Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields.

Abstract

Molecular dynamics (MD) simulations of peptides and proteins offer atomic-level detail into many biological processes, although the degree of insight depends on the accuracy of the force fields used to represent them. Protein folding is a key example in which the accurate reproduction of folded-state conformations of proteins and kinetics of the folding processes in simulation is a longstanding goal. Although there have been a number of recent successes, challenges remain in capturing the full complexity of folding for even secondary-structure elements. In the present work, we have used all-atom MD simulations to study the folding properties of one such element, the C-terminal β-hairpin of the B1 domain of streptococcal protein G (GB1). Using replica-exchange umbrella sampling simulations, we examined the folding free energy of two fixed-charge CHARMM force fields, CHARMM36 and CHARMM22*, as well as a polarizable force field, the CHARMM Drude-2013 model, which has previously been shown to improve the folding properties of α-helical peptides. The CHARMM22* and Drude-2013 models are in rough agreement with experimental studies of GB1 folding, while CHARMM36 overstabilizes the β-hairpin. Additional free-energy calculations show that small adjustments to the atomic polarizabilities in the Drude-2013 model can improve both the backbone solubility and folding properties of GB1 without significantly affecting the model's ability to properly fold α-helices. We also identify a non-native salt bridge in the β-turn region that overstabilizes the β-hairpin in the C36 model. Finally, we demonstrate that tryptophan fluorescence is insufficient for capturing the full β-hairpin folding pathway.