The dynamics of chymotrypsin inhibitor 2 (CI2) in water, as well as in 10M urea, have been studied by Molecular Dynamics simulations. The analysis aims at investigating how local protein processes are affected by urea and how the perturbation by urea on the local level manifests itself in the kinetics of the global unfolding. The results show that the effect of urea on local processes depends upon the type of process at hand. An isolated two-residue contact on the surface of CI2 has a decreased frequency of rupture in the urea solvent. This is in contrast to the increased frequency of rupture of the hydrogen bonds in secondary structure elements in the urea solvent. It is proposed that the increase in the unfolding rates of complex protein processes is based upon the retardation of the refolding rate of small scale, isolated processes.
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