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SLIM: An improved generalized B orn implicit membrane model
Author(s) -
Setzler Julia,
Seith Carolin,
Brieg Martin,
Wenzel Wolfgang
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23717
Subject(s) - electrostatics , dielectric , membrane , statistical physics , computer science , poisson distribution , algorithm , scheme (mathematics) , biological system , mathematics , physics , chemistry , quantum mechanics , mathematical analysis , biology , biochemistry , statistics
In most implicit continuum models, membranes are represented as heterogeneous dielectric environments, but their treatment within computationally efficient generalized Born (GB) models is challenging. Despite several previous attempts, an adequate description of multiple dielectric regions in implicit GB‐based membrane models that reproduce the qualitative and quantitative features of Poisson–Boltzmann (PB) electrostatics remains an unmet prerequisite of qualitatively correct implicit membrane models. A novel scheme (SLIM) to decompose one environment consisting of multiple dielectric regions into a sum of multiple environments consisting only of two dielectric regions each is proposed to solve this issue. These simpler environments can be treated with established GB methods. This approach captures qualitative features of PB electrostatic that are not present in previous models. Simulations of three membrane proteins demonstrate that this model correctly reproduces known properties of these proteins in agreement with experimental or other computational studies. © 2014 Wiley Periodicals, Inc.