Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields
详细信息 查看全文
- 作者：Evgeni Penev ; Joel Ireta ; Joan-Emma Shea
- 刊名：Journal of Physical Chemistry B
- 出版年：2008
- 出版时间：June 5, 2008
- 年：2008
- 卷：112
- 期：22
- 页码：6872 - 6877
- 全文大小：1295K
- 年卷期：v.112,no.22(June 5, 2008)
- ISSN：1520-5207
文摘
We present a novel method for comparing the long-range part of force fields in the presence of a maximally cooperative network of nonbonded interactions. The method is based on mapping the potential energy surface of an infinite polypeptide chain in the gas phase by using cylindrical coordinates (the twist and pitch) as geometry descriptors. We apply our method to an infinite polyalanine chain and consider the AMBER99, AMBER99SB, CHARMM27, and OPLS-AA/L fixed partial-charge force fields and the protein-specific version of the AMOEBA polarizable force field. Results from our analysis are compared to those obtained from high-level density-functional theory (DFT) calculations. We find that all force fields produce stronger stabilization of the helical conformations as compared to DFT, with only AMBER99/AMBER99SB satisfactorily reproducing all three helical conformations (π, α, and 310).