title: Common spatial arrangements of backbone fragments in homologous and non-homologous proteins.
abstract: We have developed a new method of detecting common spatial arrangements of backbone fragments in proteins. This method allows corresponding fragments to occur in a different order in respective amino acid sequences. We applied this method to detect structural similarities between an acid protease, endothiapepsin, and all other proteins in the protein data bank. Significant similarities were found not only with other acid proteases but also with virus proteases and with proteins having different functions. The possible biological meaning of these similarities is discussed.
authors.affiliation: Department of Chemistry, Faculty of Science, Kyoto University, Japan.
authors.forename: N N
authors.initials: NN
authors.lastname: Alexandrov
authors.forename: K
authors.initials: K
authors.lastname: Takahashi
authors.forename: N
authors.initials: N
authors.lastname: Go
mesh_terms: D016282:Aspartic Acid Endopeptidases / Q000737:chemistry / Q000378:metabolism; D016208:Databases, Factual; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013059:Spectrum Analysis, Raman
chemical_list: D010446:Peptide Fragments; D016282:Aspartic Acid Endopeptidases; C042466:Endothia aspartic proteinase