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Biophysics of Proteins at Surfaces: Assembly, Activation, Signaling
Poster Abstracts
27-POS
Board 27
Replica-Exchange Molecular-Dynamics Simulations of Mixed Lipid Bilayer Systems
Takaharu Mori
, Yuji Sugita.
RIKEN, Wako-shi, Saitama, Japan.
Conformational sampling is fundamentally important for simulating complex bio-molecular
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 bio-molecules such as proteins, nucleic acids, carbohydrates, and also of lipid
membranes. Recently, we have proposed a new generalized-ensemble algorithm for membrane
systems, which we call the surface-tension REMD method (γ-REMD) [1]. 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. In this
study, we carried out γ-REMD simulation for a pure DPPC lipid bilayer [1], and also T-REMD,
γ-REMD, and γT-REMD simulations for a mixed POPC/DMPC lipid bilayer [2]. In the DPPC
simulation, we found that lateral diffusion of lipid molecules was enhanced compared with
conventional MD simulation. In the POPC/DMPC simulations, lateral diffusion in the same lipid
phase was enhanced in all REMD simulations. As for "mixing" of two lipid components,
however, it was enhanced in T-REMD, while it was suppressed in γ-REMD. In γT-REMD, both
enhancement and suppression were observed, presumably because lateral diffusion is accelerated
at high temperature while it is suppressed under high surface tension. We suggest that surface
tension affects the degree of mixing of lipid components in biological membranes.
[1] T. Mori, J. Jung, and Y. Sugita, J. Chem. Theory Comput., 9, 5629-5640 (2013).
[2] J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita , WIREs
Comput. Mol. Sci., doi: 10.1002/wcms.1220 (2015).