Sowdhamini R, Srinivasan N, Shoichet B, Santi D V, Ramakrishnan C, Balaram P
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Protein Eng. 1989 Nov;3(2):95-103. doi: 10.1093/protein/3.2.95.
A computer modeling procedure for assessing the stereochemical suitability of pairs of residues in proteins as potential sites for introduction of cystine disulfide crosslinks has been developed. Residue pairs with C alpha-C alpha distances of less than or equal to 6.5 A and C beta-C beta distances of less than or equal to 4.5 A are chosen for geometrical fixation of S atoms using the program MODIP. The stereochemistry of the modeled disulfides is evaluated using limits for the structural parameters of the various torsion angles and S-S bond length in the disulfide bridge. The ability of the procedure to correctly model disulfides has been checked with examples of cystine peptides of known crystal structures and 103 disulfide bridges from 25 available protein crystal structures determined at less than or equal to 2 A resolution. An analysis of results on three proteins with engineered disulfides, T4 lysozyme, dihydrofolate reductase and subtilisin, is presented. Two positions for the introduction of 'stereochemically optimal' disulfides are identified in subtilisin.
已开发出一种计算机建模程序，用于评估蛋白质中残基对作为引入胱氨酸二硫键交联潜在位点的立体化学适宜性。使用MODIP程序选择Cα-Cα距离小于或等于6.5 Å且Cβ-Cβ距离小于或等于4.5 Å的残基对，以对S原子进行几何固定。使用二硫键桥中各种扭转角和S-S键长度的结构参数限制来评估模拟二硫键的立体化学。已通过已知晶体结构的胱氨酸肽实例以及25个分辨率小于或等于2 Å的可用蛋白质晶体结构中的103个二硫键桥来检验该程序正确模拟二硫键的能力。本文对三种具有工程化二硫键的蛋白质（T4溶菌酶、二氢叶酸还原酶和枯草杆菌蛋白酶）的结果进行了分析。在枯草杆菌蛋白酶中确定了两个引入“立体化学最佳”二硫键的位置。
