Transition model
Introduction
Helix-coil transition models are formalized statistical mechanics techniques developed to describe the conformations of linear polymers in solution. The models are commonly, but not exclusively, applied to polypeptides as a measure of the relative fraction of the molecule in alpha-helix conformation versus the fraction in random coil conformation. The main interest in investigating the formation of alpha helices is that the main features of protein folding are found, but in the simplest possible version.[1].
Most helix-coil models contain parameters for the probability of helix nucleation from a coil region and the propagation of the helix through the sequence once nucleated. Since polypeptides are directional and have different N-terminal and C-terminal ends, the propagation parameters may differ for each of the directions.
Some common models would be the Zimm-Bragg model and the Lifson-Roig model), and their extensions and variations.
The energy of the polyadenine host helix in aqueous solution is:.
where m - is the number of residues in the helix.[2].
References
- [1] ↑ Doig AJ (2008). «The alpha-Helix as the Simplest Protein Model: Helix–Coil Theory, Stability, and Design». En Muñoz V, ed. Protein Folding, Misfolding and Aggregation: Classical Themes and Novel Approaches. Royal Society of Chemistry.
- [2] ↑ Chakrabartty A, Baldwin RL (1995). «Stability of alpha-helices». Adv Protein Chem 46: 141-176.