Protein Folding Energy Funnel
Funneled landscape guides chains to native structure
Energy: 0.0 k_BT
Q (fraction native): 0.00
RMSD: 0.0 Å
Energy Funnel Hypothesis (Wolynes, Bryngelson, Dill): Evolution has shaped protein sequences so their energy landscape resembles a funnel — the native state is at the bottom, and most paths lead downhill toward it. The funnel is parameterized by two axes: Q (fraction of native contacts formed, 0→1) and entropy S (conformational disorder). The free energy F=E−TS creates a barrier determined by temperature. Above the folding temperature T_f, the denatured ensemble is favored; below it, the native state wins. Coarse-grained Gō-models retain only native interactions, producing a perfect funnel — a useful approximation for exploring topology-driven folding.