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Int. J. Mol. Sci. 2009, 10(3), 1013-1030; doi:10.3390/ijms10031013

Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

1
Department of Chemistry / Stanford Unversity, Stanford, California 94305, USA
2
Biophysics Program / Stanford University, Stanford, California 94305, USA
*
Author to whom correspondence should be addressed.
Received: 15 January 2009 / Revised: 4 March 2009 / Accepted: 9 March 2009 / Published: 10 March 2009
(This article belongs to the Special Issue Protein Folding 2009)
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Abstract

Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of ~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 DPDP-II folds at time scales longer than 240 ns, or that DPDP-II is not a well-defined three-stranded β-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another.
Keywords: Ultrafast folding; downhill folding; DPDP; DPDP-II; designed beta- sheet proteins Ultrafast folding; downhill folding; DPDP; DPDP-II; designed beta- sheet proteins
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MDPI and ACS Style

Voelz, V.A.; Luttmann, E.; Bowman, G.R.; Pande, V.S. Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation. Int. J. Mol. Sci. 2009, 10, 1013-1030.

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