protein secondary structure
heuristic prediction of protein structure
Biochemistry and Biotechnology
Wiley InterScience Backfile Collection 1832-2000
The tertiary structure of the α-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the α/β-class of supersecondary structures. The two-domain structure of the α-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a β-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the α-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the β-sheet eliminated all but one structure. The native structure is predicted to have a parallel β-sheet flanked on both sides by α-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for β2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.
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