Literature DB >> 33513017

EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations.

Semen Yesylevskyy1,2, Himanshu Khandelia3,4.   

Abstract

The EnCurv method for maintaining membrane curvature in molecular dynamics simulations is introduced. The method allows maintaining any desired curvature in a sector of lipid membrane bent in a single plane without adding any unphysical interactions into the system and without restrictions on lateral and transversal lipid diffusion and distribution. The current implementation is limited to the membranes curved in a single plane but generalization to arbitrary curvature and membrane topology is possible. The method is simple, easy to implement, and scales linearly with the system size. EnCurv is agnostic to the force field, simulation parameters, and membrane composition. The proof of principle implementation (https://github.com/yesint/EnCurv) is compatible with the majority of modern simulation packages and shows consistent results on the model systems.

Entities:  

Year:  2021        PMID: 33513017     DOI: 10.1021/acs.jctc.0c00800

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  4 in total

Review 1.  Computational Studies of Lipid Droplets.

Authors:  Siyoung Kim; Jessica M J Swanson; Gregory A Voth
Journal:  J Phys Chem B       Date:  2022-03-09       Impact factor: 2.991

2.  Coarse-Grained Simulations Suggest Potential Competing Roles of Phosphoinositides and Amphipathic Helix Structures in Membrane Curvature Sensing of the AP180 N-Terminal Homology Domain.

Authors:  Alexis Belessiotis-Richards; Andreas H Larsen; Stuart G Higgins; Molly M Stevens; Alfredo Alexander-Katz
Journal:  J Phys Chem B       Date:  2022-04-08       Impact factor: 3.466

3.  Amphiphilic anti-SARS-CoV-2 drug remdesivir incorporates into the lipid bilayer and nerve terminal membranes influencing excitatory and inhibitory neurotransmission.

Authors:  Natalia Krisanova; Natalia Pozdnyakova; Artem Pastukhov; Marina Dudarenko; Oleg Shatursky; Olena Gnatyuk; Uliana Afonina; Kyrylo Pyrshev; Galina Dovbeshko; Semen Yesylevskyy; Tatiana Borisova
Journal:  Biochim Biophys Acta Biomembr       Date:  2022-04-22       Impact factor: 4.019

Review 4.  Molecular Dynamics Simulations of Curved Lipid Membranes.

Authors:  Andreas Haahr Larsen
Journal:  Int J Mol Sci       Date:  2022-07-22       Impact factor: 6.208

  4 in total

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