An extended sampling of the configurational space of HPr from E. coli

Proteins
B L de GrootH J Berendsen

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.

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Citations

Aug 22, 2008·The Journal of Chemical Physics·W Michael BrownJean-Paul Watson
Sep 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Isabella DaidoneJeremy C Smith
Apr 16, 1998·Protein Science : a Publication of the Protein Society·L S CavesM Karplus
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Dec 12, 2012·Physical Chemistry Chemical Physics : PCCP·Hua WanShan Chang
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Oct 27, 2016·Physical Chemistry Chemical Physics : PCCP·Daohui Zhao, Jian Zhou
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Jan 13, 2006·The Journal of Physical Chemistry. a·Sara NúñezSteven D Schwartz
Oct 20, 2005·Journal of the American Chemical Society·Isabella DaidoneAndrea Amadei

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