title: 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Leeds, England. aalten@cshl.org
authors.forename: D M
authors.initials: DM
authors.lastname: van Aalten
authors.forename: D A
authors.initials: DA
authors.lastname: Conn
authors.forename: B L
authors.initials: BL
authors.lastname: de Groot
authors.forename: H J
authors.initials: HJ
authors.lastname: Berendsen
authors.forename: J B
authors.initials: JB
authors.lastname: Findlay
authors.forename: A
authors.initials: A
authors.lastname: Amadei
mesh_terms: 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
chemical_list: D011506:Proteins