title: Codon number shapes peptide redundancy in the universal proteome composition.
abstract: The proteomes catalogued in the UniRef100 database were collected into a single proteome set and examined for actual versus theoretical pentapeptide occurrences. We found a highly diversified degree of pentapeptide redundancy. Numerically, 953 pentamers are expressed only once in the protein world, whereas 103 pentamers occur more than 50,000 times. Moreover, it seems that 417 potentially possible pentapeptides are not present in the protein world. On the whole, tracing the redundancy profile of the protein world as a function of pentapeptide occurrences reveals a quasi-Gaussian curve, with tails representing scarcely and repeatedly occurring 5-mers. Analysis of physico-chemical-biological parameters shows that codon number is the main factor influencing and favoring specific pentapeptide frequencies in the universal proteome composition. That is, when compared to the set of never-expressed 5-mers, the pentapeptides frequently represented in the universal proteome are endowed with a higher number of multi-codonic amino acids. In contrast, the bulkiness degree and the hydrophobicity level play a smaller role. Unexpectedly, the heat of formation of pentapeptide appears to have the least influence.
authors: Department of Computer Science, University of Saskatchewan, Saskatoon, Canada.
authors: Anthony
authors: A
authors: Kusalik
authors: Brett
authors: B
authors: Trost
authors: Mik
authors: M
authors: Bickis
authors: Candida
authors: C
authors: Fasano
authors: Giovanni
authors: G
authors: Capone
authors: Darja
authors: D
authors: Kanduc
mesh_terms: D000595:Amino Acid Sequence; D003062:Codon; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000235:genetics*; D020543:Proteome / Q000032:analysis / Q000235:genetics; D020539:Sequence Analysis, Protein
chemical_list: D003062:Codon; D010455:Peptides; D020543:Proteome