OPTIMAL PROTEIN-STRUCTURE ALIGNMENTS BY MULTIPLE LINKAGE CLUSTERING - APPLICATION TO DISTANTLY RELATED PROTEINS

被引:63
作者
BOUTONNET, NS
ROOMAN, MJ
OCHAGAVIA, ME
RICHELLE, J
WODAK, SJ
机构
[1] FREE UNIV BRUSSELS,UNITE CONFORMAT MACROMOLEC BIOL,B-1050 BRUSSELS,BELGIUM
[2] INST BIOL PHYS CHIM,BIOCHIM THEOR LAB,F-75005 PARIS,FRANCE
[3] CTR INGN GENET & BIOTECNOL,HAVANA 10600,CUBA
来源
PROTEIN ENGINEERING | 1995年 / 8卷 / 07期
关键词
BACKBONE SUPERPOSITION; CONSENSUS MOTIFS; RIGID-BODY MOVEMENTS; STRUCTURE COMPARISON;
D O I
10.1093/protein/8.7.647
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A fully automatic procedure for aligning two protein structures is presented, It uses as sole structural similarity measure the root mean square (r.m.s.) deviation of superimposed backbone atoms (N, C-alpha,C- C and O) and is designed to yield optimal solutions with respect to this measure, In a first step, the procedure identifies protein segments with similar conformations in both proteins. In a second step, a novel multiple linkage clustering algorithm is used to identify segment combinations which yield optimal global structure alignments, Several structure alignments can usually be obtained for a given pair of proteins, which are exploited here to define automatically the common structural core of a protein family, Furthermore, an automatic analysis of the clustering trees is described which enables detection of rigid-body movements between structure elements, To illustrate the performance of our procedure, we apply it to families of distantly related proteins, One groups the three alpha+beta proteins ubiquitin, ferredoxin and the B1-domain of protein G. Their common structure motif consists of four beta-strands and the only a-helix, with one strand and the helix being displaced as a rigid body relative to the remaining three beta-strands. The other family consists of beta-proteins from the Greek key group, in particular actinoxanthin, the immunoglobulin variable domain and plastocyanin, Their consensus motif, composed of five beta-strands and a turn, is identified, mostly intact, in all Greek key proteins except the trypsins, and interestingly also in three other beta-protein families, the lipocalins, the neuraminidases and the lectins, This result provides new insights into the evolutionary relationships in the very diverse group of all beta-proteins.
引用
收藏
页码:647 / 662
页数:16
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