title: Improving the prediction of secondary structure of 'TIM-barrel' enzymes.
abstract: The information contained in aligned sets of homologous protein sequences should improve the score of secondary structure prediction. Seven different enzymes having the (beta/alpha)8 or TIM-barrel fold were used to optimize the prediction with regard to this class of enzymes. The alpha-helix, beta-strand and loop propensities of the Garnier-Osguthorpe-Robson method were averaged at aligned residue positions, leading to a significant improvement over the average score obtained from single sequences. The increased accuracy correlates with the average sequence variability of the aligned set. Further improvements were obtained by using the following averaged properties as weights for the averaged state propensities: amphipathic moment and alpha-helix; hydropathy and beta-strand; chain flexibility and loop. The clustering of conserved residues at the C-terminal ends of the beta-strands was used as an additional positive weight for beta-strand propensity and increased the prediction of otherwise unpredicted beta-strands decisively. The automatic weighted prediction method identifies greater than 95% of the secondary structure elements of the set of seven TIM-barrel enzymes.
authors.affiliation: Abteilung Biophysikalische Chemie, University of Basel, Switzerland.
authors.forename: T
authors.initials: T
authors.lastname: Niermann
authors.forename: K
authors.initials: K
authors.lastname: Kirschner
mesh_terms: D000595:Amino Acid Sequence; D002238:Carbohydrate Epimerases / Q000737:chemistry*; D004798:Enzymes / Q000737:chemistry*; D005634:Fructose-Bisphosphate Aldolase / Q000737:chemistry; D007209:Indole-3-Glycerol-Phosphate Synthase / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010751:Phosphopyruvate Hydratase / Q000737:chemistry; D011487:Protein Conformation; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D014305:Triose-Phosphate Isomerase / Q000737:chemistry; D014367:Tryptophan Synthase / Q000737:chemistry; D000516:alpha-Amylases / Q000737:chemistry
chemical_list: D004798:Enzymes; D000516:alpha-Amylases; D007209:Indole-3-Glycerol-Phosphate Synthase; D005634:Fructose-Bisphosphate Aldolase; D010751:Phosphopyruvate Hydratase; D014367:Tryptophan Synthase; D002238:Carbohydrate Epimerases; D014305:Triose-Phosphate Isomerase