Journal of Physical Chemistry B, Vol.122, No.49, 11355-11362, 2018
Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model
A continuum solvent model based on screened Coulomb potentials has been simplified and parametrized to sample native-like structures in replica-exchange simulations of each of six different peptides and miniproteins. Low-energy, native, and non-native structures were used to iteratively refine 11 parameter values. The centroid of the largest cluster of structures sampled in simulations initiated from an extended conformation represents the predicted structure. The main-chain rms deviation of this prediction from the experimental structure was 0.47 angstrom for the 12-residue Trp-zip2, 0.86 angstrom for the 14-residue MBH12, 2.53 angstrom for the 17-residue U(1-17)T9D, 2.03 angstrom for the 20-residue BS1, 1.08 angstrom for the 20-residue Trp-cage, and 3.64 angstrom for the 35-residue villin headpiece subdomain HP35. The centroid of the sixth largest cluster sampled for HP35 deviated by 0.91 angstrom. The CHARMM22/CMAP force field was used, with an additional psi torsion term for residues other than glycine and proline. Six parameters govern the dielectric response of the continuum solvent, and four values of surface tension approximate nonpolar effects. An atom's self energy and interaction energies are screened independently, each depending on whether the atom is part of a charged group, a neutral hydrogen-bonding main-chain group, or any other neutral group. The parameters inferred result in strong main-chain hydrogen bonds, consistent with the view that protein folding is dominated by the formation of these bonds.(1,2) Conformations of MBH12 and BSI were excluded from the energy-function refinement, suggesting the parameters, referred to as SCP18, are transferable. An efficient estimate of solvent-accessible surface area is also described.