Literature DB >> 21647243

Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields.

Brad A Bauer1, Timothy R Lucas, David J Meninger, Sandeep Patel.   

Abstract

We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5-5.5 kcal/mol barriers for water permeation into bilayers. Barriers are highest when water coordination within the bilayer is prevented, and also when using force fields that accurately reproduce experimental alkane hydration free energies. The magnitude of the average water dipole moment decreases from 2.6 Debye (in bulk) to 1.88 Debye (in membrane interior). This variation correlates with the change in a water molecule's coordination number.

Entities:  

Year:  2011        PMID: 21647243      PMCID: PMC3107520          DOI: 10.1016/j.cplett.2011.04.052

Source DB:  PubMed          Journal:  Chem Phys Lett        ISSN: 0009-2614            Impact factor:   2.328


  18 in total

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Authors:  M A Wilson; A Pohorille
Journal:  J Am Chem Soc       Date:  1996-07-17       Impact factor: 15.419

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Authors:  D Huster; A J Jin; K Arnold; K Gawrisch
Journal:  Biophys J       Date:  1997-08       Impact factor: 4.033

3.  Distribution of amino acids in a lipid bilayer from computer simulations.

Authors:  Justin L MacCallum; W F Drew Bennett; D Peter Tieleman
Journal:  Biophys J       Date:  2008-01-22       Impact factor: 4.033

4.  A molecular-dynamics study of lipid bilayers: effects of the hydrocarbon chain length on permeability.

Authors:  Taisuke Sugii; Shu Takagi; Yoichiro Matsumoto
Journal:  J Chem Phys       Date:  2005-11-08       Impact factor: 3.488

5.  Simulation-based methods for interpreting x-ray data from lipid bilayers.

Authors:  Jeffery B Klauda; Norbert Kucerka; Bernard R Brooks; Richard W Pastor; John F Nagle
Journal:  Biophys J       Date:  2006-01-27       Impact factor: 4.033

6.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Authors:  Jeffery B Klauda; Richard M Venable; J Alfredo Freites; Joseph W O'Connor; Douglas J Tobias; Carlos Mondragon-Ramirez; Igor Vorobyov; Alexander D MacKerell; Richard W Pastor
Journal:  J Phys Chem B       Date:  2010-06-17       Impact factor: 2.991

7.  Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields.

Authors:  Lula Rosso; Ian R Gould
Journal:  J Comput Chem       Date:  2008-01-15       Impact factor: 3.376

8.  Modification of the CHARMM force field for DMPC lipid bilayer.

Authors:  Carl-Johan Högberg; Alexei M Nikitin; Alexander P Lyubartsev
Journal:  J Comput Chem       Date:  2008-11-15       Impact factor: 3.376

9.  Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models.

Authors:  Joseph E Davis; Obaidur Rahaman; Sandeep Patel
Journal:  Biophys J       Date:  2009-01       Impact factor: 4.033

10.  Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment.

Authors:  Justin L MacCallum; W F Drew Bennett; D Peter Tieleman
Journal:  J Gen Physiol       Date:  2007-04-16       Impact factor: 4.086

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  9 in total

Review 1.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

Review 2.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

Review 3.  Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems.

Authors:  Timothy R Lucas; Brad A Bauer; Sandeep Patel
Journal:  Biochim Biophys Acta       Date:  2011-09-24

4.  Force Fields for Small Molecules.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2019

5.  Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields.

Authors:  Timothy R Lucas; Brad A Bauer; Joseph E Davis; Sandeep Patel
Journal:  J Comput Chem       Date:  2011-10-14       Impact factor: 3.376

6.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

7.  Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.

Authors:  Christopher T Lee; Jeffrey Comer; Conner Herndon; Nelson Leung; Anna Pavlova; Robert V Swift; Chris Tung; Christopher N Rowley; Rommie E Amaro; Christophe Chipot; Yi Wang; James C Gumbart
Journal:  J Chem Inf Model       Date:  2016-04-14       Impact factor: 4.956

8.  Two Relations to Estimate Membrane Permeability Using Milestoning.

Authors:  Lane W Votapka; Christopher T Lee; Rommie E Amaro
Journal:  J Phys Chem B       Date:  2016-05-27       Impact factor: 2.991

9.  A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

Authors:  Huiying Chu; Xiangda Peng; Yan Li; Yuebin Zhang; Guohui Li
Journal:  Molecules       Date:  2017-12-31       Impact factor: 4.411

  9 in total

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