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. 1997 Dec;73(6):2891–2896. doi: 10.1016/S0006-3495(97)78317-6

Protein dynamics derived from clusters of crystal structures.

D M van Aalten 1, D A Conn 1, B L de Groot 1, H J Berendsen 1, J B Findlay 1, A Amadei 1
PMCID: PMC1181194  PMID: 9414203

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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Selected References

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