Details

Autor(en) / Beteiligte

• Thukral, Lipi
• Smith, Jeremy C
• Daidone, Isabella

Titel

Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations

Ist Teil von

• Journal of the American Chemical Society, 2009-12, Vol.131 (50), p.18147-18152

Ort / Verlag

United States: American Chemical Society

Erscheinungsjahr

2009

Quelle

MEDLINE

Beschreibungen/Notizen

• The folding of a 15-residue β-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 μs-long for a total of 37.5 μs, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1−1.5 μs obtained from the simulations is in good agreement with experiment [ Xu Y. ; et al. J. Am. Chem. Soc. 2003, 125, 15388−15394 ]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the β-hairpin.