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Conformational diffusion and helix formation kinetics.

G Hummer1, A E García, S Garde

  • 1Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA. hummer@helix.nih.gov

Physical Review Letters
|September 8, 2000
PubMed
Summary
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Helix formation kinetics in peptides are quantitatively described by a diffusive search model. This model explains nonexponential kinetics and temperature jump experiment findings in explicit solvent.

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Molecular Dynamics

Background:

  • Understanding peptide folding is crucial for protein science.
  • Kinetics of helix formation influence biological function.
  • Atomistic simulations provide detailed insights into molecular processes.

Purpose of the Study:

  • To quantitatively describe helix formation kinetics in peptides.
  • To investigate the influence of time, temperature, and sequence.
  • To model these processes in explicit solvent using atomistic simulations.

Main Methods:

  • Utilized fully atomistic peptide models.
  • Employed explicit solvent simulations.
  • Developed a quantitative model based on diffusive search within the coil state.

Related Experiment Videos

  • Analyzed barrierless transitions into the helical state.

    • Main Results:

    • Established a quantitative description of helix formation kinetics.
    • Demonstrated that conformational diffusion governs these kinetics.
    • Observed nonexponential kinetics.
    • Identified jump-width dependences in temperature jump experiments.

    Conclusions:

    • The diffusive search model accurately describes peptide helix formation.
    • Conformational diffusion is a key mechanism.
    • Findings are consistent with experimental observations like temperature jump experiments.