title: A structure-based method for derivation of all-atom potentials for protein folding.
abstract: A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a C(alpha) distance rms from the native structure of less than 2 A. Similar results were obtained for the hairpin and helices by using different potentials. We derived potentials for several different proteins and found a high correlation between the derived parameters, suggesting that a potential of this form eventually could be found that folds multiple, unrelated proteins at the atomic level of detail.
authors.affiliation: Department of Biophysics, Harvard University, 240 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Edo
authors.initials: E
authors.lastname: Kussell
authors.forename: Jun
authors.initials: J
authors.lastname: Shimada
authors.forename: Eugene I
authors.initials: EI
authors.lastname: Shakhnovich
mesh_terms: D001703:Biophysics / Q000379:methods*; D002244:Carbon / Q000737:chemistry*; D003208:Concanavalin A / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013211:Staphylococcus aureus / Q000378:metabolism; D013696:Temperature; D013997:Time Factors
chemical_list: D003208:Concanavalin A; D002244:Carbon