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Int J Mol Sci. 2009 Mar;10(3):1013-30. doi: 10.3390/ijms10031013. Epub 2009 Mar 10.

Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation.

Author information

1
Department of Chemistry, Stanford Unversity, California 94305, USA. vvoelz@stanford.edu

Abstract

Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of approximately 140 +/- 20 ns was published. We performed massively parallel molecular dynamics simulations in explicit solvent to probe the structural events involved in this relaxation. While our simulations produce similar relaxation rates, the structural ensemble is broad. We observe the formation of turn structure, but only very weak interaction in the strand regions, which is consistent with the lack of strong backbone-backbone NOEs in previous structural NMR studies. These results suggest that either (D)P(D)P-II folds at time scales longer than 240 ns, or that (D)P(D)P-II is not a well-defined three-stranded beta-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another.

KEYWORDS:

DPDP; DPDP-II; Ultrafast folding; designed beta-sheet proteins; downhill folding

PMID:
19399235
PMCID:
PMC2672016
DOI:
10.3390/ijms10031013
[Indexed for MEDLINE]
Free PMC Article

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