|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|
|Date Published||1996 Nov|
|Keywords||Bacterial Proteins, Computer Simulation, Escherichia coli, Magnetic Resonance Spectroscopy, Models, Molecular, Phosphoenolpyruvate Sugar Phosphotransferase System, Protein Conformation, Protein Structure, Secondary, Reproducibility of Results|
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.