All-atom structure prediction and folding simulations of a stable protein.
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.
Simmerling
Carlos
C
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
Strockbine
Bentley
B
Roitberg
Adrian E
AE
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
D009842:Oligopeptides