A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information.
Description
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries - Journal of Chemical Theory and Computation (ACS Publications)
%0 Journal Article
%1 Jefferys2015Alchembed
%A Jefferys, Elizabeth
%A Sands, Zara A.
%A Shi, Jiye
%A Sansom, Mark S. P.
%A Fowler, Philip W.
%D 2015
%J Journal of Chemical Theory and Computation
%K membrane-insertion membrane-systems molecular-dynamics
%N 6
%P 2743-2754
%R 10.1021/ct501111d
%T Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
%U /brokenurl# http://dx.doi.org/10.1021/ct501111d
%V 11
%X A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information.
@article{Jefferys2015Alchembed,
abstract = { A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information. },
added-at = {2016-03-15T21:18:56.000+0100},
author = {Jefferys, Elizabeth and Sands, Zara A. and Shi, Jiye and Sansom, Mark S. P. and Fowler, Philip W.},
biburl = {https://www.bibsonomy.org/bibtex/23bb497d4327cd8b05f6bfe6ddbf10232/salotz},
description = {Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries - Journal of Chemical Theory and Computation (ACS Publications)},
doi = {10.1021/ct501111d},
eprint = {http://dx.doi.org/10.1021/ct501111d},
interhash = {ec663cc79b6b32535d194b82193c407f},
intrahash = {3bb497d4327cd8b05f6bfe6ddbf10232},
journal = {Journal of Chemical Theory and Computation},
keywords = {membrane-insertion membrane-systems molecular-dynamics},
note = {PMID: 26089745},
number = 6,
pages = {2743-2754},
timestamp = {2016-03-15T21:18:56.000+0100},
title = {Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries},
url = {/brokenurl# http://dx.doi.org/10.1021/ct501111d },
volume = 11,
year = 2015
}