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Extent of protein–protein interactions and quasi‐equivalence in viral capsids
Author(s) -
Shepherd Craig M.,
Reddy Vijay S.
Publication year - 2004
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.20311
Subject(s) - capsid , protein subunit , biophysics , chemistry , microbiology and biotechnology , biology , virus , virology , gene , genetics
Viral capsids are composed of multiple copies of one or a few gene products that self‐assemble on their own or in the presence of the viral genome and/or auxiliary proteins into closed shells (capsids). We have analyzed 75 high‐resolution virus capsid structures by calculating the average fraction of the solvent‐accessible surface area of the coat protein subunits buried in the viral capsids. This fraction ranges from 0 to 1 and represents a normalized protein–protein interaction (PPI) index and is a measure of the extent of protein–protein interactions. The PPI indices were used to compare the extent of association of subunits among different capsids. We further examined the variation of the PPI indices as a function of the molecular weight of the coat protein subunit and the capsid diameter. Our results suggest that the PPI indices in T=1 and pseudo ‐T=3 capsids vary linearly with the molecular weight of the subunit and capsid size. This is in contrast to quasi‐equivalent capsids with T≥3, where the extent of protein–protein interactions is relatively independent of the subunit and capsid sizes. The striking outcome of this analysis is the distinctive clustering of the “T=2” capsids, which are distinguished by higher subunit molecular weights and a much lower degree of protein–protein interactions. Furthermore, the calculated residual (R sym ) of the fraction buried surface areas of the structurally unique subunits in capsids with T>1 was used to calculate the quasi‐equivalence of different subunit environments. Proteins 2005. © 2004 Wiley‐Liss, Inc.