Abstract
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 macromolecules enables DNA packing in the cell nucleus and plays an important role in the regulation of transcription and gene expression. Nucleosome assembly and functioning depend on the ionic environment and electrical characteristics of the medium to a great extent. Maps of monovalent ion distribution in the DNA-histone system have been analyzed in the present work and the preferred location of the ions has been determined. A method for the calculation of distribution of certain physical parameter values in the computational cell incorporating the drifting macromolecule has been put forward. Distribution of the electrostatic potential around a nucleosome has been considered.
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Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., and Richmond, T.J., Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 angstrom resolution, J. Mol. Biol., 2002, vol. 319, no. 5, pp. 1097–1113.
Vasudevan, D., Chua, E.Y.D., and Davey, C.A., Crystal structures of nucleosome core particles containing the '601' strong positioning sequence, J. Mol. Biol., 2010, vol. 403, no. 1, pp. 1–10.
Thiriet, C., Replication-independent core histone dynamics at transcriptionally active loci in vivo, Gene Dev., 2005, vol. 19, no. 6, pp. 677–682.
Studitsky, V.M., Clark, D.J., and Felsenfeld, G., Overcoming a nucleosomal barrier to transcription, Cell, 1995, vol. 83, no. 1, pp. 19–27.
Andrews, A.J. and Luger, K., A coupled equilibrium approach to study nucleosome thermodynamics, Methods Enzymol., 2011, vol. 488, pp. 265–285.
Banks, D.D. and Gloss, L.M., Equilibrium folding of the core histones: the h3–h4 tetramer is less stable than the h2a–h2b dimer, Biochemistry, 2003, vol. 42, no. 22, pp. 6827–6839.
Davey, C.A. and Richmond, T.J., DNA-dependent divalent cation binding in the nucleosome core particle, Proc. Natl. Acad. Sci. USA, 2002, vol. 99, no. 17, pp. 11169–11174.
Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J.L., Dror, R.J., and Shaw, D.E., Improved sidechain torsion potentials for the Amber ff99sb protein force field, Proteins, 2010, vol. 78, no. 8, pp. 1950–1958.
Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M.R., Smith, J.C., Kasson, P.M., van der Spoel, D., Hess, B., and Lindahl, E., Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics, 2013, vol. 29, no. 7, pp. 845–854.
Humphrey, W., Dalke, A., and Schulten, K., Vmd: visual molecular dynamics, J. Mol. Graphics Modell., 1996, vol. 14, no. 1, pp. 33–38.
Aksimentiev, A. and Schulten, K., Imaging alphahemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map, Biophys. J., 2005, vol. 88, no. 6, pp. 3745–3761.
Savelyev, A. and Papoian, G.A., Electrostatic, steric, and hydration interaction favor Na+ condensation around DNA compared with K+, J. Am. Chem. Soc., 2006, vol. 128, no. 45, pp. 14506–14518.
Sadovnichy, V., Tikhonravov, A., Voevodin, V., and Opanasenko, V., in Contemporary High Performance Computing: from Petascale Toward Exascale, Jeffery, S.V., Ed., Boca Raton, FL: CRC Press, 2013, pp. 283–307.
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Original Russian Text © G.A. Armeev, K.V. Shaitan, A.K. Shaitan, 2015, published in Vestnik Moskovskogo Universiteta. Biologiya, 2015, No. 4, pp. 24–28.
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Armeev, G.A., Shaitan, K.V. & Shaitan, A.K. Molecular dynamics study of the ionic environment and electrical characteristics of nucleosomes. Moscow Univ. Biol.Sci. Bull. 70, 173–176 (2015). https://doi.org/10.3103/S0096392515040033
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DOI: https://doi.org/10.3103/S0096392515040033