title: Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.
abstract: Do Gō-type model potentials provide a valid approach for studying protein folding? They have been widely used for this purpose because of their simplicity and the speed of simulations based on their use. The essential assumption in such models is that only contact interactions existing in the native state determine the energy surface of a polypeptide chain, even for non-native configurations sampled along folding trajectories. Here we use an all-atom molecular mechanics energy function to investigate the adequacy of Gō-type potentials. We show that, although the contact approximation is accurate, non-native contributions to the energy can be significant. The assumed relation between residue-residue interaction energies and the number of contacts between them is found to be only approximate. By contrast, individual residue energies correlate very well with the number of contacts. The results demonstrate that models based on the latter should give meaningful results (e.g., as used to interpret phi values), whereas those that depend on the former are only qualitative, at best.
authors.affiliation: ISIS, Laboratoire de Chimie Biophysique, Université Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Paci
authors.forename: Michele
authors.initials: M
authors.lastname: Vendruscolo
authors.forename: Martin
authors.initials: M
authors.lastname: Karplus
mesh_terms: D003198:Computer Simulation; D004735:Energy Transfer; D046911:Macromolecular Substances; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D046911:Macromolecular Substances; D011506:Proteins; D012997:Solvents