An extended sampling of the configurational space of HPr from E

An extended sampling of the configurational space of HPr from E. coli

B. L. de Groot¹, A. Amadei¹, R. M. Scheek¹, N. A. J. van Nuland², Dr. H. J. C. Berendsen^{1 *}

¹Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, the University of Groningen, AG Groningen, The Netherlands
²Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, Oxford, United Kingdom

^*Correspondence to H. J. C. Berendsen, GBB, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands

Keywords

protein structure • molecular dynamics • essential dynamics • nuclear magnetic resonance • nuclear Overhauser effect • distance restraints

FULL TEXT

Abstract

Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) to obtain an extended sampling of the configurational space of proteins, using an adapted form of molecular dynamics (MD) simulations, based on the essential dynamics (ED) (Amadei et al., Proteins 17:412-425, 1993) method. In the present study, this ED sampling technique is applied to the histidine-containing phosphocarrier protein HPr from Escherichia coli. We find a cluster of conformations that is an order of magnitude larger than that found for a usual MD simulation of comparable length. The structures in this cluster are geometrically and energetically comparable to NMR structures. Moreover, on average, this large cluster satisfies nearly all NMR-derived distance restraints. © 1996 Wiley-Liss, Inc.

Received: 30 May 1996; Accepted: 31 May 1996