title: Extent of protein-protein interactions and quasi-equivalence in viral capsids.
abstract: 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>or=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.
authors.affiliation: Department of Molecular Biology, TPC-06, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: Craig M
authors.initials: CM
authors.lastname: Shepherd
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Reddy
mesh_terms: D001665:Binding Sites; D001703:Biophysics / Q000379:methods; D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins / Q000737:chemistry*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D008970:Molecular Weight; D027383:Papillomaviridae / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D014764:Viral Proteins / Q000737:chemistry; D014771:Virion / Q000378:metabolism; D019065:Virus Assembly
chemical_list: D036022:Capsid Proteins; D011506:Proteins; D014764:Viral Proteins