Open AccessAlchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
Author(s) -
Elizabeth Jefferys,
Zara A. Sands,
Jiye Shi,
Mark S. P. Sansom,
Philip W. Fowler
Publication year - 2015
Publication title -
journal of chemical theory and computation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.001
H-Index - 185
eISSN - 1549-9626
pISSN - 1549-9618
DOI - 10.1021/ct501111d
Subject(s) - van der waals force , core (optical fiber) , membrane protein , computer science , membrane , force field (fiction) , code (set theory) , molecular dynamics , range (aeronautics) , biological system , chemistry , computational science , materials science , molecule , biology , computational chemistry , biochemistry , artificial intelligence , telecommunications , organic chemistry , set (abstract data type) , composite material , programming language
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.