Paper Citing NAMD - Abstract
Staritzbichler, Rene; Anselmi, Claudio; Forrest, Lucy R.; Faraldo-Gomez, Jose D.
GRIFFIN: A Versatile Methodology for Optimization of Protein-Lipid Interfaces for Membrane Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1167-1176, APR 2011
As new atomic structures of membrane proteins are resolved, they reveal increasingly complex transmembrane topologies and highly irregular surfaces with crevices and pores. In many cases, specific interactions formed with the lipid membrane are functionally crucial, as is the overall lipid composition. Compounded with increasing protein size, these characteristics pose a challenge for the construction of simulation models of membrane proteins in lipid environments; clearly, that these models are sufficiently realistic bears upon the reliability of simulation-based studies of these systems. Here, we introduce GRIFFIN (GRId-based Force Field INput), which uses a versatile framework to automate and improve a widely used membrane-embedding protocol. Initially, GRIFFIN carves out lipid and water molecules from a volume equivalent to that of the protein, to conserve the system density. In the subsequent optimization phase GRIFFIN adds an implicit grid-based protein force field to a molecular dynamics simulation of the precarved membrane. In this force field, atoms inside the implicit protein volume experience an outward force that will expel them from that volume, whereas those outside are subject to electrostatic and van der Waals interactions with the implicit protein. At each step of the simulation, these forces are updated by GRIFFIN and combined with the intermolecular forces of the explicit lipid water system. This procedure enables the construction of realistic and reproducible starting configurations of the protein membrane interface within a reasonable time frame and with minimal intervention. GRIFFIN is a stand-alone tool designed to work alongside any existing molecular dynamics package, such as NAMD or GROMACS.
