title: Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands.
abstract: In an effort to better understand beta-sheet assembly, we have investigated the evolutionary behavior of neighboring residues on adjacent antiparallel beta-strands. Residue pairs were classified according to solvent exposure as well as by whether their backbone NH and C==O groups are hydrogen bonded. The conservation and covariation of 19,241 pairs in 219 sequence alignments was analyzed. Buried pairs were found to be the most conserved, while stronger covariation was detected in the solvent-exposed pairs. However, residues on neighboring strands showed a degree of conservation and covariation similar to that of well-separated residues on the same strand, suggesting that evolutionary pressure to maintain complementarity between pairs on neighboring strands is weak. Moreover, in spite of the preference of certain amino acid pairs to occupy neighboring positions on adjacent strands, such favored pairs are neither more strongly mutually conserved nor covary more strongly than pairs of the same type in non-interacting positions. Although the beta-sheet pairs did not show outstanding evolutionary coupling, in many protein families significant conservation and covariation patterns were detected for some of the residue pairs. Overall, the weak evolutionary conservation and covariation of the beta-sheet pairs indicates that sheet structure is unlikely to be dictated by specific side-chain interactions.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Mandel-Gutfreund
authors.forename: S M
authors.initials: SM
authors.lastname: Zaremba
authors.forename: L M
authors.initials: LM
authors.lastname: Gregoret
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D019992:Databases as Topic; D019143:Evolution, Molecular; D005346:Fibroblast Growth Factors / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D007375:Interleukin-1 / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012997:Solvents
chemical_list: D007375:Interleukin-1; D011506:Proteins; D012997:Solvents; D005346:Fibroblast Growth Factors