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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.

SUBMITTER: Jefferys E 

PROVIDER: S-EPMC4467903 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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

Jefferys Elizabeth E   Sands Zara A ZA   Shi Jiye J   Sansom Mark S P MS   Fowler Philip W PW  

Journal of chemical theory and computation 20150514 6


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, <i>alchembed</i>, 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  ...[more]

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