Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Biochimica Et Biophysica Acta
Takaharu MoriYuji Sugita

Abstract

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

References

Jul 31, 1979·The Journal of Membrane Biology·H J GallaE Sackmann
May 1, 1990·Biochemistry·J L Popot, D M Engelman
Sep 1, 1996·Biophysical Journal·F Jähnig
Apr 4, 1997·Science·K R MacKenzieD M Engelman
Dec 5, 1988·Physical Review Letters·A M Ferrenberg, R H Swendsen
Jan 6, 1992·Physical Review Letters·B A Berg, T Neuhaus
May 1, 1999·Proteins·T Lazaridis, M Karplus
May 8, 1999·Biophysical Journal·R S Cantor
Mar 15, 2000·Journal of Molecular Biology·W P Russ, D M Engelman
Oct 14, 2000·Annual Review of Physical Chemistry·D Bashford, D A Case
Nov 7, 2000·Biochimica Et Biophysica Acta·J F Nagle, S Tristram-Nagle
Feb 19, 2002·Chemical Reviews·Christopher J. Cramer, Donald G. Truhlar
Jun 19, 2002·Accounts of Chemical Research·Leonor Saiz, Michael L Klein
Sep 6, 2002·Journal of Computational Chemistry·Alexey OnufrievDonald Bashford
Jan 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Chikashi ToyoshimaDavid H MacLennan
Jul 2, 2003·Proteins·Themis Lazaridis
Jul 3, 2003·Nature Reviews. Molecular Cell Biology·David H MacLennan, Evangelia G Kranias
Sep 10, 2003·Journal of Computational Chemistry·Wonpil ImCharles L Brooks
Jun 25, 2004·Protein Science : a Publication of the Protein Society·Stephen H White
Jul 23, 2004·The Journal of Chemical Physics·Hironori Kokubo, Yuko Okamoto
Jul 23, 2004·The Journal of Chemical Physics·Donald HamelbergJ Andrew McCammon
Apr 20, 2005·Current Opinion in Structural Biology·Nathan A Baker
Apr 30, 2005·Proceedings of the National Academy of Sciences of the United States of America·Wonpil Im, Charles L Brooks

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Citations

Apr 21, 2016·Biochimica Et Biophysica Acta·James C Gumbart, Sergei Noskov
Feb 10, 2017·The Journal of Physical Chemistry. B·Juan R PerillaPeijun Zhang
Nov 20, 2016·Journal of Computational Chemistry·Sunhwan JoWonpil Im
May 23, 2017·The Journal of Physical Chemistry. B·David Stelter, Tom Keyes
Sep 5, 2017·Reports on Progress in Physics·Helen MillerMark C Leake
Mar 2, 2018·Annual Review of Biophysics·Sander BoonstraAntoine M van Oijen
Oct 5, 2017·Critical Reviews in Biochemistry and Molecular Biology·Bian LiJens Meiler
Sep 7, 2018·Physical Chemistry Chemical Physics : PCCP·Elisa PieriNicolas Ferré
Jun 9, 2016·Nature Structural & Molecular Biology·Patrick Barth, Alessandro Senes
Oct 8, 2019·Soft Matter·David Stelter, Tom Keyes
Oct 2, 2019·The Journal of Membrane Biology·Mikhail N RyazantsevMichael F Brown
Jul 3, 2017·The Journal of Chemical Physics·Damián A GrilloMarta B Ferraro
Jun 10, 2018·The Journal of Chemical Physics·Damián A GrilloMarta B Ferraro
Nov 22, 2019·Frontiers in Molecular Biosciences·Laura Orellana
Aug 28, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Guilherme Volpe Bossa, Sylvio May
Jul 13, 2019·Annual Review of Cell and Developmental Biology·Michael Feig, Yuji Sugita
Jan 16, 2021·International Journal of Molecular Sciences·Francisco Ramos-Martín, Nicola D'Amelio
Jan 12, 2021·Chemical Reviews·Jovan DamjanovicYu-Shan Lin
Jun 19, 2021·Journal of Chemical Information and Modeling·Takaharu MoriYuji Sugita
Aug 1, 2021·Biochimica Et Biophysica Acta. Biomembranes·Gerard DuartLuis Martinez-Gil
Jun 7, 2018·Journal of Chemical Theory and Computation·Jan K MarzinekPeter J Bond
Oct 31, 2019·Journal of Chemical Theory and Computation·Benjamin Bouvier
Sep 7, 2017·Journal of Chemical Theory and Computation·Thomas J PiggotJonathan W Essex
Dec 13, 2018·Journal of Chemical Information and Modeling·Stephanie A BrockeMichael Feig
Jan 10, 2019·Chemical Reviews·Siewert J MarrinkMark S P Sansom
Nov 26, 2019·Journal of Chemical Theory and Computation·Takaharu Mori, Yuji Sugita
Feb 13, 2019·Chemical Reviews·Richard M VenableRichard W Pastor
Feb 14, 2019·Chemical Reviews·Valentina CorradiD Peter Tieleman
Feb 21, 2019·Chemical Reviews·Alison N LeonardJeffery B Klauda

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