Effects of Interactions with the GroEL Cavity on Protein Folding Rates

University of Cambridge, Department of Chemistry, Cambridge, United Kingdom.
Biophysical Journal (Impact Factor: 3.97). 03/2013; 104(5):1098-106. DOI: 10.1016/j.bpj.2013.01.034
Source: PubMed


Encapsulation of proteins in chaperonins is an important mechanism by which the cell prevents the accumulation of misfolded species in the cytosol. However, results from theory and simulation for repulsive cavities appear to be inconsistent with recent experimental results showing, if anything, a slowdown in folding rate for encapsulated Rhodanese. We study the folding of Rhodanese in GroEL, using coarse-grained molecular simulations of the complete system including chaperonin and substrate protein. We find that, by approximating the substrate:GroEL interactions as repulsive, we obtain a strong acceleration in rate of between one and two orders of magnitude; a similar result is obtained by representing the chaperonin as a simple spherical cavity. Remarkably, however, we find that using a carefully parameterized, sequence-based potential to capture specific residue-residue interactions between Rhodanese and the GroEL cavity walls induces a very strong reduction of the folding rates. The effect of the interactions is large enough to completely offset the effects of confinement, such that folding in some cases can be even slower than that of the unconfined protein. The origin of the slowdown appears to be stabilization-relative to repulsive confinement-of the unfolded state through binding to the cavity walls, rather than a reduction of the diffusion coefficient along the folding coordinate.

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    • "How does GroEL/ES catalyze the folding of the DapA TIM barrel? Theory predicts that steric confinement of unfolded protein in a repulsive (net-negatively charged) cage can accelerate folding by one to two orders of magnitude by restricting the conformational freedom of folding intermediates and making the formation of local and long-range contacts, including those present in the transition state, more favorable (Baumketner et al., 2003; Hayer-Hartl and Minton, 2006; Sirur and Best, 2013). Our results with the single ring variant of GroEL, SREL, show that folding catalysis is achieved upon a single round of protein encapsulation within the SREL/ES cage. "
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    ABSTRACT: The GroEL/ES chaperonin system functions as a protein folding cage. Many obligate substrates of GroEL share the (βα)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known. Here, we analyzed the folding of DapA at peptide resolution using hydrogen/deuterium exchange and mass spectrometry. During spontaneous folding, all elements of the DapA TIM barrel acquire structure simultaneously in a process associated with a long search time. In contrast, GroEL/ES accelerates folding more than 30-fold by catalyzing segmental structure formation in the TIM barrel. Segmental structure formation is also observed during the fast spontaneous folding of a structural homolog of DapA from a bacterium that lacks GroEL/ES. Thus, chaperonin independence correlates with folding properties otherwise enforced by protein confinement in the GroEL/ES cage. We suggest that folding catalysis by GroEL/ES is required by a set of proteins to reach native state at a biologically relevant timescale, avoiding aggregation or degradation.
    Cell 05/2014; 157(4):922-34. DOI:10.1016/j.cell.2014.03.038 · 32.24 Impact Factor
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    Biophysical Journal 03/2013; 104(5):964-5. DOI:10.1016/j.bpj.2013.01.036 · 3.97 Impact Factor
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    ABSTRACT: Three structurally similar domains from α-spectrin have been shown to fold very differently. First, there is a contrast in the folding mechanism, as probed by Φ-value analysis, between the R15 domain and the R16 and R17 domains. Second, there are very different contributions from internal friction to folding: the folding rate of the R15 domain was found to be inversely proportional to solvent viscosity, showing no apparent frictional contribution from the protein, but in the other two domains, a large internal friction component was evident. Non-native misdocking of helices has been suggested to be responsible for this phenomenon. Here, I study the folding of these three proteins with minimalist coarse-grained models based on a funneled energy landscape. Remarkably, I find that, despite the absence of non-native interactions, the differences in folding mechanism of the domains are well captured by the model, and the agreement of the Φ-values with experiment is fairly good. On the other hand, within the context of this model, there are no significant differences in diffusion coefficient along the chosen folding coordinate, and the model cannot explain the large differences in folding rates between the proteins found experimentally. These results are nonetheless consistent with the expectations from the energy landscape perspective of protein folding, namely, that the folding mechanism is primarily determined by the native-like interactions present in the Go̅-like model, with missing non-native interactions being required to explain the differences in "internal friction" seen in experiment.
    The Journal of Physical Chemistry B 08/2013; 117(42). DOI:10.1021/jp403305a · 3.30 Impact Factor
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