Next Article in Journal
Dietary Protection Against Free Radicals: A Case for Multiple Testing to Establish Structure-activity Relationships for Antioxidant Potential of Anthocyanic Plant Species
Next Article in Special Issue
Importance of Translational Entropy of Water in Biological Self-Assembly Processes like Protein Folding
Previous Article in Journal
Neuropathology and Therapeutic Intervention in Spinal and Bulbar Muscular Atrophy
Previous Article in Special Issue
Multiple, but Concerted Cellular Activities of the Human Protein Hap46/BAG-1M and Isoforms
Open AccessArticle

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.
Int. J. Mol. Sci. 2009, 10(3), 1013-1030; https://doi.org/10.3390/ijms10031013
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)
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. View Full-Text
Keywords: Ultrafast folding; downhill folding; DPDP; DPDP-II; designed beta- sheet proteins Ultrafast folding; downhill folding; DPDP; DPDP-II; designed beta- sheet proteins
Show Figures

Graphical abstract

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.

Show more citation formats Show less citations formats

Article Access Map by Country/Region

1
Only visits after 24 November 2015 are recorded.
Search more from Scilit
 
Search
Back to TopTop