Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
AUTOR(ES)
Pitera, Jed W.
FONTE
National Academy of Sciences
RESUMO
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 Å Cα rms positional deviation from structures in the corresponding NMR ensemble. These folded states are thermodynamically stable with a simulated melting temperature of ≈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.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=164630Documentos Relacionados
- Trp-cage: Folding free energy landscape in explicit water
- High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study
- Error and efficiency of replica exchange molecular dynamics simulations
- How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations
- Web design: production and analysis guide