An extended sampling of the configurational space of HPr fromE. coli

Autor:	Herman J. C. Berendsen, N. A. J. Van Nuland, Ruud M. Scheek, B. L. de Groot, Andrea Amadei
Rok vydání:	1996
Předmět:	Chemistry Thermodynamics Sampling (statistics) Nuclear magnetic resonance spectroscopy Nuclear Overhauser effect Space (mathematics) Biochemistry Phosphocarrier protein HPr Molecular dynamics Crystallography Protein structure Structural Biology Cluster (physics) Molecular Biology
Zdroj:	Proteins: Structure, Function, and Genetics. 26:314-322
ISSN:	1097-0134 0887-3585
DOI:	10.1002/(sici)1097-0134(199611)26:3<314::aid-prot7>3.0.co;2-d
Popis:	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.
Databáze:	OpenAIRE
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