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Evolutionary information hidden in a single protein structure
Author(s) -
Shih ChienHua,
Chang ChihMin,
Lin YeongShin,
Lo WeiCheng,
Hwang JennKang
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24058
Subject(s) - protein superfamily , conserved sequence , sequence (biology) , computational biology , protein evolution , protein structure , biology , peptide sequence , set (abstract data type) , protein sequencing , genetics , evolutionary biology , computer science , biochemistry , gene , programming language
Abstract The knowledge of conserved sequences in proteins is valuable in identifying functionally or structurally important residues. Generating the conservation profile of a sequence requires aligning families of homologous sequences and having knowledge of their evolutionary relationships. Here, we report that the conservation profile at the residue level can be quantitatively derived from a single protein structure with only backbone information. We found that the reciprocal packing density profiles of protein structures closely resemble their sequence conservation profiles. For a set of 554 nonhomologous enzymes, 74% (408/554) of the proteins have a correlation coefficient > 0.5 between these two profiles. Our results indicate that the three‐dimensional structure, instead of being a mere scaffold for positioning amino acid residues, exerts such strong evolutionary constraints on the residues of the protein that its profile of sequence conservation essentially reflects that of its structural characteristics. Proteins 2012;. © 2012 Wiley Periodicals, Inc.