Keskin O, Bahar I
Chemical Engineering Department and Polymer Research Center, Bogazici University, Istanbul, Turkey.
Fold Des. 1998;3(6):469-79. doi: 10.1016/S1359-0278(98)00064-9.
Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features.
A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (r.m.s.d.) of 2.40 A with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 A and decreases to 1.35 A when conformational correlations and directional effects in inter-residue couplings are considered.
An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.
多个研究小组已经提出了蛋白质侧链的原子水平旋转异构体文库。另一方面，尽管低分辨率方法是探索全局结构特征的唯一有效途径，但粗粒度模型中侧链基团的构象尚未得到分析。
提出了一种与粗粒度模型兼容的、基于特定残基主链的侧链异构体文库。这些异构体状态用于已知主链结构的侧链堆积。对于50个测试蛋白质，预测的侧链位置相对于晶体结构的均方根偏差（r.m.s.d.）为2.40埃。核心残基的均方根偏差为1.60埃，当考虑残基间耦合中的构象相关性和方向效应时，该值降至1.35埃。
提出了一种在粗粒度模型蛋白质中分配侧链位置的自动化方法，并在互联网上提供；该方法能令人满意地解释侧链堆积，尤其是在核心区域。
