Oas Lab (2/13/99)
The diagram above shows the calculated folding mechanism through 38 different partially folded substates of wild type monomeric lambda repressor based on the diffusion-collision theory of Karplus & Weaver (Nature 260:404-406, 1976). The calculated overall folding rate agrees with the experimentally measured rate (Huang & Oas, Proc. Nat. Acad. Sci, USA 92:6878-6882, 1995). Each numbered circle corresponds to one the five helices in the molecule, in either the unfolded (white) or unfolded (black) conformations. The colored bars in each sub-state represent one of eight inter-helical "bonds" that form via a diffusion/collision reaction. The width of lines between substates corresponds to the relative rates of substate formation. Notice that the substate with all helices formed except helix 3 (a particularly unstable helix with 2 glycine residues) represents the bottleneck in the folding reaction. This substate is predicted to transiently accumulate to a significant population (represented by the darkness of each substate symbol.) These calculations are described in: