Title | An extended sampling of the configurational space of HPr from E. coli. |
Publication Type | Journal Article |
Year of Publication | 1996 |
Authors | de Groot, B. L., A. Amadei, R. M. Scheek, N. A. J. van Nuland, and H. J. Berendsen |
Journal | Proteins |
Volume | 26 |
Issue | 3 |
Pagination | 314-22 |
Date Published | 1996 Nov |
ISSN | 0887-3585 |
Keywords | Bacterial 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. |
DOI | 10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D |
Alternate Journal | Proteins |
PubMed ID | 8953652 |
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