Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E, Room 2020, Salt Lake City, Utah 84112-0850, USA.
Faraday Discuss. 2010;144:347-57; discussion 445-81. doi: 10.1039/b901996k.
An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of 1/2 a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented.
提出了一种用于膜蛋白体系大规模粗粒模拟的整体多尺度模拟策略。该蛋白质被建模为一个非均匀弹性网络，而脂质则使用混合分析-系统（HAS）方法建模，在这两种情况下，都使用从分子动力学模拟获得的原子级信息来参数化模型。这种方法的一个特点是，从一开始就在模拟中使用脂质体长度尺度（即，大约一百万个脂质体加上蛋白质）。提出了一种从分子尺度信息开发高度粗粒模型的方法，并给出了脂质体中 N-BAR 结构域蛋白重排的结果。
