title: Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.
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.
authors.affiliation: Department of Biochemistry, University of Oxford , Oxford OX1 3QU, United Kingdom.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Jefferys
authors.affiliation: UCB NewMedicines , Chemin du Foriest, 1420 Braine-l'Alleud, Belgium.
authors.forename: Zara A
authors.initials: ZA
authors.lastname: Sands
authors.affiliation: UCB NewMedicines , Chemin du Foriest, 1420 Braine-l'Alleud, Belgium.
authors.forename: Jiye
authors.initials: J
authors.lastname: Shi
authors.affiliation: Department of Biochemistry, University of Oxford , Oxford OX1 3QU, United Kingdom.
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
authors.affiliation: Department of Biochemistry, University of Oxford , Oxford OX1 3QU, United Kingdom.
authors.forename: Philip W
authors.initials: PW
authors.lastname: Fowler