The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.
The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.
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DOI：
10.1016/j.bpj.2012.01.061
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发表时间：
2012-05
影响因子：
3.4
通讯作者：
A. Zhou;C. O’Hern;L. Regan
中科院分区：
文献类型：
--
作者：
A. Zhou;C. O’Hern;L. Regan
The energy functions used to predict protein structures typically include both molecular-mechanics and knowledge-based terms. In contrast, our approach is to develop robust physics- and geometry-based methods. Here, we investigate to what extent simple hard-sphere models can be used to predict side-chain conformations. The distributions of the side-chain dihedral angleχ1of Val and Thr in proteins of known structure show distinctive features: Val side chains predominantly adoptχ1= 180°, whereas Thr side chains typically adoptχ1= 60° and 300° (i.e.,χ1= ±60° org− andg+configurations). Several hypotheses have been proposed to explain these differences, including interresidue steric clashes and hydrogen-bonding interactions. In contrast, we show that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using onlylocalsteric interactions in a dipeptide mimetic. Our results emphasize the power of simple physical approaches and their importance for future advances in protein engineering and design.
