Cooperative Helix Formation in the (AAQAA)3 Peptide Obtained with the Drude Polarizable Force Field

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Molecular simulations can provide atomic-level details of protein folding. However, their accuracy is limited by approximations made in the underlying empirical force fields. Recently we presented a force field for peptides and proteins that includes explicit treatment of electronic polarization based on the classical Drude oscillator model.[1] The Drude force field was found to maintain protein native structures during microsecond molecular dynamics simulations of multiple folded proteins, and leads to significant variability of backbone and side chain dipole moments as a function of environment.[2] Here we report replica exchange simulations of the helix-forming (AAQAA)3 peptide and the β-sheet-forming GB1 hairpin using this fully polarizable model. Polarizable simulations of (AAQAA)3 reveal the presence of folding cooperativity consistent with experimental observations. The cooperativity is significantly larger than that modeled by currently available non-polarizable force fields and is shown to be directly associated with enhanced dipole moments of the peptide backbone upon helix formation.[3] The GB1 hairpin is found to be less stable with the Drude force field compared to the experimental observation. Results from these extensive condensed phase simulations of peptide folding will be utilized, together with QM calculations of model alanine polypeptide systems, to further refine the backbone parameters in the Drude protein force field. In summary, our results demonstrate that the inclusion of explicit electronic polarizability leads to a fundamentally improved model of the physical forces dictating the structure and dynamics of polypeptides. [1] P. Lopes, J. Huang, J. Shim, Y. Luo, H. Li, B. Roux, and A.D. MacKerell, J. Chem. Theo. Comput., 2013, 9, 5430. [2] J. Huang, P. Lopes, B. Roux, and A.D. MacKerell, J. Phys. Chem. Lett., 2014, 5, 3144. [3] J. Huang and A.D. MacKerell, Biophys. J., 2014, 107, 991.