title: Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent.
abstract: 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 alpha-helical peptides, A21 and the Fs, by using two different classical potentials and both water models. We find that when using GB/SA: (i) A21 is predicted to be more helical than the Fs peptide at all temperatures; (ii) the native structure of the Fs 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 phi(psi) 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.
authors: Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, T10 MS K710, Los Alamos, NM 87545, USA.
authors: Hugh
authors: H
authors: Nymeyer
authors: Angel E
authors: AE
authors: García
mesh_terms: D000465:Algorithms; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents; D013816:Thermodynamics; D014867:Water
chemical_list: D010455:Peptides; D012997:Solvents; D014867:Water