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

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.