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

TitleAn extended sampling of the configurational space of HPr from E. coli.
Publication TypeJournal Article
Year of Publication1996
Authorsde Groot, B. L., A. Amadei, R. M. Scheek, N. A. J. van Nuland, and H. J. Berendsen
JournalProteins
Volume26
Issue3
Pagination314-22
Date Published1996 Nov
ISSN0887-3585
KeywordsBacterial Proteins, Computer Simulation, Escherichia coli, Magnetic Resonance Spectroscopy, Models, Molecular, Phosphoenolpyruvate Sugar Phosphotransferase System, Protein Conformation, Protein Structure, Secondary, Reproducibility of Results
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.

DOI10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D
Alternate JournalProteins
PubMed ID8953652