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  Helix nucleation kinetics from molecular simulations in explicit solvent

Hummer, G., García, A. E., & Garde, S. (2001). Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins: Structure, Function, and Genetics, 42(1), 77-84.

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 Urheber:
Hummer, Gerhard1, Autor                 
García, Angel E.2, Autor
Garde, Shekhar2, Autor
Affiliations:
1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, USA, ou_persistent22              
2External Organizations, ou_persistent22              

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Schlagwörter: Alanine, Computer Simulation, Glycine, Hydrogen Bonding, Kinetics, Models, Molecular, Peptides, Protein Folding, Protein Structure, Secondary, Solvents, Temperature, Thermodynamics, Time Factors
 Zusammenfassung: We study the reversible folding/unfolding of short Ala and Gly-based peptides by molecular dynamics simulations of all-atom models in explicit water solvent. A kinetic analysis shows that the formation of a first alpha-helical turn occurs within 0.1-1 ns, in agreement with the analyses of laser temperature jump experiments. The unfolding times exhibit Arrhenius temperature dependence. For a rapidly nucleating all-Ala peptide, the helix nucleation time depends only weakly on temperature. For a peptide with enthalpically competing turn-like structures, helix nucleation exhibits an Arrhenius temperature dependence, corresponding to the unfolding of enthalpic traps in the coil ensemble. An analysis of structures in a "transition-state ensemble" shows that helix-to-coil transitions occur predominantly through breaking of hydrogen bonds at the helix ends, particularly at the C-terminus. The temperature dependence of the transition-state ensemble and the corresponding folding/unfolding pathways illustrate that folding mechanisms can change with temperature, possibly complicating the interpretation of high-temperature unfolding simulations. The timescale of helix formation is an essential factor in molecular models of protein folding. The rapid helix nucleation observed here suggests that transient helices form early in the folding event.

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Sprache(n): eng - English
 Datum: 2000-05-012000-08-292001-01-01
 Publikationsstatus: Erschienen
 Seiten: 8
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: BibTex Citekey: hummer_helix_2001
 Art des Abschluß: -

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Titel: Proteins: Structure, Function, and Genetics
  Andere : Proteins: Struct., Funct., Genet.
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: New York, NY : John Wiley & Sons
Seiten: - Band / Heft: 42 (1) Artikelnummer: - Start- / Endseite: 77 - 84 Identifikator: ISSN: 0887-3585
CoNE: https://pure.mpg.de/cone/journals/resource/954925553393