SYSTEMATIC ANALYSIS OF DOMAIN MOTIONS IN PROTEINS FROM CONFORMATIONALCHANGE - NEW RESULTS ON CITRATE SYNTHASE AND T4 LYSOZYME

Methods developed originally to analyze domain motions from simulation [Proteins 27:425-437, 1997] are adapted and extended for the analysis of X-ray conformers and for proteins with more than two domains. The method can be applied as an automatic procedure to any case where more than one conformation is available. The basis of the methodology is t hat domains can be recognized ham the difference in the parameters gov erning their quasi-rigid body motion, and in particular their rotation vectors. A clustering algorithm is used to determine clusters of rota tion vectors corresponding to main-chain segments that form possible d ynamic domains. Domains are accepted for further analysis on the basis of a ratio of interdomain to intradomain fluctuation, and Chasles' th eorem is used to determine interdomain screw axes. Finally residues in volved in lie interdomain motion are identified, The methodology is te sted on citrate synthase and the M6I mutant of T4 lysozyme. In both ca ses new aspects to their conformational change are revealed, as are in dividual residues intimately involved in their dynamics, For citrate s ynthase the beta sheet is identified to be part of the hinging mechani sm. In the case of T4 lysozyme, one of the four transitions in the pat hway from the closed to the open conformation, furnished four dynamic domains rather than the expected two. This result indicates that the n umber of dynamic domains a protein possesses may not be a constant of the motion. (C) 1998 Wiley-Liss, Inc.