Boundary condition effects on the dynamic and electric properties of hydration layers

The Journal of Physical Chemistry. a
Balasubramanian ChandramouliGiuseppe Brancato

Abstract

Water solvation has a central role in several biochemical processes ranging from protein folding to biomolecular recognition and enzyme catalysis. Because of its importance, the structure and dynamics of hydration layers around biological macromolecules have been the targets of a great number of experimental and computational studies. In the present contribution, we have investigated the effects of periodic boundary conditions (PBCs), as used in conjunction with molecular dynamics (MD) simulations, on the dynamic and electric properties of water layers. In particular, we have systematically performed MD simulations of neat water and biomolecules in aqueous solutions by imposing a different external dielectric constant, a generally overlooked parameter in PBC simulations. The effect of the system size has also been addressed. Overall, our results consistently indicate that the dipole moment properties of water layers, and specifically the dipole moment fluctuations and the reorientational correlation functions, can be sensitive to the choice of the external boundary conditions, whereas other molecular properties, such as the self-diffusion coefficient and the reorientational relaxation times, are not affected. We think that our ...Continue Reading

References

Jan 1, 1996·Annual Review of Biophysics and Biomolecular Structure·R G Bryant
Oct 29, 1998·Protein Science : a Publication of the Protein Society·Y XueS Young
Apr 8, 2000·Current Opinion in Structural Biology·H J Berendsen, S Hayward
Jan 12, 2002·Current Opinion in Structural Biology·M T Zanni, R M Hochstrasser
Apr 15, 2004·Chemical Reviews·Samir Kumar Pal, Ahmed H Zewail
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Aug 13, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Bertil Halle
Jun 11, 2005·The Journal of Chemical Physics·Giuseppe BrancatoAndrea Amadei
Aug 2, 2005·Angewandte Chemie·J Luis Pérez LustresNikolaus P Ernsting
Aug 13, 2005·The Journal of Chemical Physics·Gabriele PetraglioMichele Parrinello
Sep 15, 2005·Chemical Reviews·Biman Bagchi
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Oct 1, 1952·Proceedings of the National Academy of Sciences of the United States of America·J G Kirkwood, J B Shumaker
May 13, 2006·Annual Review of Biophysics and Biomolecular Structure·Yaakov Levy, José N Onuchic
Jun 16, 2006·The Journal of Chemical Physics·Giuseppe BrancatoVincenzo Barone
Jul 21, 2006·The Journal of Physical Chemistry. B·Alex H de VriesPhilippe H Hünenberger
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Dec 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Simon EbbinghausMartina Havenith
Feb 6, 2008·Journal of the American Chemical Society·Simon EbbinghausMartina Havenith
Mar 18, 2008·The Journal of Physical Chemistry. B·David N LeBard, Dmitry V Matyushov
Apr 17, 2008·The Journal of Chemical Physics·Giuseppe BrancatoVincenzo Barone
Nov 19, 2008·Physical Chemistry Chemical Physics : PCCP·Dusan BratkoAlenka Luzar
Jun 29, 2010·The Journal of Physical Chemistry. B·David N LeBard, Dmitry V Matyushov
Jan 14, 2011·Quarterly Reviews of Biophysics·Tamar SchlickXia Xiao
Jan 1, 1986·Annual Review of Physical Chemistry·S W De LeeuwE R Smith
Feb 1, 2012·The Journal of Physical Chemistry. B·Susmita Roy, Biman Bagchi
Feb 18, 2012·Journal of the American Chemical Society·Fabio SterponeDamien Laage
May 15, 2012·Annual Review of Biophysics·Ron O DrorDavid E Shaw
May 3, 2014·The Journal of Chemical Physics·V Ballenegger
Aug 19, 2015·The Journal of Physical Chemistry Letters·Mauro Del BenBen Slater

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Citations

Oct 7, 2016·Physical Chemistry Chemical Physics : PCCP·Marina MacchiagodenaVincenzo Barone
May 22, 2018·Physical Chemistry Chemical Physics : PCCP·Jayangika N Dahanayake, Katie R Mitchell-Koch
Feb 15, 2018·Journal of Chemical Theory and Computation·Julija ZavadlavMatej Praprotnik
Sep 7, 2021·The Journal of Physical Chemistry. B·Archita Maiti, Snehasis Daschakraborty

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