PMID: 7526400Nov 22, 1994Paper

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

Proceedings of the National Academy of Sciences of the United States of America
T B Woolf, B Roux

Abstract

A molecular dynamics simulation of the gramicidin A channel in an explicit dimyristoyl phosphatidylcholine bilayer was generated to study the details of lipid-protein interactions at the microscopic level. Solid-state NMR properties of the channel averaged over the 500-psec trajectory are in excellent agreement with available experimental data. In contrast with the assumptions of macroscopic models, the membrane/solution interface region is found to be at least 12 A thick. The tryptophan side chains, located within the interface, are found to form hydrogen bonds with the ester carbonyl groups of the lipids and with water, suggesting their important contribution to the stability of membrane proteins. Individual lipid-protein interactions are seen to vary from near 0 to -50 kcal/mol. The most strongly interacting conformations are short-lived and have a nearly equal contribution from both van der Waals and electrostatic energies. This approach for performing molecular dynamics simulations of membrane proteins in explicit phospholipid bilayers should help in studying the structure, dynamics, and energetics of lipid-protein interactions.

References

Apr 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·J C OwickiH M McConnell
Sep 20, 1992·Journal of Molecular Biology·M S Weiss, G E Schulz
Dec 11, 1992·Biochimica Et Biophysica Acta·I PascherS Sundell
Apr 16, 1990·Biochemical and Biophysical Research Communications·M A DaviesR Mendelsohn
Feb 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·R W PastorM Karplus
Jan 1, 1986·Annual Review of Biophysics and Biophysical Chemistry·D M EngelmanA Goldman
Aug 1, 1984·Biophysical Journal·O G Mouritsen, M Bloom
May 15, 1983·Journal of Molecular Biology·B A Lewis, D M Engelman
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·M A Swairjo, B A Seaton
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·B Roux, M Karplus

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Citations

Aug 31, 2000·Proteins·A GrossfieldT B Woolf
Jun 16, 2004·European Biophysics Journal : EBJ·Bryan M van der EndeJames H Davis
Aug 1, 1995·Current Opinion in Structural Biology·R A Reithmeier
Mar 26, 1998·Biochimica Et Biophysica Acta·D P TielemanH J Berendsen
Apr 12, 2001·Current Opinion in Structural Biology·D J Tobias
Aug 1, 1997·Current Opinion in Structural Biology·K M Merz
Sep 20, 2012·Journal of Chemical Information and Modeling·Thomas H Schmidt, Christian Kandt
Oct 6, 2012·Chemical Reviews·Christopher MaffeoAleksei Aksimentiev
Mar 14, 2008·Journal of the American Chemical Society·Allison A LanghamYiannis N Kaznessis
Jul 1, 1996·Nature Structural Biology·B L StoddardP A Bash
Aug 5, 2009·Physical Chemistry Chemical Physics : PCCP·Ulrich SternbergAnne S Ulrich
Oct 12, 2011·Lab on a Chip·Rogan CarrAleksei Aksimentiev
Apr 1, 1997·Journal of Biomolecular Structure & Dynamics·D R Garmer
Mar 14, 2001·Journal of Biomolecular Structure & Dynamics·D Roy, C Mukhopadhyay
May 25, 2002·Journal of Biomolecular Structure & Dynamics·Debjani Roy, Chaitali Mukhopadhyay
Sep 6, 2003·Journal of Biomolecular Structure & Dynamics·Norbert GarnierMonique Genest
Jun 7, 2008·Journal of Biomolecular Structure & Dynamics·Y HoundonougboG S Jas
Oct 19, 2011·The Journal of General Physiology·Taekyung KwonThaddeus A Bargiello
Sep 27, 2013·Journal of the Royal Society, Interface·Milica TodorovićTsuyoshi Miyazaki
Nov 10, 2001·Annual Review of Biomedical Engineering·J M Nitsche
Dec 18, 2013·The Journal of Chemical Physics·Shan-Yan ChangYan Sun
Apr 16, 2014·Proceedings of the National Academy of Sciences of the United States of America·Andrew S ThomsonBrad S Rothberg
Jan 31, 2016·Biochimica Et Biophysica Acta·Anna PavlovaJames C Gumbart
Dec 27, 2015·Biochimica Et Biophysica Acta·Ernest Awoonor-Williams, Christopher N Rowley
Dec 14, 2011·Advanced Drug Delivery Reviews·Tim WernerW Bret Church
Jan 25, 2011·Biophysical Chemistry·Yong ZhaiRoland Winter
Mar 8, 2016·Biochimica Et Biophysica Acta·Matti Javanainen, Hector Martinez-Seara
Nov 23, 2006·Journal of Structural Biology·Shirley W I Siu, Rainer A Böckmann
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
May 21, 2009·Proteins·Veronica Zobnina, Irena Roterman
Apr 5, 2007·Proteins·Cen Gao, Harry A Stern

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