Protein dynamics derived from clusters of crystal structures

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 chang...

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Bibliographic Details
Published in:Biophysical journal 1997-12, Vol.73 (6), p.2891-2896
Main Authors: van Aalten, D.M., Conn, D.A., de Groot, B.L., Berendsen, H.J., Findlay, J.B., Amadei, A.
Format: Article
Language:English
Subjects:
Animals
Biophysical Phenomena
Biophysics
Crystallization
Crystallography, X-Ray
Models, Molecular
Protein Conformation
Proteins - chemistry
Thermodynamics
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Summary: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.
ISSN:0006-3495
1542-0086
DOI:10.1016/S0006-3495(97)78317-6