Work

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries

Year: 2015

Type: article

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.

Source: Journal of Chemical Theory and Computation

DOI: 10.1021/ct501111d

Authors: Elizabeth Jefferys, Zara A. Sands, Jiye Shi, Mark S. P. Sansom, Philip W. Fowler

Institution: University of Oxford

Language: English

Topic: Lipid Membrane Structure and Behavior

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $240

Funders: Wellcome Trust, Union Chimique Belge, Partnership for Advanced Computing in Europe AISBL, Biotechnology and Biological Sciences Research Council