Application of a chaperone‐based refolding method to two‐ and three‐dimensional off‐lattice protein models

A model of protein–chaperone interaction as a two‐phase (unfolding/refolding) iterative annealing mechanism able to promote structural segregation of hydrophobic and hydrophilic monomers and thereby facilitate access to nativelike states has recently been applied successfully to two 22‐mers of the Honeycutt and Thirumalai BLN (hydrophobic, hydrophilic, neutral) heteropolymer model. This technique is here applied to a much wider data set: 94 8‐mers of the off‐lattice protein model originally presented in two dimensions by Stillinger and Head‐Gordon, and later extended into three dimensions by Irbäck and Potthast; the model chaperone is shown to be equally successful, and by progressive elaboration of the chaperone model as in the earlier BLN model work, to be utilizing very similar underlying mechanisms. It is demonstrated that on average, contacts with the model chaperone give rise to a consistent movement in structure space in the direction of more nativelike structures; this method of global minimization does not therefore rely fundamentally on random search. Insofar as the responses to the chaperone of the two‐ and three‐dimensional forms of the substrate model do differ, this can be interpreted as reflecting the different handling of hydrophilic monomers in the models—in particular, whether there is active repulsion between these and monomers of hydrophobic character. The chaperone‐induced refolding method is also tested on a set of 220 9‐mer chains of each version of the substrate model, where it is seen that the two‐dimensional model, with its more clearly distinguished roles for the hydrophobic and hydrophilic monomers, shows a more favorable scaling behavior. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 146–160, 2002