Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme

Autor: Steven Hayward, H.J.C. Berendsen
Rok vydání: 1998
Předmět:
Zdroj: Proteins: Structure, Function, and Genetics. 30:144-154
ISSN: 1097-0134
0887-3585
DOI: 10.1002/(sici)1097-0134(19980201)30:2<144::aid-prot4>3.0.co;2-n
Popis: 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 that domains can be recog- nized from the difference in the parameters governing their quasi-rigid body motion, and in particular their rotation vectors. A cluster- ing algorithm is used to determine clusters of rotation vectors corresponding to main-chain segments that form possible dynamic domains. Domains are accepted for further analysis on the basis of a ratio of interdomain to intrado- main fluctuation, and Chasles' theorem is used to determine interdomain screw axes. Finally residues involved in the interdomain motion are identified. The methodology is tested on citrate synthase and the M6I mutant of T4 lysozyme. In both cases new aspects to their conformational change are revealed, as are individual residues intimately involved in their dynamics. For citrate synthase the beta sheet is identified to be part of the hinging mecha- nism. In the case of T4 lysozyme, one of the four transitions in the pathway from the closed to the open conformation, furnished four dy- namic domains rather than the expected two. This result indicates that the number of dy- namic domains a protein possesses may not be a constant of the motion. Proteins 30:144-154
Databáze: OpenAIRE
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