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Biophysical Journal 73: 2891-2896 (1997)
© 1997 the Biophysical Society

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Protein dynamics derived from clusters of crystal structures.

D M van Aalten, D A Conn, B L de Groot, H J Berendsen, J B Findlay and A Amadei

Department of Biochemistry and Molecular Biology, University of Leeds, England. aalten@cshl.org

ABSTRACT

A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins.




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Copyright © 1997 by the Biophysical Society.