Jefferys, Elizabeth; Sands, Zara A.; Shi, Jiye; Sansom, Mark S. P.; Fowler, Philip W.
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2743-2754, JUN 2015

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.

DOI:10.1021/ct501111d

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