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Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins

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Published on: January 6, 2017

Testing the diffusing boundary model for the helix-coil transition in peptides.

Sabine Neumaier¹, Andreas Reiner, Maren Büttner

¹Munich Center for Integrated Protein Science and Department of Chemistry, Technische Universität München, D-85747 Garching, Germany.

Proceedings of the National Academy of Sciences of the United States of America

|July 24, 2013

Summary

This summary is machine-generated.

Peptide helix dynamics are governed by boundary diffusion, a 1D process. Helix unfolding can also occur via coil nucleation, and stabilizing motifs slow boundary diffusion.

Keywords:

-value protein folding α-helix capping

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Area of Science:

Biophysics
Chemical Kinetics

Background:

Peptide alpha-helix dynamics and their kinetic mechanisms have been debated.
Recent experiments suggest helix-coil dynamics involve boundary movement along the peptide chain.

Purpose of the Study:

To test the diffusing boundary model for helix-coil dynamics in peptides of varying lengths.
To investigate the influence of amino acid replacements on helix dynamics.

Main Methods:

Triplet-triplet energy transfer measurements.
Simulations using a kinetic linear Ising model.
Analysis of local and nonlocal effects of amino acid substitutions.

Main Results:

Boundary diffusion follows a classical 1D Einstein-type process (D = 2.7e7 aa^2/s).
Coil nucleation contributes to unfolding in helices longer than 40 amino acids.
Helix-stabilizing capping motifs reduce boundary diffusion rates.
Single amino acid replacements locally affect dynamics (phi_f = 0.35), indicating pre-existing propensities in the transition state.

Conclusions:

The diffusing boundary model accurately describes helix-coil dynamics in peptides.
Helix unfolding involves both boundary diffusion and coil nucleation for longer helices.
Amino acid replacements have local effects on folding/unfolding and nonlocal effects on unfolding, consistent with the diffusing boundary model.