title: Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids.
abstract: The conservation level of a residue is a useful measure about the importance of that residue in protein structure and function. Much information about sequence conservation comes from aligning homologous sequences. Profiles showing the variation of the conservation level along the sequence are usually interpreted in evolutionary terms and dictated by site similarities of a proper set of homologous sequences. Here, we report that, of the viral icosahedral capsids, the sequence conservation profile can be determined by variations in the distances between residues and the centroid of the capsid - with a direct inverse proportionality between the conservation level and the centroid distance - as well as by the spatial variations in local packing density. Examining both the centroid and the packing density models against a dataset of 51 crystal structures of nonhomologous icosahedral capsids, we found that many global patterns and minor features derived from the viral structures are consistent with those present in the sequence conservation profiles. The quantitative link between the level of conservation and structural features like centroid-distance or packing density allows us to look at residue conservation from a structural viewpoint as well as from an evolutionary viewpoint.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C.
authors.forename: Chih-Min
authors.initials: CM
authors.lastname: Chang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C.
authors.forename: Yu-Wen
authors.initials: YW
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C.
authors.forename: Chi-Wen
authors.initials: CW
authors.lastname: Lee
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C.
authors.forename: Tsun-Tsao
authors.initials: TT
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C.
authors.forename: Chung-Shiuan
authors.initials: CS
authors.lastname: Shih
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan, R.O.C; Department of Bioinformatics and Medical Engineering, Asia University, Taichung City 41354, Taiwan, R.O.C.
authors.forename: Jenn-Kang
authors.initials: JK
authors.lastname: Hwang
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D002213:Capsid / Q000648:ultrastructure*; D036022:Capsid Proteins / Q000737:chemistry*; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D066264:Datasets as Topic; D000229:Dependovirus / Q000737:chemistry / Q000648:ultrastructure; D029968:Escherichia coli Proteins / Q000737:chemistry; D019143:Evolution, Molecular; D008958:Models, Molecular; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry; D019065:Virus Assembly
chemical_list: D036022:Capsid Proteins; D029968:Escherichia coli Proteins; D044925:Oxidoreductases Acting on CH-CH Group Donors; C100153:2,4-dienoyl-CoA reductase