Helix Formation in a Pentapeptide Experiment and Force-field Dependent Dynamics

We used a combined approach of experiment and simulation to determine the helical population and folding pathway of a small helix forming blocked pentapeptide Ac-(Ala)(5)-NH2 Experimental structural characterization of this blocked peptide was carried out with far UV circular dichroism spectroscopy FTIR and NMR measurements These measurements confirm the presence of the alpha-helical state in a buffer solution Direct molecular dynamics and replica-exchange simulations of the pentapeptide were performed using several popular force fields with explicit solvent The simulations yielded statistically reliable estimates of helix populations melting curves, folding, and nucleation times De distributions of conformer populations ate used to measure folding cooperativity Finally, a statistical analysis of the sample of helix-coil transition paths was performed The details of the calculated helix populations folding kinetics and pathways vary with the employed force field Interestingly the helix populations, folding and unfolding times obtained from most of the studied force fields are in qualitative agreement with each other and with available experimental data with the deviations corresponding to several kcal/mol in energy at 300 K Most of the force fields also predict qualitatively similar transition paths with unfolding initiated at the C-terminus Accuracy of potential energy parameters rather than conformational sampling may be the limiting factor in current molecular simulations