Parisien Marc, Major François
Department of Computer Science and Operations Research, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada.
Proteins. 2007 Sep 1;68(4):824-9. doi: 10.1002/prot.21475.
The formation of beta-sheet domains in proteins involves five energetically important factors: the formation of networks of hydrogen bonds and hydrophobic faces, and the residue propensities, or preferences, to be found at the edges of the beta-sheet, to adopt the extended conformation, and to make contact with other residues. These relative energy contributions define a potential energy function. Here, we show how optimizing this potential energy function reveals the formation of hydrophobic faces as the utmost factor. The potential energy function was optimized to minimize the Z-scores of the native topologies among the exhaustive sets of over 400 different beta-sheets. These results corroborate with experimental data that showed the environment of a protein is an important modulator of beta-sheet folding. The contact propensities were found to be the least important, which could explain the poor predictive power of beta-strand alignment methods based on pair-wise contact matrices.
蛋白质中β-折叠结构域的形成涉及五个在能量方面很重要的因素：氢键网络和疏水表面的形成，以及在β-折叠边缘出现、采用伸展构象并与其他残基接触的残基倾向或偏好。这些相对能量贡献定义了一个势能函数。在此，我们展示了优化该势能函数如何揭示疏水表面的形成是最为关键的因素。通过优化势能函数，使超过400种不同β-折叠的详尽集合中的天然拓扑结构的Z分数最小化。这些结果与实验数据相符，实验数据表明蛋白质的环境是β-折叠折叠的重要调节因素。发现接触倾向是最不重要的，这可以解释基于成对接触矩阵的β-链比对方法预测能力较差的原因。
