{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["100(13)"],"submitter":["Pitera JW"],"pubmed_abstract":["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."],"journal":["Proceedings of the National Academy of Sciences of the United States of America"],"pagination":["7587-92"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC164630"],"repository":["biostudies-literature"],"pubmed_title":["Understanding folding and design: replica-exchange simulations of \"Trp-cage\" miniproteins."],"pmcid":["PMC164630"],"pubmed_authors":["Swope W","Pitera JW"],"additional_accession":[]},"is_claimable":false,"name":"Understanding folding and design: replica-exchange simulations of \"Trp-cage\" miniproteins.","description":"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.","dates":{"release":"2003-01-01T00:00:00Z","publication":"2003 Jun","modification":"2025-04-26T15:58:00.538Z","creation":"2019-03-27T00:35:19Z"},"accession":"S-EPMC164630","cross_references":{"pubmed":["12808142"],"doi":["10.1073/pnas.1330954100"]}}