Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 100, Issue 13, Pages 7587-7592Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1330954100
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Replica-exchange molecular dynamics simulations in implicit solvent have been carried out to study the folding thermodynamics of a designed 20-residue peptide, or miniprotein. The simulations in this study used the AMBER (parm94) force field along with the generalized Born/solvent-accessible surface area implicit solvent model, and they spanned a range of temperatures from 273 to 630 K. Starting from a completely extended initial conformation, simulations of one peptide sequence sample conformations that are <1.0 Angstrom C-alpha rms positional deviation from structures in the corresponding NMR ensemble.. These folded states are thermodynamically stable with a simulated melting temperature of approximate to400 K, and they satisfy the majority of experimentally observed NMR restraints. Simulations of a related mutant peptide show a degenerate ensemble of states at low temperature, in agreement with experimental results.
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