We used this data in the research article Shaytan et al., 2016 [1]. The trajectory files are supplemented by TCL scripts providing advanced visualization capabilities.

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 experiments with single molecules involving X-ray lasers. The delivery of the sample into the X-ray beam is performed by a microdroplet injector in these experiments; and the approach time is in the microsecond range. A version of molecular-dynamics simulation for all-atom modeling of an irreversible isothermal evaporation process is developed. The parameters of the isothermal evaporation of a water–protein droplet that contains sodium and chloride ions at concentrations of approximately 0.3 M have been determined in computational experiments for different temperatures. The in silico experiments showed that the energy of irreversible evaporation at the initial stages of the process was virtually the same as the specific heat of evaporation for water. An exact analytical solution of the problem for the kinetics of irreversible adiabatic evaporation has been obtained in the limit of the high heat conductivity of the droplet (or a droplet size not exceeding ~100 Å). This solution contains parameters that were derived from simulation of the isothermal evaporation of the droplets. The kinetics of the evaporation and adiabatic cooling of the droplet were shown to be scalable according to the size of the droplet. Estimation of the rate of freezing of the water–protein droplet upon adiabatic evaporation in a vacuum chamber revealed the necessity of using additional procedures for stabilizing the temperature in the droplet nucleus that contains the protein molecule. Isothermal or quasi-isothermal conditions are more favorable for the investigation of macro-molecular structural rearrangements that are related to the functioning of the object. However, the effects of dehydration and a sharp increase in the ionic strength of the aqueous microenvironment of the protein must be taken into account in this case.

Investigation of histone-DNA binding energy as a function of DNA unwrapping 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 replication and transcription. This interaction can be described in terms of a free energy profile. In this paper, we calculated the free energy profile during DNA unwrapping from the histone octamer. The calculations were carried out using the MM/PBSA method. The calculated profiles are in good agreement with experimental data published earlier. The obtained results indicate the applicability of the technique for studying the effect of posttranslational modifications of histones and histone variants on nucleosome energy, which is important for understanding the mechanisms of transcriptional regulation in chromatin.

Nucleosome structure relaxation during DNA unwrapping: Molecular dynamics simulation study

Effects of local relaxation of the nucleosome structure after DNA unwrapping from the histone octamer are considered in this paper. The influence of charge distribution in histones on the kinetics of DNA rewrapping was studied. It was shown that ionic environment rapidly stabilizes during relaxation simulation of the system by molecular dynamics. In the case of short relaxation, a rapid irreversible restoration of the structure, which is similar to a crystal one, occurs. In the case of longer relaxation, DNA rewrapping does not occur despite the absence of apparent differences in the ionic environment of DNA. The change in the quadrupole moment of the system during relaxation was shown.

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 nanoparticles made of Escherichia coli polar lipids and compared lipodisc nanoparticles that contained the photosensitive protein complex of the sensory rhodopsin with its cognate transducer from the halobacterium Natronomonas pharaonis with empty lipodisc nanoparticles that contained no protein. The lipodisc nanoparticles were characterized by dynamic light scattering, transmission electron microscopy and atomic force microscopy. We found that the diameter of lipodisc nanoparticles was not affected by incorporation of the protein complexes, which makes them a prospective platform for single-molecule studies of membrane proteins.

6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations.

6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations Alexey K. Shaytan*, Grigoriy A. Armeev, Alexander Goncearenco, Victor B. Zhurkin, David Landsman and Anna R. Panchenko National Center for Biotechnology Information, NLM, NIH, MD 20894; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA *Email: alexey.shaytan@nih.gov, Phone: (301) 496-6226

Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

Hydroxyl-radical footprinting (HRF) is a powerful method for probing structures of nucleic acid–protein complexes with single-nucleotide resolution in solution. To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA (HYDROID), to quantify HRF data and integrate them with atomistic structural models. The stages of the HYDROID protocol are extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at each nucleotide and theoretical estimation of the DNA cleavage frequency from atomistic structural models, followed by comparison of experimental and theoretical results. Example scripts for each step of HRF data analysis and interpretation are provided for several nucleosome systems; they can be easily adapted to analyze user data. As input, HYDROID requires polyacrylamide gel electrophoresis (PAGE) images of HRF products and optionally can use a molecular model of the DNA–protein complex. The HYDROID protocol can be used to quantify HRF over DNA regions of up to 100 nucleotides per gel image. In addition, it can be applied to the analysis of RNA–protein complexes and free RNA or DNA molecules in solution. Compared with other methods reported to date, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available. The complete protocol takes ~3 h. Users should be familiar with the command-line interface, the Python scripting language and Protein Data Bank (PDB) file formats. A graphical user interface (GUI) with basic functionality (HYDROID_GUI) is also available.Hydroxyl-radical footprinting provides a wealth of data on the structure of nucleic acid–protein complexes. HYDROID is a software tool used to quantify footprinting data from gel electrophoresis images and integrate them with structural models.