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Protein dynamics derived from clusters of crystal structures.

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.

SUBMITTER: van Aalten DM

PROVIDER: S-EPMC1181194 | biostudies-other | 1997 Dec

REPOSITORIES: biostudies-other

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Protein dynamics derived from clusters of crystal structures.

van Aalten D M DM Conn D A DA de Groot B L BL Berendsen H J HJ Findlay J B JB Amadei A A

Biophysical journal 19971201 6

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 ...[more]

PMID: 9414203

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