PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

详细信息    查看全文

• 作者：Marco Pasi ; Richard Lavery ; Nicoletta Ceres
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2013
• 出版时间：January 8, 2013
• 年：2013
• 卷：9
• 期：1
• 页码：785-793
• 全文大小：534K
• 年卷期：v.9,no.1(January 8, 2013)
• ISSN：1549-9626

文摘

We present a coarse-grain protein model PaLaCe (Pasi鈥揕avery鈥揅eres) that has been developed principally to allow fast computational studies of protein mechanics and to clarify the links between mechanics and function. PaLaCe uses a two-tier protein representation with one to three pseudoatoms representing each amino acid for the main nonbonded interactions, combined with atomic-scale peptide groups and some side chain atoms to allow the explicit representation of backbone hydrogen bonds and to simplify the treatment of bonded interactions. The PaLaCe force field is composed of physics-based terms, parametrized using Boltzmann inversion of conformational probability distributions derived from a protein structure data set, and iteratively refined to reproduce the experimental distributions. PaLaCe has been implemented in the MMTK simulation package and can be used for energy minimization, normal mode calculations, and molecular or stochastic dynamics. We present simulations with PaLaCe that test its ability to maintain stable structures for folded proteins, reproduce their dynamic fluctuations, and correctly model large-scale, force-induced conformational changes.