biostudies-literature00680Unknown100(13)Pitera JWReplica-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 A Calpha rms positional deviation from structures in the corresponding NMR ensemble. These folded states are thermodynamically stable with a simulated melting temperature of approximately 400 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.Proceedings of the National Academy of Sciences of the United States of America7587-92https://www.ebi.ac.uk/biostudies/studies/S-EPMC164630biostudies-literatureUnderstanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.PMC164630Swope WPitera JW68falseUnderstanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.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 A Calpha rms positional deviation from structures in the corresponding NMR ensemble. These folded states are thermodynamically stable with a simulated melting temperature of approximately 400 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.2003-01-01T00:00:00Z2003 Jun2024-11-09T01:43:19.765Z2019-03-27T00:35:19ZS-EPMC1646301280814210.1073/pnas.1330954100