Coarse-graining methods for computational biology

MG Saunders, GA Voth - Annual review of biophysics, 2013 - annualreviews.org
Connecting the molecular world to biology requires understanding how molecular-scale
dynamics propagate upward in scale to define the function of biological structures. To …

[HTML][HTML] Force field development for lipid membrane simulations

AP Lyubartsev, AL Rabinovich - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
With the rapid development of computer power and wide availability of modelling software
computer simulations of realistic models of lipid membranes, including their interactions with …

Structural basis of membrane bending by the N-BAR protein endophilin

C Mim, H Cui, JA Gawronski-Salerno, A Frost, E Lyman… - Cell, 2012 - cell.com
Functioning as key players in cellular regulation of membrane curvature, BAR domain
proteins bend bilayers and recruit interaction partners through poorly understood …

Machine learning-driven multiscale modeling: bridging the scales with a next-generation simulation infrastructure

HI Ingólfsson, H Bhatia, F Aydin… - Journal of Chemical …, 2023 - ACS Publications
Interdependence across time and length scales is common in biology, where atomic
interactions can impact larger-scale phenomenon. Such dependence is especially true for a …

Mechanism of membrane curvature sensing by amphipathic helix containing proteins

H Cui, E Lyman, GA Voth - Biophysical journal, 2011 - cell.com
There are several examples of membrane-associated protein domains that target curved
membranes. This behavior is believed to have functional significance in a number of …

Membrane tension controls the assembly of curvature-generating proteins

M Simunovic, GA Voth - Nature communications, 2015 - nature.com
Abstract Proteins containing a Bin/Amphiphysin/Rvs (BAR) domain regulate membrane
curvature in the cell. Recent simulations have revealed that BAR proteins assemble into …

Linear aggregation of proteins on the membrane as a prelude to membrane remodeling

M Simunovic, A Srivastava… - Proceedings of the …, 2013 - National Acad Sciences
Adhesion and insertion of curvature-mediating proteins can induce dramatic structural
changes in cell membranes, allowing them to participate in several key cellular tasks. The …

Recent development in computer simulations of lipid bilayers

AP Lyubartsev, AL Rabinovich - Soft Matter, 2011 - pubs.rsc.org
Rapid development of computer power during the last decade has made molecular
simulations of lipid bilayers feasible for many research groups, which, together with the …

Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model

YZ Ohkubo, TV Pogorelov, MJ Arcario… - Biophysical journal, 2012 - cell.com
Characterizing atomic details of membrane binding of peripheral membrane proteins by
molecular dynamics (MD) has been significantly hindered by the slow dynamics of …

α-Synuclein induces both positive mean curvature and negative Gaussian curvature in membranes

AR Braun, E Sevcsik, P Chin, E Rhoades… - Journal of the …, 2012 - ACS Publications
Using a combination of X-ray scattering, fluorescence correlation spectroscopy, coarse-
grained molecular dynamics (MD) simulations and potential of mean force calculations, we …