An extended sampling of the configurational space of HPr fromE. coli
- 1 November 1996
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 26 (3), 314-322
- https://doi.org/10.1002/(sici)1097-0134(199611)26:3<314::aid-prot7>3.0.co;2-d
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.Keywords
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