title: Protein fragments: functional and structural roles of their coevolution networks.
abstract: Small protein fragments, and not just residues, can be used as basic building blocks to reconstruct networks of coevolved amino acids in proteins. Fragments often enter in physical contact one with the other and play a major biological role in the protein. The nature of these interactions might be multiple and spans beyond binding specificity, allosteric regulation and folding constraints. Indeed, coevolving fragments are indicators of important information explaining folding intermediates, peptide assembly, key mutations with known roles in genetic diseases, distinguished subfamily-dependent motifs and differentiated evolutionary pressures on protein regions. Coevolution analysis detects networks of fragments interaction and highlights a high order organization of fragments demonstrating the importance of studying at a deeper level this structure. We demonstrate that it can be applied to protein families that are highly conserved or represented by few sequences, enlarging in this manner, the class of proteins where coevolution analysis can be performed and making large-scale coevolution studies a feasible goal.
authors.affiliation: Université Pierre et Marie Curie, UMR 7238, Équipe de Génomique Analytique, Paris, France.
authors.forename: Linda
authors.initials: L
authors.lastname: Dib
authors.forename: Alessandra
authors.initials: A
authors.lastname: Carbone
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D016229:Amyloid beta-Peptides / Q000737:chemistry; D017124:Conserved Sequence; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism*; D060066:Protein Interaction Maps; D055550:Protein Stability; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D000596:Amino Acids; D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D011506:Proteins; D000251:Adenosine Triphosphatases