Alpha-Helix Folding: Hydrogen-Bond Cooperativity

Conditions

Temperature 300 K

Chain length 20 residues

Sequence

Live State

Helix content Q

i,i+4 H-bonds

Radius of gyration R_g

0.0 Å

Helical residue (Cα) Coil residue (Cα) Breaker residue (proline) Backbone i→i+4 H-bond

How it works

Each residue can be coil or helical. A helical run of 4 or more consecutive residues forms one backbone hydrogen bond between the C=O of residue i and the N–H of residue i+4 for every extra residue in the run. Folding is driven by Metropolis Monte-Carlo on a Zimm–Bragg-style free energy:

ΔG_bond(T) = ΔH − TΔS         (per i,i+4 H-bond, ΔH scaled by residue helix propensity)
ΔG_nuc(T)  = −RT·ln(σ)         (one-off cost to start a NEW helical run, σ ≈ 10⁻³)
E(state)   = Σ over runs [ ΔG_nuc + bonds(run)·ΔG_bond ]

At each Monte-Carlo step one residue's coil/helix flag is proposed to flip; the move is accepted if it lowers E, or accepted with probability exp(−ΔE / RT) otherwise (real thermal fluctuation). Because ΔG_nuc is large and positive, extending an existing helical run is always cheaper than starting a new one — this is why helices nucleate at one spot and then propagate, exactly as in real proteins (this is the same cooperativity captured by the classic Zimm–Bragg helix–coil transition theory).

Temperature — raises T in ΔG_bond, tipping the balance toward the entropically-favoured coil (thermal denaturation).
Sequence — scales ΔH per residue by its helix propensity: alanine-like residues fold strongly, glycine-like residues barely fold, and a proline breaker can never enter the helical state, splitting any helix that tries to cross it.
The 3D backbone blends between an ideal α-helix (radius 2.3 Å, rise 1.5 Å/residue, 100°/residue turn) and a fixed random-coil path per residue, in proportion to how "helical" that residue currently is.

Drag to rotate · scroll to zoom

⚠ Couldn't load the 3D engineThree.js failed to load from the CDN. Check your connection and reload.