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Comparison of conformational characteristics in structurally similar protein pairs
Author(s) -
Flores T.P.,
Orengo C.A.,
Moss D.S.,
Thornton J.M.
Publication year - 1993
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560021104
Subject(s) - chemistry , protein structure , computational biology , crystallography , biophysics , stereochemistry , biology , biochemistry
Although it is known that three‐dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the main‐chain coordinates. In this study, we align the structures of 90 pairs of homologous proteins having sequence identities ranging from 5 to 100%. Their structures are compared as a function of sequence identity, including not only consideration of C α coordinates but also accessibility, Ooi numbers, secondary structure, and side‐chain angles. We discuss how these properties change as the sequences become less similar. This will be of practical use in homology modeling, especially for modeling very distantly related or analogous proteins. We also consider how the average size and number of insertions and deletions vary as sequences diverge. This study presents further quantitative evidence that structure is remarkably well conserved in detail, as well as at the topological level, even when the sequences do not show similarity that is significant statistically.