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Experiments and comprehensive simulations of the formation of a helical turn
Jas, Gouri S. Hegefeld, Wendy A. Májek, Peter Kuczera, Krzysztof Elber, Ron
Jas, Gouri S.
Hegefeld, Wendy A.
Májek, Peter
Kuczera, Krzysztof
Elber, Ron
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Abstract
We consider the kinetics and thermodynamics of a helical turn formation in the peptide Ac-WAAAH-NH2. NMR measurements indicate that the peptide has significant tendency to form a structure of a helical turn, while temperature dependent CD establishes the helix fraction at different temperatures. Molecular Dynamics and Milestoning simulations agree with experimental observables and suggests an atomically detailed picture for the turn formation. Using a network representation two alternative mechanisms of folding are identified: (i) a direct cooperative mechanism from the unfolded to the folded state without intermediate formation of hydrogen bonds and (ii) an indirect mechanism with structural intermediates with two residues in a helical conformation. This picture is consistent with kinetic measurements that reveal two experimental time scales of sub nanosecond and several nanoseconds.
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Date
2012-06-14
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American Chemical Society
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Keywords
Folding, Pentatpeptide, Molecular Dynamics, NMR, Circular dichroism, Milestoning
Citation
Jas, G. S., Hegefeld, W., Májek, P., Kuczera, K., & Elber, R. (2012). Experiments and comprehensive simulations of the formation of a helical turn. The Journal of Physical Chemistry. B, 116(23), 6598–6610. http://doi.org/10.1021/jp211645s