Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study

Biophysical Journal
V A MakarovB M Pettitt

Abstract

Effects of the macromolecular solute on the translational mobility of surrounding solvent water, and Na+ and Cl- ions are investigated by molecular dynamics (MD) simulation. Using MD trajectories of myoglobin and d(C5T5) . d(G5A5) DNA decamer of high quality and length, we determine the average diffusion coefficients for all solvent species as a function of distance from the closest solute atom. We examine solvent mobility in the directions parallel and perpendicular to the solute surface and in proximity to three different classes of solute atoms (oxygens, nitrogens, and carbons). The nature and the magnitude of the solute effects on water diffusion appear to be very similar for protein and DNA decamer. The overall diffusion rate at the interface is lower than in the bulk. The rate is higher than the average in the direction parallel to the solute surface, and lower in the direction normal to the surface, up to 15 A away from the solute. The rate is also lower in the solvation shells of the macromolecules, producing characteristic depressions in the radial profiles of the diffusion coefficient that can be correlated with peaks in the corresponding radial distribution functions. The magnitude of these depressions is small compa...Continue Reading

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jan 1, 1991·Annual Review of Biophysics and Biophysical Chemistry·M M Teeter
Oct 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·M Levitt, R Sharon
Apr 11, 1995·Proceedings of the National Academy of Sciences of the United States of America·J B ClarageG N Phillips
Mar 1, 1994·Biophysical Journal·V LounnasG N Phillips
May 13, 1998·Biopolymers·V A MakarovB M Pettitt
Apr 1, 1996·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·A R Bizzarri, S Cannistraro

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Citations

Dec 24, 2002·Journal of Computational Chemistry·Francesca Massi, John E Straub
Apr 8, 2000·Current Opinion in Structural Biology·D L Beveridge, K J McConnell
Mar 14, 2008·Journal of the American Chemical Society·Allison A LanghamYiannis N Kaznessis
Feb 23, 2012·Journal of the American Chemical Society·Ryuhei HaradaMichael Feig
Oct 30, 2010·The Journal of Physical Chemistry. B·Nikolay A Simakov, Maria G Kurnikova
Aug 9, 2008·Physical Chemistry Chemical Physics : PCCP·Feng DongNathan A Baker
Mar 3, 2005·The Journal of Chemical Physics·Zhi-Jie Tan, Shi-Jie Chen
Feb 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Samir Kumar PalAhmed H Zewail
Dec 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Simon EbbinghausMartina Havenith
Apr 27, 2004·Journal of Biomolecular Structure & Dynamics·I Stoica
Aug 12, 2004·Nucleic Acids Research·Péter Várnai, Krystyna Zakrzewska
Jan 1, 2011·Annual Review of Chemical and Biomolecular Engineering·Sumanth N JamadagniShekhar Garde
Feb 24, 2012·PLoS Computational Biology·Priyanka PrakashAlemayehu A Gorfe
Mar 3, 2011·Medical Physics·Gary D FullertonIvan L Cameron
Dec 5, 2012·The Journal of Chemical Physics·F Y HansenA Miskowiec
Sep 8, 2010·The Journal of Chemical Physics·J ServantieA R Atilgan
Oct 2, 2009·The Journal of Chemical Physics·Jun FengB Montgomery Pettitt
Mar 21, 2003·Biophysical Chemistry·David A C BeckValerie Daggett
Jun 15, 2011·Biophysical Chemistry·Nicholus Bhattacharjee, Parbati Biswas
Dec 16, 2005·Proteins·Chuanying ChenB Montgomery Pettitt
Dec 7, 2000·Biophysical Journal·V A MakarovB M Pettitt
May 19, 2006·Biochemical and Biophysical Research Communications·Miguel RodríguezGünter Siegel
Sep 4, 2015·The Journal of Physical Chemistry. B·Sebastian LorchAna-Nicoleta Bondar
Jul 17, 2007·Biophysical Journal·Alla OleinikovaIvan Brovchenko
Feb 8, 2006·Biophysical Journal·Alfonso De SimoneFranca Fraternali
Feb 13, 2001·Biophysical Journal·S R KimuraC J Camacho
Aug 31, 2002·Biophysical Journal·Jung-Hsin LinJ Andrew McCammon
Jul 29, 1999·Biophysical Journal·G S Lakshmikanth, G Krishnamoorthy
Jul 22, 2016·Journal of Chemical Theory and Computation·Michael SchauperlKlaus R Liedl
Jan 28, 2006·The Journal of Chemical Physics·Taner E DiramaAlexei P Sokolov
Dec 28, 2006·The Journal of Chemical Physics·Subrata PalBiman Bagchi
Jun 15, 2007·The Journal of Chemical Physics·Rajesh K Murarka, Teresa Head-Gordon
Aug 4, 2007·The Journal of Chemical Physics·Koji UmezawaHeisaburo Shindo
Jul 11, 2006·The Journal of Chemical Physics·C SchröderO Steinhauser
Jul 23, 2005·The Journal of Chemical Physics·Taner E DiramaAlexei P Sokolov
Mar 21, 2017·The Journal of Physical Chemistry. B·Jeremy M MoixIbtissam Echchgadda
Feb 27, 1999·Journal of Molecular Biology·M Feig, B M Pettitt
Feb 16, 2002·Journal of Molecular Biology·C K ReddyB Jayaram
Jun 22, 2017·The Journal of Physical Chemistry. B·Viren PattniMatthias Heyden
Mar 11, 2018·The Journal of Membrane Biology·Konstantina Karathanou, Ana-Nicoleta Bondar
Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shubhra Ghosh Dastidar, Chaitali Mukhopadhyay
May 27, 2010·Chemical Society Reviews·Biman Bagchi, Biman Jana
Dec 7, 2006·Physical Chemistry Chemical Physics : PCCP·Damián E BikielDarío A Estrin

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