Moult J, James M N
Biochemistry Department, University of Alberta, Edmonton, Canada.
Proteins. 1986 Oct;1(2):146-63. doi: 10.1002/prot.340010207.
The feasibility of determining the conformation of segments of a polypeptide chain up to six residues in length in globular proteins by means of a systematic search through the possible conformations has been investigated. Trial conformations are generated by using representative sets of phi, psi, and chi angles that have been derived from an examination of the distributions of these angles in refined protein structures. A set of filters based on simple rules that protein structures obey is used to reduce the number of conformations to a manageable total. The most important filters are the maintenance of chain integrity and the avoidance of too-short van der Waals contacts with the rest of the protein and with other portions of the segment under construction. The procedure is intended to be used with approximate models so that allowance is made throughout for errors in the rest of the structure. All possible main chains are first constructed and then all possible side-chain conformations are built onto each of these. The electrostatic energy, including a solvent screening term, and the exposed hydrophobic area are evaluated for each accepted conformation. The method has been tested on two segments of chain in the trypsin like enzyme from Streptomyces griseus. It is found that there is a wide spread of energies among the accepted conformations, and the lowest energy ones have satisfactorily small root mean square deviations from the X-ray structure.
通过对可能的构象进行系统搜索来确定球状蛋白质中长度达六个残基的多肽链片段构象的可行性已得到研究。通过使用从对精细蛋白质结构中这些角度的分布进行检查而得出的代表性的φ、ψ和χ角集来生成试验构象。使用一组基于蛋白质结构所遵循的简单规则的筛选器，将构象数量减少到可管理的总数。最重要的筛选器是保持链的完整性以及避免与蛋白质的其余部分以及正在构建的片段的其他部分形成过短的范德华接触。该程序旨在与近似模型一起使用，以便始终考虑结构其余部分中的误差。首先构建所有可能的主链，然后将所有可能的侧链构象构建到这些主链中的每一个上。对每个接受的构象评估静电能，包括溶剂筛选项，以及暴露的疏水面积。该方法已在来自灰色链霉菌的类胰蛋白酶的两个链段上进行了测试。发现接受的构象之间能量分布广泛，并且能量最低的构象与X射线结构的均方根偏差令人满意地小。
