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 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.
van Aalten
D M
DM
Department of Biochemistry and Molecular Biology, University of Leeds, England. aalten@cshl.org
Conn
D A
DA
de Groot
B L
BL
Berendsen
H J
HJ
Findlay
J B
JB
Amadei
A
A
D000818:Animals; D055592:Biophysical Phenomena; D001703:Biophysics; D003460:Crystallization; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins