Kinetics of cytochrome C folding: Atomically detailed simulations

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Abstract
The vast range of time scales (from nanoseconds to seconds) during protein folding is a challenge for experiments and computations. To make concrete predictions on folding mechanisms, atomically detailed simulations of protein folding, using potentials derived from chemical physics principles, are desired. However, due to their computational complexity, straightforward molecular dynamics simulations of protein folding are impossible today. An alternative algorithm is used that makes it possible to compute approximate atomically detailed long time trajectories (the Stochastic Difference Equation in Length). This algorithm is used to compute 26 atomically detailed folding trajectories of cytochrome c (a millisecond process). The early collapse of the protein chain (with marginal formation of secondary structure), and the earlier formation of the N and C helices (compare to the 60's helix) are consistent with the experiment. The existence of an energy barrier upon entry to the molten globule is examined as well. In addition to (favorable) comparison to experiments, we show that non‐native contacts drive the formation of the molten globule. In contrast to popular folding models, the non‐native contacts do not form off‐pathway kinetic traps in cytochrome c. Proteins 2003;51:245–257.
Funding Information
  • NIH
  • NSF