Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity

The chaperonin system, GroEL and GroES of Escherichia coli enable certain p roteins to fold under conditions when spontaneous folding is prohibitively slow as to compete with other non-productive channels such as aggregation. We investigated the plausible mechanisms of GroEL-mediated folding using si mple lattice models. In particular, we have investigated protein folding in a confined environment, such as those offered by the GroEL, to decipher wh ether rate and yield enhancement can occur when the substrate protein is al lowed to fold within the cavity of the chaperonins. The GroEL cavity is mod eled as a cubic box and a simple bead model is used to represent the substr ate chain. We consider three distinct characteristic of the confining envir onment. First, the cavity is taken to be a passive Anfinsen cage in which t he walls merely reduce the available conformation space. We find that at te mperatures when the native conformation is stable, the folding rate is reta rded in the Anfinsen cage. We then assumed that the interior of the wall is hydrophobic. In this case the folding times exhibit a complex behavior. Wh en the strength of the interaction between the polypeptide chain and the ca vity is too strong or too weak we find that the rates of folding are retard ed compared to spontaneous folding. There is an optimum range of the intera ction strength that enhances the rates. Thus, above this value there is an inverse correlation between the folding rates and the strength of the subst rate-cavity interactions. The optimal hydrophobic walls essentially pull th e kinetically trapped states which leads to a smoother the energy landscape . It is known that upon addition of ATP and GroES the interior cavity of Gr oEL offers a hydrophilic-like environment to the substrate protein. In orde r to mimic this within the context of the dynamic Anfinsen cage model, we a llow for changes in the hydrophobicity of the walls of the cavity. The dura tion for which the walls remain hydrophobic during one cycle of ATP hydroly sis is allowed to vary. These calculations show that frequent cycling of th e wall hydrophobicity can dramatically reduce the folding times and increas e the yield as well under non-permissive conditions. Examination of the str uctures of the substrate proteins before and after the change in hydrophobi city indicates that there is global unfolding involved. Ln addition, it is found that a fraction of the molecules kinetically partition to the native state in accordabce with the iterative annealing mechanism. Thus, frequent "unfoldase" activity of chaperonins leading to global unfolding of the poly peptide chain results in enhancement of the folding rates and yield of the folded protein. We suggest that chaperonin efficiency can be greatly enhanc ed if the cycling time is reduced. The calculations are used to interpret a few experiments on chaperonin-mediated protein folding. (C) 1999 Academic Press.