An extended sampling of the configurational space of HPr from E. coli.
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.
de Groot
B L
BL
Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, The Netherlands.
Amadei
A
A
Scheek
R M
RM
van Nuland
N A
NA
Berendsen
H J
HJ
D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004926:Escherichia coli; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results
D001426:Bacterial Proteins; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr