Is alanine dipeptide a good model for representing the torsional preferences of protein backbones?

被引:74
作者
Feig, Michael [1 ,2 ]
机构
[1] Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA
[2] Michigan State Univ, Dept Chem, E Lansing, MI 48824 USA
基金
美国国家科学基金会;
关键词
D O I
10.1021/ct800153n
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The conformational preference for different phi/Psi backbone torsion angles is a key determinant of peptide and protein secondary structure. Often, dipeptides are used as models for understanding protein backbone dynamics and to derive force field parameters. Here, the question is examined to what extent the conformational preferences in dipeptides reflect the backbone dynamics in polypeptides and proteins and to what extent an alanine dipeptide-based backbone torsion parametrization can lead to accurate reproduction of amino acid dependent phi/Psi preferences in protein structures. Results from a comparison of the analysis of Protein Data Bank (PDB) structures with long simulations of selected proteins and amino acid dipeptides suggest that a common alanine dipeptide-based torsion potential does in fact lead to excellent agreement between protein simulations and PDB structures. At the same time, the phi/Psi preferences in the dipeptides are significantly different, suggesting that dipeptides are not good model systems for studying protein backbone dynamics.
引用
收藏
页码:1555 / 1564
页数:10
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