Sutcliffe M J, Haneef I, Carney D, Blundell T L
Department of Crystallography, Birkbeck College, London, UK.
Protein Eng. 1987 Oct-Nov;1(5):377-84. doi: 10.1093/protein/1.5.377.
An approach is described for modelling the three-dimensional structure of a protein from the tertiary structures of several homologous proteins that have been determined by X-ray analysis. A method is developed for the simultaneous superposition of several protein molecules and for the calculation of an 'average structure' or 'framework'. Investigation of the convergence properties of this method, in the case of both weighted and unweighted least squares, demonstrates that both give a unique answer and the latter is robust for an homologous family of proteins. Multi-dimensional scaling is used to subgroup of the proteins with respect to structural homology. The framework calculated on the basis of the family of homologous proteins, or of an appropriate subgroup, is used to align fragments of the known protein structures of high sequence homology with the unknown. This alignment provides a basis for model building the tertiary structure. Different techniques for using the framework to model the mainchain of various globins and an immunoglobulin domain in the structurally conserved regions are investigated.
本文描述了一种从通过X射线分析确定的几种同源蛋白质的三级结构对蛋白质三维结构进行建模的方法。开发了一种用于同时叠加几个蛋白质分子并计算“平均结构”或“框架”的方法。对该方法在加权和非加权最小二乘法情况下的收敛特性进行研究表明，两者都能给出唯一答案，并且后者对于同源蛋白质家族具有鲁棒性。多维标度用于根据结构同源性对蛋白质进行亚分组。基于同源蛋白质家族或适当亚组计算的框架用于将高序列同源性的已知蛋白质结构片段与未知结构进行比对。这种比对为构建三级结构模型提供了基础。研究了使用框架对各种球蛋白的主链和结构保守区域中的免疫球蛋白结构域进行建模的不同技术。
