title: Protein Repeats from First Principles.
abstract: Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.
authors.affiliation: Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
authors.forename: Pablo
authors.initials: P
authors.lastname: Turjanski
authors.affiliation: Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, Argentina.
authors.forename: R Gonzalo
authors.initials: RG
authors.lastname: Parra
authors.affiliation: Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, Argentina.
authors.forename: Rocío
authors.initials: R
authors.lastname: Espada
authors.affiliation: Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
authors.forename: Verónica
authors.initials: V
authors.lastname: Becher
authors.affiliation: Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, Argentina.
authors.forename: Diego U
authors.initials: DU
authors.lastname: Ferreiro
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology; D030562:Databases, Protein; D008390:Markov Chains; D015233:Models, Statistical; D000072417:Protein Domains; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins