Ion-specificity in α-helical folding kinetics

Details Ion-specificity in α-helical folding kinetics Ion-specificity in α-helical folding kinetics

2010-11-15

arxiv.org/abs/1011.3472v1

J. Phys. Chem. B 114, 13815-13822 (2010)

Physics

Condensed Matter

Soft Condensed Matter

15 pages, 8 figures

Scientific paper

10.1021/jp107495f

The influence of the salts KCl, NaCl, and NaI at molar concentrations on the {\alpha}-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics simulations and a diffusional analysis. The mean first passage times for folding and unfolding are found to be highly salt-specific. In particular, the folding times increase about one order of magnitude for the sodium salts. The drastic slowing down can be traced back to long-lived, compact configurations of the partially folded peptide, in which sodium ions are tightly bound by several carbonyl and carboxylate groups. This multiple trapping is found to lead to a non-exponential residence time distribution of the cations in the first solvation shell of the peptide. The analysis of {\alpha}-helical folding in the framework of diffusion in a reduced (one-dimensional) free energy landscape further shows that the salt not only specifically modifies equilibrium properties, but also induces kinetic barriers due to individual ion binding. In the sodium salts, for instance, the peptide's configurational mobility (or "diffusivity") can decrease about one order of magnitude. This study demonstrates the highly specific action of ions and highlights the intimate coupling of intramolecular friction and solvent effects in protein folding.

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