Covell D G, Jernigan R L
Frederick Cancer Research Facility, Program Resources, Inc., Frederick, Maryland 21701.
Biochemistry. 1990 Apr 3;29(13):3287-94. doi: 10.1021/bi00465a020.
A new method is presented to examine the complete range of folded topologies accessible in the compact state of globular proteins. The procedure is to generate all conformations, with volume exclusion, upon a lattice in a space restricted to the individual protein's known compact conformational space. Using one lattice point per residue, we find 10(2)-10(4) possible compact conformations for the five small globular proteins studied. Subsequently, these conformations are evaluated in terms of residue-specific, pairwise contact energies that favor nonbonded, hydrophobic interactions. Native structures for the five proteins are always found within the best 2% of all conformers generated. This novel method is simple and general and can be used to determine a small group of most favorable overall arrangements for the folding of specific amino acid sequences within a restricted space.
本文提出了一种新方法，用于研究球状蛋白质紧密状态下可及的完整折叠拓扑结构范围。具体步骤是在一个受单个蛋白质已知紧密构象空间限制的空间晶格上，通过体积排除法生成所有构象。每个残基使用一个晶格点，我们发现所研究的五个小球状蛋白质有10² - 10⁴种可能的紧密构象。随后，根据有利于非键合疏水相互作用的残基特异性成对接触能对这些构象进行评估。这五种蛋白质的天然结构总是在所生成的所有构象中最佳的2%以内被找到。这种新方法简单且通用，可用于在受限空间内确定一小部分特定氨基酸序列折叠时最有利的整体排列。
