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PubMed2001

Unfolding rates for the diffusion-collision model.

In the diffusion-collision model, the unfolding rates are given by the likelihood of secondary structural cluster dissociation. In this work, we introduce an unfolding rate calculation for proteins whose secondary structural elements are alpha helices, modeled from thermal escape over a barrier that arises from the free energy in buried hydrophobic residues. Our results are in good agreement with currently accepted values for the attempt rate.

Biophysical Phenomena↗

PubMed2001

Diffusion-collision model study of misfolding in a four-helix bundle protein.

Proteins with complex folding kinetics will be susceptible to misfolding at some stage in the folding process. We simulate this problem by using the diffusion-collision model to study non-native kinetic intermediate misfolding in a four-helix bundle protein. We find a limit on the size of the pairwise hydrophobic area loss in non-native intermediates, such that burying above this limit creates long-lasting non-native kinetic intermediates that would disrupt folding and prevent formation of the native state. Our study of misfolding suggests a method for limiting the production of misfolded kinetic intermediates for helical proteins and could, perhaps, lead to more efficient production of proteins in bulk.

Diffusion↗