Journal of Physical Chemistry B, Vol.120, No.1, 33-41, 2016
Folding Simulations of an alpha-Helical Hairpin Motif alpha t alpha with Residue-Specific Force Fields
alpha-Helical hairpin (two-helix bundle) is a structure motif composed of two interacting helices connected by a turn or a short loop. It is an important model for protein folding studies, filling the gap between isolated alpha-helix and larger all-alpha domains. Here, we present, for the first time, successful folding simulations of an alpha-helical hairpin. Our RSFF1 and RSFF2 force fields give very similar predicted structures of this ata peptide, which is in good agreement with its NMR structure. Our simulations also give site-specific stability of alpha-helix formation in good agreement with amide hydrogen exchange experiments. Combining the folding free energy landscapes and analyses of structures sampled in five different ranges of the fraction of native contacts (Q), a folding mechanism of alpha t alpha is proposed. The most stable sites of Q9-E15 in helix-1 and E24-A30 in helix-2 close to the loop region act as the folding initiation sites. The formation of interhelix side-chain contacts also initiates near the loop region, but some residues in the central parts of the two helices also form contacts quite early. The two termini fold at a final stage, and the loop region remains flexible during the whole folding process. This mechanism is similar to the zipping out pathway of beta-hairpin folding.