PMID:8953652

Citation	de Groot, BL, Amadei, A, Scheek, RM, van Nuland, NA and Berendsen, HJ (1996) An extended sampling of the configurational space of HPr from E. coli. Proteins 26:314-22
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.
Links	PubMed Online version:<314::AID-PROT7>3.0.CO;2-D 10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D
Keywords	Bacterial Proteins/chemistry; Computer Simulation; Escherichia coli; Magnetic Resonance Spectroscopy; Models, Molecular; Phosphoenolpyruvate Sugar Phosphotransferase System/chemistry; Protein Conformation; Protein Structure, Secondary; Reproducibility of Results
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