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

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

1email, 1email, 2email and 2,* email
Received: 15 January 2009; in revised form: 4 March 2009 / Accepted: 9 March 2009 / Published: 10 March 2009
(This article belongs to the Special Issue Protein Folding)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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
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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.

AMA Style

Voelz VA, Luttmann E, Bowman GR, Pande VS. Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation. International Journal of Molecular Sciences. 2009; 10(3):1013-1030.

Chicago/Turabian Style

Voelz, Vincent A.; Luttmann, Edgar; Bowman, Gregory R.; Pande, Vijay S. 2009. "Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation." Int. J. Mol. Sci. 10, no. 3: 1013-1030.


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