title: A general method to quantify quasi-equivalence in icosahedral viruses.
abstract: A quantitative, atom-based, method is described for comparing protein subunit interfaces in icosahedral virus capsids with quasi-equivalent surface lattices. An integrated, normalized value (between 0 and 1) based on equivalent residue contacts (Q-score) is computed for every pair of subunit interactions and scores that are significantly above zero readily identify interfaces that are quasi-equivalent to each other. The method was applied to all quasi-equivalent capsid structures (T=3, 4, 7 and 13) in the Protein Data Bank and the Q-scores were interpreted in terms of their structural underpinnings. The analysis allowed classification of T=3 structures into three groups with architectures that resemble different polyhedra with icosahedral symmetry. The preference of subunits to form dimers in the T=4 human Hepatitis B virus capsid (HBV) was clearly reflected in high Q-scores of quasi-equivalent dimers. Interesting differences between the classical T=7 capsid and polyoma-like capsids were also identified. Application of the method to the outer-shell of the T=13 Blue tongue virus core (BTVC) highlighted the modest distortion between the interfaces of the general trimers and the strict trimers of VP7 subunits. Furthermore, the method identified the quasi 2-fold symmetry in the inner capsids of the BTV and reovirus cores. The results show that the Q-scores of various quasi-symmetries represent a "fingerprint" for a particular virus capsid architecture allowing particle classification into groups based on their underlying structural and geometric features.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: K V
authors.initials: KV
authors.lastname: Damodaran
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Reddy
authors.forename: John E
authors.initials: JE
authors.lastname: Johnson
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins / Q000737:chemistry*; D030562:Databases, Protein; D006801:Humans; D008433:Mathematics; D008958:Models, Molecular; D008961:Models, Structural; D008962:Models, Theoretical; D010942:Plant Viruses / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D036022:Capsid Proteins