title: Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.
abstract: Conformational sampling is fundamentally important for simulating complex biomolecular systems. The generalized-ensemble algorithm, especially the temperature replica-exchange molecular dynamics method (T-REMD), is one of the most powerful methods to explore structures of biomolecules such as proteins, nucleic acids, carbohydrates, and also of lipid membranes. T-REMD simulations have focused on soluble proteins rather than membrane proteins or lipid bilayers, because explicit membranes do not keep their structural integrity at high temperature. Here, we propose a new generalized-ensemble algorithm for membrane systems, which we call the surface-tension REMD method. Each replica is simulated in the NPγT ensemble, and surface tensions in a pair of replicas are exchanged at certain intervals to enhance conformational sampling of the target membrane system. We test the method on two biological membrane systems: a fully hydrated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer and a WALP23-POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane system. During these simulations, a random walk in surface tension space is realized. Large-scale lateral deformation (shrinking and stretching) of the membranes takes place in all of the replicas without collapse of the lipid bilayer structure. There is accelerated lateral diffusion of DPPC lipid molecules compared with conventional MD simulation, and a much wider range of tilt angle of the WALP23 peptide is sampled due to large deformation of the POPC lipid bilayer and through peptide-lipid interactions. Our method could be applicable to a wide variety of biological membrane systems.
authors.affiliation: RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.|RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Takaharu
authors.initials: T
authors.lastname: Mori
authors.affiliation: RIKEN Advanced Institute for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Jaewoon
authors.initials: J
authors.lastname: Jung
authors.affiliation: RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.|RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.|RIKEN Advanced Institute for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita