Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.

Biophysical Journal
Lei Zhou, Steven A Siegelbaum

Abstract

Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our ...Continue Reading

References

Jun 16, 1977·Nature·J A McCammonM Karplus
Jul 22, 1976·Nature·J A McCammonP G Wolynes
Feb 5, 1985·Journal of Molecular Biology·M LevittP S Stern
Dec 1, 1987·Biophysical Journal·M KarplusB M Pettitt
Aug 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·B Brooks, M Karplus
Jun 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·N GoT Nishikawa
Nov 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·B Brooks, M Karplus
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·P J Steinbach, B R Brooks
Oct 1, 1996·Protein Science : a Publication of the Protein Society·D van der SpoelH J Vogel
Oct 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·J Ma, M Karplus
Apr 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·D I SvergunG Zaccai
Apr 27, 1992·Physical Review Letters·A E García
May 14, 1999·Current Opinion in Structural Biology·A Kitao, N Go
Jan 14, 2000·Nature Structural Biology·D VitkupM Karplus
Mar 21, 2000·Nature·A OstermannG U Nienhaus
Apr 8, 2000·Current Opinion in Structural Biology·H J Berendsen, S Hayward
Jan 4, 2001·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·B Hess
Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Apr 5, 2001·Protein Engineering·F Tama, Y H Sanejouand
Apr 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Franci Merzel, Jeremy C Smith
Jun 19, 2002·Accounts of Chemical Research·Martin Karplus
May 22, 2003·Journal of Molecular Biology·Dudley H WilliamsMin Zhou
Jun 18, 2004·Journal of Molecular Biology·Qiang CuiMartin Karplus
Jul 21, 2004·Journal of Computational Chemistry·Jason Wagoner, Nathan A Baker
Aug 13, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jeremy C SmithStefan Fischer
Jan 25, 2005·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Martin KarplusWei Yang
Jul 23, 2005·Chembiochem : a European Journal of Chemical Biology·Steve W Homans
Aug 16, 2005·Biophysical Journal·Adam W Van Wynsberghe, Qiang Cui
Dec 20, 2005·Biophysical Journal·Paula Petrone, Vijay S Pande

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Citations

Oct 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Mingyang Lu, Jianpeng Ma
Sep 12, 2009·Theoretical Biology & Medical Modelling·Bruno S AndradeAngelo A Duarte
Aug 10, 2011·The Journal of Chemical Physics·Reza SoheilifardGregory J Rodin
Dec 29, 2010·Biochemistry Research International·Saravana Prakash Thirumuruganandham, Herbert M Urbassek
Aug 21, 2008·Proteins·Adam D SchuylerGregory S Chirikjian
Apr 3, 2014·Proteins·Hyuntae Na, Guang Song
Jan 22, 2013·Journal of Molecular Biology·Mingyang Lu, Jianpeng Ma
Oct 7, 2008·Biochimica Et Biophysica Acta·E A DisalvoG J Gordillo
Nov 8, 2013·Molecular Based Mathematical Biology·Chuan LiEmil Alexov
Sep 4, 2012·Journal of Computational Chemistry·An GhyselsBernard R Brooks
Jul 20, 2016·Science China. Life Sciences·Jingsong ZhouJianxun Yi
Dec 8, 2009·Journal of Chemical Theory and Computation·Laurence Leherte, Daniel P Vercauteren
Dec 6, 2018·Journal of Chemical Theory and Computation·Patrick DigginsRaffaello Potestio

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Methods Mentioned

BETA
NMR
x-ray crystallography
PCA
BLAS
neutron scattering
light-scattering

Software Mentioned

DIAGRTB
CHARMM
GROMACS
NMA
CGNM
ENM
PARDISO
AANM
BNM
GROMOS96

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