Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 1997 Dec;73(6):2891-6.
doi: 10.1016/S0006-3495(97)78317-6.

Protein dynamics derived from clusters of crystal structures

D M van Aalten  1 , D A Conn, B L de Groot, H J Berendsen, J B Findlay, A Amadei
Affiliations

Protein dynamics derived from clusters of crystal structures

D M van Aalten et al. Biophys J. 1997 Dec.

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.

PubMed Disclaimer

References

    1. Science. 1995 Jun 2;268(5215):1312-8 - PubMed
    1. J Biomol Struct Dyn. 1996 Feb;13(4):615-25 - PubMed
    1. Protein Eng. 1997 Apr;10(4):381-7 - PubMed
    1. Biochemistry. 1995 Mar 28;34(12):4041-55 - PubMed
    1. Protein Eng. 1995 Nov;8(11):1129-35 - PubMed