Literature DB >> 25679020

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields.

Åge A Skjevik1, Benjamin D Madej, Callum J Dickson, Knut Teigen, Ross C Walker, Ian R Gould.   

Abstract

This communication reports the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations. Using two different lipid force fields we show simulations started from random mixtures of lipids and water in which four different types of phospholipids self-assemble into organized bilayers in under 1 microsecond.

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Year:  2015        PMID： 25679020      PMCID： PMC5084445          DOI： 10.1039/c4cc09584g

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  25 in total

1.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

Authors:  Romelia Salomon-Ferrer; Andreas W Götz; Duncan Poole; Scott Le Grand; Ross C Walker
Journal:  J Chem Theory Comput       Date:  2013-08-20       Impact factor: 6.006

2.  Back to the future: mechanics and thermodynamics of lipid biomembranes.

Authors:  E Evans; W Rawicz; B A Smith
Journal:  Faraday Discuss       Date:  2013       Impact factor: 4.008

3.  Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field.

Authors:  Wataru Shinoda; Russell DeVane; Michael L Klein
Journal:  J Phys Chem B       Date:  2010-05-27       Impact factor: 2.991

4.  Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains.

Authors:  Norbert Kucerka; Stephanie Tristram-Nagle; John F Nagle
Journal:  J Membr Biol       Date:  2006-04-08       Impact factor: 1.843

5.  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

6.  Self-assembling of peptide/membrane complexes by atomistic molecular dynamics simulations.

Authors:  Santi Esteban-Martín; Jesús Salgado
Journal:  Biophys J       Date:  2006-11-03       Impact factor: 4.033

7.  Effect of chain length and unsaturation on elasticity of lipid bilayers.

Authors:  W Rawicz; K C Olbrich; T McIntosh; D Needham; E Evans
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

8.  Closer look at structure of fully hydrated fluid phase DPPC bilayers.

Authors:  Norbert Kucerka; Stephanie Tristram-Nagle; John F Nagle
Journal:  Biophys J       Date:  2006-04-14       Impact factor: 4.033

9.  Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles.

Authors:  Siewert J Marrink; Alan E Mark
Journal:  J Am Chem Soc       Date:  2003-12-10       Impact factor: 15.419

10.  Lipid14: The Amber Lipid Force Field.

Authors:  Callum J Dickson; Benjamin D Madej; Age A Skjevik; Robin M Betz; Knut Teigen; Ian R Gould; Ross C Walker
Journal:  J Chem Theory Comput       Date:  2014-01-30       Impact factor: 6.006
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  15 in total

1.  Interaction of Scots Pine Defensin with Model Membrane by Coarse-Grained Molecular Dynamics.

Authors:  Elena Ermakova; Yuriy Zuev
Journal:  J Membr Biol       Date:  2017-02-18       Impact factor: 1.843

2.  Formation and Properties of a Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed through Molecular Dynamics Simulations.

Authors:  Haoyuan Jing; Yanbin Wang; Parth Rakesh Desai; Kumaran S Ramamurthi; Siddhartha Das
Journal:  Langmuir       Date:  2020-05-12       Impact factor: 3.882

3.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
Journal:  Prog Mol Biol Transl Sci       Date:  2020-02-26       Impact factor: 3.622

4.  A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field.

Authors:  Benjamin D Madej; Ian R Gould; Ross C Walker
Journal:  J Phys Chem B       Date:  2015-09-11       Impact factor: 2.991

5.  Establishment and evaluation of glucose-modified nanocomposite liposomes for the treatment of cerebral malaria.

Authors:  Ya Tian; Zhongyuan Zheng; Xi Wang; Shuzhi Liu; Liwei Gu; Jing Mu; Xiaojun Zheng; Yujie Li; Shuo Shen
Journal:  J Nanobiotechnology       Date:  2022-07-06       Impact factor: 9.429

6.  Simulation of lipid bilayer self-assembly using all-atom lipid force fields.

Authors:  Åge A Skjevik; Benjamin D Madej; Callum J Dickson; Charles Lin; Knut Teigen; Ross C Walker; Ian R Gould
Journal:  Phys Chem Chem Phys       Date:  2016-04-01       Impact factor: 3.676

7.  Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description.

Authors:  Irene Marzuoli; Christian Margreitter; Franca Fraternali
Journal:  J Chem Theory Comput       Date:  2019-09-09       Impact factor: 6.006

8.  Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR.

Authors:  Soohaeng Yoo Willow; Ming Yuan; Oscar Juárez; David D L Minh
Journal:  Proteins       Date:  2021-06-14

9.  CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

Authors:  Jumin Lee; Xi Cheng; Jason M Swails; Min Sun Yeom; Peter K Eastman; Justin A Lemkul; Shuai Wei; Joshua Buckner; Jong Cheol Jeong; Yifei Qi; Sunhwan Jo; Vijay S Pande; David A Case; Charles L Brooks; Alexander D MacKerell; Jeffery B Klauda; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2015-12-03       Impact factor: 6.006

10.  Shear-induced microstructures and dynamics processes of phospholipid cylinders in solutions.

Authors:  Yue Shan; Xiaowei Qiang; Jianzhu Ye; Xianghong Wang; Linli He; Shiben Li
Journal:  Sci Rep       Date:  2019-10-28       Impact factor: 4.379
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