Title: On the relationship between the sequence conservation and the packing density profiles of the protein complexes
Authors: Chang, Chih-Min
Huang, Yu-Wen
Shih, Chien-Hua
Hwang, Jenn-Kang
Institude of Bioinformatics and Systems Biology
Keywords: protein structure;sequence conservation;weighted contact number
Issue Date: 1-Jul-2013
Abstract: We have recently showed that the weighted contact number profiles (or the packing density profiles) of proteins are well correlated with those of the corresponding sequence conservation profiles. The results suggest that a protein structure may contain sufficient information about sequence conservation comparable to that derived from multiple homologous sequences. However, there are ambiguities concerning how to compute the packing density of the subunit of a protein complex. For the subunits of a complex, there are different ways to compute its packing density - one including the packing contributions of the other subunits and the other one excluding their contributions. Here we selected two sets of enzyme complexes. Set A contains complexes with the active sites comprising residues from multiple subunits, while set B contains those with the active sites residing on single subunits. In Set A, if the packing density profile of a subunit is computed considering the contributions of the other subunits of the complex, it will agree better with the sequence conservation profile. But in Set B the situations are reversed. The results may be due to the stronger functional and structural constraints on the evolution processes on the complexes of Set A than those of Set B to maintain the enzymatic functions of the complexes. The comparison of the packing density and the sequence conservation profiles may provide a simple yet potentially useful way to understanding the structural and evolutionary couplings between the subunits of protein complexes. Proteins 2013; 81:1192-1199. (c) 2013 Wiley Periodicals, Inc.
URI: http://dx.doi.org/10.1002/prot.24268
ISSN: 0887-3585
DOI: 10.1002/prot.24268
Volume: 81
Issue: 7
Begin Page: 1192
End Page: 1199
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