Literature DB >> 19477311

Coarse-grained modeling of lipids.

Sandra V Bennun1, Matthew I Hoopes, Chenyue Xing, Roland Faller.   

Abstract

Molecular modeling of phospholipids on many scales has progressed significantly over the last years. Here we review several membrane models on intermediate to large length scales restricting ourselves to particle based coarse-grained models with implicit and explicit solvent. We explain similarities and differences as well as their connection to experiments and fine-grained models. We neglect any field descriptions on larger scales. We discuss then a few examples where we focus on studies of lipid phase behavior as well as supported lipid bilayers as these examples can only be meaningfully studied using large-scale models to date.

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Year:  2009        PMID: 19477311     DOI: 10.1016/j.chemphyslip.2009.03.003

Source DB:  PubMed          Journal:  Chem Phys Lipids        ISSN: 0009-3084            Impact factor:   3.329


  14 in total

1.  An implicit solvent coarse-grained lipid model with correct stress profile.

Authors:  Alex J Sodt; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2010-05-28       Impact factor: 3.488

Review 2.  Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides.

Authors:  Gianfranco Bocchinfuso; Sara Bobone; Claudia Mazzuca; Antonio Palleschi; Lorenzo Stella
Journal:  Cell Mol Life Sci       Date:  2011-05-17       Impact factor: 9.261

3.  Hysteresis and the Cholesterol Dependent Phase Transition in Binary Lipid Mixtures with the Martini Model.

Authors:  Clement Arnarez; Alexis Webb; Eric Rouvière; Edward Lyman
Journal:  J Phys Chem B       Date:  2016-12-15       Impact factor: 2.991

4.  Impact of Surface Polarity on Lipid Assembly under Spatial Confinement.

Authors:  Bradley S Harris; Yuqi Huang; Arpad Karsai; Wan-Chih Su; Pallavi D Sambre; Atul N Parikh; Gang-Yu Liu; Roland Faller
Journal:  Langmuir       Date:  2022-06-07       Impact factor: 4.331

5.  Molecular dynamics simulations of DPPC bilayers using "LIME", a new coarse-grained model.

Authors:  Emily M Curtis; Carol K Hall
Journal:  J Phys Chem B       Date:  2013-04-16       Impact factor: 2.991

Review 6.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

Review 7.  Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives.

Authors:  Christian Solís-Calero; Joaquín Ortega-Castro; Juan Frau; Francisco Muñoz
Journal:  Oxid Med Cell Longev       Date:  2015-04-21       Impact factor: 6.543

Review 8.  Atomistic Monte Carlo simulation of lipid membranes.

Authors:  Daniel Wüstner; Heinz Sklenar
Journal:  Int J Mol Sci       Date:  2014-01-24       Impact factor: 5.923

9.  The power of coarse graining in biomolecular simulations.

Authors:  Helgi I Ingólfsson; Cesar A Lopez; Jaakko J Uusitalo; Djurre H de Jong; Srinivasa M Gopal; Xavier Periole; Siewert J Marrink
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-05

10.  Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules.

Authors:  Pavel Buslaev; Ivan Gushchin
Journal:  Sci Rep       Date:  2017-09-13       Impact factor: 4.379

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