Predicting conformational switches in proteins. |
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Authors: | M. Young K. Kirshenbaum K. A. Dill S. Highsmith |
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Affiliation: | Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA. |
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Abstract: | We describe a new computational technique to predict conformationally switching elements in proteins from their amino acid sequences. The method, called ASP (Ambivalent Structure Predictor), analyzes results from a secondary structure prediction algorithm to identify regions of conformational ambivalence. ASP identifies ambivalent regions in 16 test protein sequences for which function involves substantial backbone rearrangements. In the test set, all sites previously described as conformational switches are correctly predicted to be structurally ambivalent regions. No such regions are predicted in three negative control protein sequences. ASP may be useful as a guide for experimental studies on protein function and motion in the absence of detailed three-dimensional structural data. |
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Keywords: | ASP conformational switch PHD secondary structure preferences structurally ambivalent sequence element |
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