An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

Journal of Computational Chemistry
Hujun ShenGuohui Li

Abstract

In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay-Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay-Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (DHH), area per lipid ( AL) and volume per lipid ( VL). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters wer...Continue Reading

References

Jul 1, 1996·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·D J CleaverM P Neal
Aug 29, 2002·Nature Structural Biology·Martin Karplus, J Andrew McCammon
May 2, 2003·Nature·Youxing JiangRoderick MacKinnon
Aug 20, 2003·Journal of Computational Chemistry·Dirk ReithFlorian Müller-Plathe
Jul 23, 2004·The Journal of Chemical Physics·Grace Brannigan, Frank L H Brown
Apr 20, 2005·Current Opinion in Structural Biology·Valentina Tozzini
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·M Karplus, J Kuriyan
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Oct 15, 2005·The Journal of Chemical Physics·Sergei Izvekov, Gregory A Voth
Apr 15, 2006·The Journal of Chemical Physics·Toshiko Ichiye, Ming-Liang Tan
Jul 21, 2006·The Journal of Physical Chemistry. B·Sergei Izvekov, Gregory A Voth
Sep 1, 2006·The Journal of Chemical Physics·Pavel A Golubkov, Pengyu Ren
Jun 16, 2007·The Journal of Physical Chemistry. B·Siewert J MarrinkAlex H de Vries
Dec 19, 2007·The Journal of Physical Chemistry. B·Mario OrsiJonathan W Essex
Aug 9, 2008·Physical Chemistry Chemical Physics : PCCP·Pavel A GolubkovPengyu Ren
Feb 21, 2009·Journal of Computational Chemistry·L MartínezJ M Martínez
Mar 14, 2009·The Journal of Physical Chemistry. B·Gary S Ayton, Gregory A Voth
Sep 30, 2009·Accounts of Chemical Research·Valentina Tozzini
Jun 16, 2010·PLoS Computational Biology·Semen O YesylevskyySiewert J Marrink
Aug 13, 2010·The Journal of Physical Chemistry. B·Zhe WuArun Yethiraj
Mar 11, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Mario OrsiJonathan W Essex
Oct 28, 2011·The Journal of Chemical Physics·Johnny WuPengyu Ren
Aug 25, 2012·The Journal of Physical Chemistry. B·Åge A SkjevikKnut Teigen
Mar 25, 2014·Journal of Chemical Theory and Computation·Hujun ShenGuohui Li
Apr 30, 2014·Journal of Computational Chemistry·Alexander Mirzoev, Alexander P Lyubartsev
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl
Nov 1, 2007·Journal of Chemical Theory and Computation·Michael J Schnieders, Jay W Ponder

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Citations

Dec 31, 2015·Journal of Chemical Theory and Computation·Guohui LiHonglei Wang
Oct 27, 2016·Journal of Chemical Theory and Computation·Min LiJohn Z H Zhang
Feb 13, 2016·Journal of Computational Chemistry·Ronald D Hills, Nicholas McGlinchey
Mar 8, 2017·Journal of Computational Chemistry·Hujun ShenYachao Zhang
Nov 23, 2019·Physical Chemistry Chemical Physics : PCCP·Matteo RicciClaudio Zannoni
Jun 2, 2021·Physical Chemistry Chemical Physics : PCCP·Hujun ShenChan Lu
Apr 7, 2020·The Journal of Physical Chemistry Letters·Qinglu Zhong, Guohui Li
Aug 3, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Hujun ShenShuiguo Wen
Jan 13, 2021·The Journal of Physical Chemistry. a·Hujun ShenMingsen Deng

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