Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family.
Two predictions have been prepared for the fold of initiation factor 5A (IF5A) starting from a set of homologous sequences. In the first, a secondary structural model was predicted for the protein in 1994, when only eleven homologs (and no eubacterial homologs) had been sequenced. The second was made recently, after genome projects had generated a total of 33 sequences for the protein family from species of all three kingdoms of life. With the second set of sequences, but not with the first, it was possible to predict that the N-terminal domain of the protein folds in a possibly open beta-barrel/sandwich core structure, with a short helix capping one side of the barrel. We place the pair of predictions in the public domain before an experimental structure is known. This example illustrates the impact of genome sequencing projects on structure prediction from sequence alignments.
Gerloff
D L
DL
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, 94143, USA.
Joachimiak
M
M
Cohen
F E
FE
Cannarozzi
G M
GM
Chamberlin
S G
SG
Benner
S A
SA
D000595:Amino Acid Sequence; D001105:Archaea; D001419:Bacteria; D019295:Computational Biology; D005057:Eukaryotic Cells; D016678:Genome; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D005810:Multigene Family; D010448:Peptide Initiation Factors / Q000737:chemistry* / Q000235:genetics; D010802:Phylogeny; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins; D016415:Sequence Alignment; D000097574:Eukaryotic Translation Initiation Factor 5A
D010448:Peptide Initiation Factors; D016601:RNA-Binding Proteins; D000097574:Eukaryotic Translation Initiation Factor 5A