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Related Experiment Videos

Helix nucleation kinetics from molecular simulations in explicit solvent.

G Hummer1, A E García, S Garde

  • 1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.

Proteins
|November 28, 2000
PubMed
Summary

Short peptides rapidly form alpha-helical turns within nanoseconds. This rapid helix nucleation suggests transient helices form early in protein folding, impacting molecular models.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Molecular Biology

Background:

  • Protein folding is a fundamental process in molecular biology.
  • Understanding peptide folding dynamics is crucial for developing accurate molecular models.
  • Short peptides serve as model systems to study complex protein folding mechanisms.

Purpose of the Study:

  • To investigate the reversible folding and unfolding kinetics of short alanine (Ala) and glycine (Gly)-based peptides.
  • To elucidate the role of temperature on peptide nucleation and unfolding pathways.
  • To analyze the structural characteristics of the transition-state ensemble during helix-to-coil transitions.

Main Methods:

  • All-atom molecular dynamics simulations in explicit water solvent.

Related Experiment Videos

  • Kinetic analysis of folding/unfolding events.
  • Comparison with experimental data from laser temperature jump experiments.
  • Analysis of transition-state ensemble structures.

    • Main Results:

    • Alpha-helical turn formation observed within 0.1-1 nanoseconds, consistent with experimental findings.
    • Unfolding times exhibit Arrhenius temperature dependence.
    • Helix nucleation in rapidly nucleating peptides shows weak temperature dependence.
    • Helix nucleation in peptides with competing structures displays Arrhenius dependence, indicating unfolding of enthalpic traps.
    • Helix-to-coil transitions primarily involve breaking hydrogen bonds at helix termini, especially the C-terminus.

    Conclusions:

    • Rapid helix nucleation is a key early event in peptide folding.
    • Folding mechanisms can be temperature-dependent, influencing the interpretation of unfolding simulations.
    • The timescale of helix formation is critical for accurate molecular models of protein folding.
    • Transient helices play a significant role in the initial stages of protein folding.