Folding Kinetics of IkB: Excursions Through the Energy Landscape

The IkB proteins, inhibitors of the transcription factor NF-kB, are comprised of tandem repeats of a conserved primary structure. The tandem repeats are stabilized as a repeated tertiary structural motif, at least when complexed with NF-kB and DNA. Structural fluctuations in the native state deviate substantially from a simple repeating pattern, as reported by site-resolved hydrogen exchange rates, NMR chemical shifts and relaxation parameters, and energetically frustrated intraprotein contacts. Here we have studied the folding of the first four ankyrin repeats of human IkB-alpha and -beta, using coarse-grained structural models to extensively simulate dynamics under structurally-parameterized Hamiltonians. The folding reaction coordinate was sampled with biasing potentials and the free energy as a function of the reaction coordinate was calculated with weighted histogram analysis. The trajectories were used to assign the thermodynamic changes between substates in the folding mechanism. Kinetic models connecting the folding substates were used to predict experimentally known (un)folding rates.