Fast in silico protein folding by introduction of alternating hydrogen bond potentials.

Biophysical Journal
M G Wolf, S W de Leeuw

Abstract

We accelerate protein folding in all-atom molecular dynamics simulations by introducing alternating hydrogen bond potentials as a supplement to the force field. The alternating hydrogen bond potentials result in accelerated hydrogen bond reordering, which leads to rapid formation of secondary structure elements. The method does not require knowledge of the native state but generates the potentials based on the development of the tertiary structure in the simulation. In protein folding, the formation of secondary structure elements, especially alpha-helix and beta-sheet, is very important, and we show that our method can fold both efficiently and with great speed.

References

Jan 1, 1984·Progress in Biophysics and Molecular Biology·E N Baker, R E Hubbard
Oct 1, 1995·Nature Structural Biology·G I MakhatadzeA M Gronenborn
Feb 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·D H WilliamsR A Maplestone
Oct 1, 1996·Biophysical Journal·J K Myers, C N Pace
Jan 1, 1997·Nature Structural Biology·K A Dill, H S Chan
Feb 27, 1999·Current Opinion in Structural Biology·C M Dobson, M Karplus
May 8, 2001·Annual Review of Biophysics and Biomolecular Structure·D Thirumalai, G H Lorimer
Mar 9, 2002·Science·F Ulrich Hartl, Manajit Hayer-Hartl
May 3, 2003·Current Opinion in Structural Biology·S GnanakaranAngel E García
Apr 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Young Min RheeVijay S Pande
Apr 20, 2004·Current Opinion in Structural Biology·Michael Feig, Charles L Brooks
Oct 2, 2004·Nature Reviews. Molecular Cell Biology·Jason C YoungF Ulrich Hartl
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Christopher D SnowVijay S Pande
Aug 30, 2005·Comptes rendus biologies·Martin Gruebele
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Mar 3, 2006·The Journal of Physical Chemistry. B·David van der SpoelNicusor Tîmneanu
Sep 15, 2006·The Journal of Physical Chemistry. B·Chunhu TanRay Luo
Jan 24, 2007·Current Opinion in Structural Biology·David J Brockwell, Sheena E Radford
Feb 27, 2007·Protein Science : a Publication of the Protein Society·Mallela M G Krishna, S Walter Englander

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Citations

Aug 10, 2011·The Journal of Physical Chemistry. B·Sairam S Mallajosyula, Alexander D MacKerell
Dec 17, 2011·Midwifery·Lucie L M MartijnMichel M Wensing
Jul 13, 2010·Journal of Chemical Theory and Computation·Neil J Bruce, Richard A Bryce

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