Prediction of protein conformational freedom from distance constraints
Article first published online: 7 DEC 1998
Copyright © 1997 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 29, Issue 2, pages 240–251, October 1997
How to Cite
de Groot, B.L., van Aalten, D.M.F., Scheek, R.M., Amadei, A., Vriend, G. and Berendsen, H.J.C. (1997), Prediction of protein conformational freedom from distance constraints. Proteins, 29: 240–251. doi: 10.1002/(SICI)1097-0134(199710)29:2<240::AID-PROT11>3.0.CO;2-O
- Issue published online: 7 DEC 1998
- Article first published online: 7 DEC 1998
- Manuscript Accepted: 6 MAY 1997
- Manuscript Received: 2 AUG 1996
- molecular dynamics;
- essential dynamics;
- protein dynamics;
A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD simulation. Although detailed aspects of dynamical mechanisms are not covered and the extent of variations are only estimated in a relative sense, applications to an IgG-binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins. The method may be used to support the design of mutants, when structural fluctuations for a large number of mutants are to be screened. The results suggest that motional freedom in proteins is ruled largely by a set of simple geometric constraints. Proteins 29:240–251, 1997. © 1997 Wiley-Liss, Inc.