title: A new bioinformatics approach to natural protein collections: permutation structure contrasts of viral and cellular systems.
abstract: Biological cells and viruses operate by different replication and symmetry paradigms. Cells are able to replicate independently and express little spatial symmetry; viruses require cells for replication while manifesting high symmetry. The author inquired whether different paradigms were reflected in the permutations of amino acid sequences. The hypothesis was that the permutation structure level and symmetry within viral protein collections exceed that of living cells. The rationale was that one symmetry aspect generally accompanies and promotes others in a system. The inquiry was readily answered given abundant sequence archives for proteins. The analysis of collections from diverse viral and cellular sources lends strong support. Additional insights into protein primary structure, the design of collections, and the role of information are provided as well.
authors.affiliation: Department of Chemistry, Loyola University Chicago, 6525 North Sheridan Road, Chicago, IL 60626, USA. dgraha1@luc.edu
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Graham
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008954:Models, Biological; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry / Q000145:classification; D020543:Proteome / Q000737:chemistry* / Q000145:classification*; D014764:Viral Proteins / Q000737:chemistry* / Q000145:classification*
chemical_list: D011506:Proteins; D020543:Proteome; D014764:Viral Proteins