Simulation of the folding equilibrium of α-helical peptides:: A comparison of the generalized born approximation with explicit solvent

We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent model with simulations using explicit solvent (transferable intermolecular potential 3 point, TIP3P) to test the GB/SA algorithm. We use the replica exchange molecular dynamics method to sample the conformational phase space of two a-helical peptides, A(21) and the F-s, by using two different classical potentials and both water models. We find that when using GB/SA: (i) A(21) is predicted to be more helical than the F-s peptide at all temperatures; (ii) the native structure of the F-s peptide is predicted to be a helical bundle instead of a single helix; and (iii) the persistence length and most probable end-to-end distance are too large in the unfolded state when compared against the explicit solvent simulations. We find that the potential of mean force in the phipsi plane is markedly different in the two solvents, making the two simulated peptides respond differently when the backbone torsions are perturbed. A fit of the temperature melting curves obtained in these simulations to a Lifson-Roig model finds that the GB/SA model has an unphysically large nucleation parameter, whereas the explicit solvent model produces values similar to experiment.