TY - JOUR
T1 - PSPICA
T2 - A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model
AU - Miyazaki, Yusuke
AU - Okazaki, Susumu
AU - Shinoda, Wataru
N1 - Funding Information:
We thank Kyle Hall and Michael Klein for helpful comments and discussions. This research was partly supported by MEXT as “Priority Issue on Post-K computer” (Building Innovative Drug Discovery Infrastructure Through Functional Control of Biomolecular Systems). This research used computational resources of the K computer provided by the RIKEN Advanced Institute for Computational Science through the HPCI System Research Project (Project ID: hp190171) and the computational facilities of Research Center for Computational Science, Okazaki, and the Institute for Solid State Physics, the University of Tokyo.
Publisher Copyright:
© 2019 American Chemical Society.
PY - 2020/1/14
Y1 - 2020/1/14
N2 - We present a coarse-grained (CG) force field (FF), pSPICA, for lipid membranes that incorporates a CG polar water model, which guarantees a reasonable dielectric response for water. Using a relatively simple functional form for the interaction, the CG parameters were systematically optimized to reproduce surface/interfacial tension, density, solvation or transfer free energy, as well as distribution functions obtained from all-atom molecular dynamics trajectory generated with the CHARMM FF, following the scheme used in the SPICA FF. Lipid membranes simulated using the present CG FF demonstrate reasonable membrane area and thickness, elasticity, and line tension, which ensure that the simulated lipid membranes exhibit proper mesoscopic morphology. The major advantages of the pSPICA FF with a polar water model were its ability to simulate membrane electroporation and its superior performance in the morphological characterization of charged lipid aggregates. We also demonstrated that the pSPICA can better describe the membrane permeation of hydrophilic segments involving a water string formation.
AB - We present a coarse-grained (CG) force field (FF), pSPICA, for lipid membranes that incorporates a CG polar water model, which guarantees a reasonable dielectric response for water. Using a relatively simple functional form for the interaction, the CG parameters were systematically optimized to reproduce surface/interfacial tension, density, solvation or transfer free energy, as well as distribution functions obtained from all-atom molecular dynamics trajectory generated with the CHARMM FF, following the scheme used in the SPICA FF. Lipid membranes simulated using the present CG FF demonstrate reasonable membrane area and thickness, elasticity, and line tension, which ensure that the simulated lipid membranes exhibit proper mesoscopic morphology. The major advantages of the pSPICA FF with a polar water model were its ability to simulate membrane electroporation and its superior performance in the morphological characterization of charged lipid aggregates. We also demonstrated that the pSPICA can better describe the membrane permeation of hydrophilic segments involving a water string formation.
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U2 - 10.1021/acs.jctc.9b00946
DO - 10.1021/acs.jctc.9b00946
M3 - Article
C2 - 31751511
AN - SCOPUS:85076740400
SN - 1549-9618
VL - 16
SP - 782
EP - 793
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
IS - 1
ER -