Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.
J Chem Theory Comput
; 11(6): 2743-2754, 2015 Jun 09.
Article
em En
| MEDLINE
| ID: mdl-26089745
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.
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MEDLINE
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En
Ano de publicação:
2015
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Article