Frenkel Zakharia M, Trifonov Edward N
Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel.
Proteins. 2007 May 1;67(2):271-84. doi: 10.1002/prot.21325.
A new method is proposed to reveal apparent evolutionary relationships between protein fragments with similar 3D structures by finding "intermediate" sequences in the proteomic database. Instead of looking for homologies and intermediates for a whole protein domain, we build a chain of intermediate short sequences, which allows one to link similar structural modules of proteins belonging to the same or different families. Several such chains of intermediates can be combined into an evolutionary tree of structural protein modules. All calculations were made for protein fragments of 20 aa residues. Three evolutionary trees for different module structures are described. The aim of the paper is to introduce the new method and to demonstrate its potential for protein structural predictions. The approach also opens new perspectives for protein evolution studies.
提出了一种新方法，通过在蛋白质组数据库中寻找“中间”序列来揭示具有相似三维结构的蛋白质片段之间明显的进化关系。我们不是为整个蛋白质结构域寻找同源性和中间体，而是构建中间短序列链，这使得人们能够将属于同一或不同家族的蛋白质的相似结构模块联系起来。几个这样的中间序列链可以组合成结构蛋白质模块的进化树。所有计算都是针对20个氨基酸残基的蛋白质片段进行的。描述了三种不同模块结构的进化树。本文的目的是介绍这种新方法，并展示其在蛋白质结构预测方面的潜力。该方法也为蛋白质进化研究开辟了新的视角。
