title: Evaluation of the sequence template method for protein structure prediction. Discrimination of the (beta/alpha)8-barrel fold.
abstract: A multiple alignment of five (beta/alpha)8-barrel enzymes has been derived from their structure. The eight beta-strands and eight alpha-helices of the (beta/alpha)8-barrel are correctly aligned and the equivalenced residues in these regions fulfil similar structural roles. Each beta-strand has a central core of usually four residues, two residues contribute side-chains to the barrel core and the other two residues are involved in beta-strand/alpha-helix contacts. However, the fold imposes no constraints on the volumes of the residues at either a local or global level: the volume of the beta-barrel core varies between 1088 A3 in glycolate oxidase and 1571 A3 in taka-amylase. Sequence motifs derived from the multiple alignment were scanned against a database of 124 protein sequences, including 17 (beta/alpha)8-barrel enzymes. The results were evaluated in terms of the discrimination of (beta/alpha)8-barrel sequences and the quality of the alignments obtained. One motif was able to identify the top 12% of high scoring sequences as forming (beta/alpha)8-barrels with 50% accuracy and the bottom 50% of sequences as not being (beta/alpha)8-barrel proteins with 100% accuracy. However, in most instances the alignments were poor. The reasons for this are discussed with reference to the (beta/alpha)8-barrel proteins and the sequence motif method in general.
authors.affiliation: Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, U.K.
authors.forename: S D
authors.initials: SD
authors.lastname: Pickett
authors.forename: M A
authors.initials: MA
authors.lastname: Saqi
authors.forename: M J
authors.initials: MJ
authors.lastname: Sternberg
mesh_terms: D000429:Alcohol Oxidoreductases / Q000737:chemistry; D019747:Aldose-Ketose Isomerases; D000595:Amino Acid Sequence; D002238:Carbohydrate Epimerases / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry*; D008722:Methods; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry; D016415:Sequence Alignment; D013698:Templates, Genetic; D014305:Triose-Phosphate Isomerase / Q000737:chemistry; D000516:alpha-Amylases / Q000737:chemistry
chemical_list: D004798:Enzymes; D000429:Alcohol Oxidoreductases; C020821:glycollate oxidase; D000516:alpha-Amylases; D012273:Ribulose-Bisphosphate Carboxylase; D002238:Carbohydrate Epimerases; D019747:Aldose-Ketose Isomerases; D014305:Triose-Phosphate Isomerase; C023298:xylose isomerase