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Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

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Published on: November 12, 2014

Statistical mechanics of helix bundles using a dynamic programming approach.

Adam Lucas¹, Liang Huang, Aravind Joshi

¹Department of Mathematics, Saint Mary's College of California, Moraga, California 94575-3517, USA.

Journal of the American Chemical Society

|March 17, 2007

Summary

A new dynamic programming model accurately predicts biomolecule folding cooperativity, including chain collapse and secondary structure formation. This model successfully explains helix-coil and helix-bundle folding transitions in peptides and proteins.

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Area of Science:

Biophysics
Computational Biology
Polymer Science

Background:

Biomolecule folding cooperativity remains poorly understood.
Existing models lack accuracy in treating both chain collapse and secondary structure formation simultaneously.
Quantitative models exist for helix-coil and coil-to-globule transitions, but not integrated approaches.

Purpose of the Study:

To develop an accurate model for predicting foldamer chain molecule folding cooperativity.
To integrate secondary structure formation and chain collapse phenomena in a unified model.
To apply the model to analyze helix-coil and helix-bundle folding in peptides and proteins.

Main Methods:

Developed a dynamic programming approach to calculate statistical mechanical partition functions for foldamer chains.
Named the approach the ascending levels model (ALM).
Applied the ALM to analyze helix-coil and helix-bundle folding, including cooperativity, in various peptide and protein systems.

Main Results:

The ALM accurately predicts heat capacity and helicity versus temperature and urea for Baldwin peptides (14- to 50-mer).
The model provides good fits for the denaturation of specific three-helix bundle proteins (F13W* and alpha3C) using temperature and guanidine.
It predicts two-state folding transitions for these proteins, with nearly higher-order transitions in Baldwin helices, and anti-cooperative folding for three-helix bundle polypeptoids.

Conclusions:

The ascending levels model offers a general and accurate method for exploring cooperativity in complex foldable polymers.
The model successfully predicts conformational distributions and folding behaviors, including stability differences between proteins and peptoids for two-helix bundles.
This approach advances the understanding of biomolecular folding mechanisms and cooperativity.