The phospho-beta-galactosidase and synaptotagmin predictions.
Two bona fide consensus predictions of secondary and tertiary structure in a protein family, made and announced before experimental structures were known, are evaluated in light of the subsequently determined experimental structures. The first, for phospho-beta-galactosidase, identified the core strands of an 8-fold alpha-beta barrel, and identified the 8-fold alpha-beta barrel itself, which was found in the subsequently determined experimental structure to be the core folding domain. The second, for synaptotagmin, identified seven out of eight beta-strands in the structure correctly, missing only a noncore strand. Three preferred "topologies" were selected from several hundred thousand possible topologies of these seven predicted strands using a rule-based analysis. The subsequently determined experimental structure showed that these seven strands in synaptotagmin adopt one of the three preferred topologies. We were unable, however, to identify the correct topology from among these three topologies.
Benner
S A
SA
Department of Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland.
Gerloff
D
D
Chelvanayagam
G
G
D000595:Amino Acid Sequence; D001400:Azurin / Q000031:analogs & derivatives / Q000737:chemistry; D002135:Calcium-Binding Proteins; D016208:Databases, Factual; D006026:Glycoside Hydrolases; D008562:Membrane Glycoproteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D050857:Synaptotagmins; D001616:beta-Galactosidase / Q000737:chemistry*
D002135:Calcium-Binding Proteins; D008562:Membrane Glycoproteins; D009419:Nerve Tissue Proteins; C047163:pseudoazurin; D001400:Azurin; D050857:Synaptotagmins; D006026:Glycoside Hydrolases; D001616:beta-Galactosidase; C022361:6-phospho-beta-galactosidase