title: All-atom structure prediction and folding simulations of a stable protein.
abstract: We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined regions of the experimental structure, our prediction has a remarkably low 0.97 A Calpha root-mean-square-deviation (rmsd) and 1.4 A for all heavy atoms. The simulated structure family displays additional features that are suggested by experimental data, yet are not evident in the family of NMR-derived structures.
authors.affiliation: Center for Structural Biology and Department of Chemistry, State University of New York - Stony Brook, Stony Brook, New York 11794, USA. carlos.simmerling@sunysb.edu
authors.forename: Carlos
authors.initials: C
authors.lastname: Simmerling
authors.forename: Bentley
authors.initials: B
authors.lastname: Strockbine
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry*; D017510:Protein Folding; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides