Experiments and Comprehensive Simulations of the Formation of a Helical Turn

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• 作者：Gouri S. Jas ; Wendy A. Hegefeld ; Peter M谩jek ; Krzysztof Kuczera ; Ron Elber
• 刊名：The Journal of Physical Chemistry B
• 出版年：2012
• 出版时间：June 14, 2012
• 年：2012
• 卷：116
• 期：23
• 页码：6598-6610
• 全文大小：494K
• 年卷期：v.116,no.23(June 14, 2012)
• ISSN：1520-5207

文摘

We investigate the kinetics and thermodynamics of a helical turn formation in the peptide Ac-WAAAH-NH₂. NMR measurements indicate that this 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 suggest an atomically detailed picture for the turn formation. Using a network representation, two alternative mechanisms of folding are identified: (i) a direct co-operative 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.