Insights into the domain and repeat architecture of target of rapamycin.
A simple and efficient protein sequence analysis strategy was developed to predict the number and location of structural repeats in the TOR protein. This strategy uses multiple HHpred alignments against proteins of known 3D structure to enable protein repeats referenced from the 3D structure to be traced back to the query protein sequence by using user-directed repeat assignments. The HHpred strategy performed with high sensitivity by predicting 100% of the repeat units within a test set of HEAT- and TPR-repeat-containing proteins of known three-dimensional structure. The HHpred strategy predicts that TOR contains 32 tandem HEAT repeats extending from the N-terminus to the FAT domain, which is itself comprised of 16 tandem TPR repeats. These findings were used to assemble a 3D atomic model for the TOR protein.
Knutson
Bruce A
BA
Fred Hutchinson Cancer Research Center, Basic Sciences Division, 1100 Fairview Ave N, P.O. Box 19024, Mailstop A1-162, Seattle, WA 98109, USA. bknutson@fhcrc.org
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D029681:Arabidopsis Proteins; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary; D020449:Repetitive Sequences, Amino Acid; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D058570:TOR Serine-Threonine Kinases
D029681:Arabidopsis Proteins; D047908:Intracellular Signaling Peptides and Proteins; D019869:Phosphatidylinositol 3-Kinases; D017346:Protein Serine-Threonine Kinases; D029701:Saccharomyces cerevisiae Proteins; D058570:TOR Serine-Threonine Kinases; C546842:MTOR protein, human; C512171:TOR protein, Arabidopsis; C083324:TOR1 protein, S cerevisiae