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Coil-helix transition in macromolecules. I. Minimal model
Karthik C Sinha1, Alexey A Gavrilov1, Artem M Rumyantsev1
1Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA.
The Journal of Chemical Physics
|August 12, 2026
Summary
A new coarse-grained model simplifies polymer coil-helix transitions. Varying hydrogen-bond spacing reveals how molecular architecture controls helix formation and cooperativity, matching natural helix behaviors.
Area of Science:
- Polymer Physics
- Computational Chemistry
- Biophysics
Background:
- The coil-helix transition is fundamental to polymer behavior and protein folding.
- Understanding the factors governing this transition, such as hydrogen-bond spacing, is crucial for designing functional polymers.
- Existing models may lack the simplicity or accuracy to capture essential thermodynamic features.
Purpose of the Study:
- To develop a minimal coarse-grained molecular dynamics model for polymer coil-helix transitions.
- To investigate the influence of hydrogen-bond spacing on transition thermodynamics and cooperativity.
- To validate the model's ability to reproduce key features of natural helix formation.
Main Methods:
- Development of a coarse-grained model incorporating Morse, volume, and bond potentials.
- Molecular dynamics simulations of polymer chains with varying hydrogen-bonding monomer spacing (i → i + m, m=4, 5, 6).
- Extraction of Zimm-Bragg parameters (propagation 's' and nucleation 'σ') to quantify helical propensity and cooperativity.
Main Results:
- The model successfully reproduces essential thermodynamic features of the coil-helix transition.
- Increased monomer spacing (larger 'm') leads to increased cooperativity (lower nucleation parameter σ).
- A larger 'm' results in a sharper coil-helix transition, consistent with experimental observations for different helix types.
Conclusions:
- A minimal coarse-grained model with a Morse potential is sufficient to capture key coil-helix transition thermodynamics.
- Hydrogen-bond spacing is a critical determinant of polymer helical propensity and transition cooperativity.
- The model provides a versatile platform for studying how molecular architecture dictates helix formation in polymers.
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