title: Structure based sequence analysis of viral and cellular protein assemblies.
abstract: It is well accepted that, in general, protein structural similarity is strongly related to the amino acid sequence identity. To analyze in great detail the correlation, distribution and variation levels of conserved residues in the protein structure, we analyzed all available high-resolution structural data of 5245 cellular complex-forming proteins and 293 spherical virus capsid proteins (VCPs). We categorized and compare them in terms of protein structural regions. In all cases, the buried core residues are the most conserved, followed by the residues at the protein-protein interfaces. The solvent-exposed surface shows greater sequence variations. Our results provide evidence that cellular monomers and VCPs could be two extremes in the quaternary structural space, with cellular dimers and oligomers in between. Moreover, based on statistical analysis, we detected a distinct group of icosahedral virus families whose capsid proteins seem to evolve much slower than the rest of the protein complexes analyzed in this work.
authors.affiliation: Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Montiel-García
authors.affiliation: Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
authors.forename: Ranjan V
authors.initials: RV
authors.lastname: Mannige
authors.affiliation: Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Reddy
authors.affiliation: Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico. Electronic address: mauricio.carrillo@cinvestav.mx.
authors.forename: Mauricio
authors.initials: M
authors.lastname: Carrillo-Tripp
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D036022:Capsid Proteins / Q000648:ultrastructure*; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D008958:Models, Molecular; D011487:Protein Conformation; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D014764:Viral Proteins / Q000737:chemistry*; D014780:Viruses / Q000235:genetics
chemical_list: D036022:Capsid Proteins; D014764:Viral Proteins
keywords: Bioinformatics; Protein complexes; Protein-protein interactions; Sequence conservation; Subunit interface; Viral capsid proteins