Dual Function of Protein Confinement in Chaperonin-Assisted Protein Folding

Escherichia coli chaperonin, GroEL, helps proteins fold under nonpermissive conditions. During the reaction cycle, GroEL undergoes allosteric transitions in response to binding of a substrate protein (SP), ATP, and the cochaperonin GroES. Using coarse-grained representations of the GroEL and GroES structures, we explore the link between allosteric transitions and the folding of a model SP, a de novo-designed four-helix bundle protein, with low spontaneous yield. The ensemble of GroEL-bound SP is less structured than the bulk misfolded structures. Upon binding, which kinetically occurs in two stages, the SP loses not only native tertiary contacts but also experiences a decrease in helical content. During multivalent binding and the subsequent ATP-driven transition of GroEL the SP undergoes force-induced stretching. Upon encapsulation, which occurs upon GroES binding, the SP finds itself in a ''hydrophilic'' cavity in which it can reach the folded conformation. Surprisingly, we find that the yield of the native state in the expanded GroEL cavity is relatively small even after it remains in it for twice the spontaneous folding time. Thus, in accord with the iterative annealing mechanism, multiple rounds of binding, partial unfolding, and release of the SP are required to enhance the yield of the folded SP.native state yield ͉ soft nanomachine ͉ force-induced stretching

Section: Groes Binding Encapsulates the Sp And Helps Foldingsupporting

confidence: 73%

Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein

Stan

Lorimer

Thirumalai

et al. 2007

“…In particular, Ϸ12 such interacting proteins have been shown in vitro to be completely dependent on GroEL͞GroES to reach the native state, and several of these proteins carry out essential cellular functions, thus providing some explanation for why groE is essential for cell growth. Such proteins require not only the binding function of GroEL, which forestalls misfolding and aggregation, but also the action of folding inside a hydrophilic, confined, cis ternary GroEL͞ GroES complex (10)(11)(12)(13). But interaction and in vitro reconstitution studies cannot uncover the primary effects of shutoff of chaperonin function in the intact physiological system.…”

mentioning

confidence: 99%

Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL

Chapman

Farr

Usaite

et al. 2006

134

171

In a newly isolated temperature-sensitive lethal Escherichia coli mutant affecting the chaperonin GroEL, we observed wholesale aggregation of newly translated proteins. After temperature shift, transcription, translation, and growth slowed over two to three generations, accompanied by filamentation and accretion (in Ϸ2% of cells) of paracrystalline arrays containing mutant chaperonin complex. A biochemically isolated inclusion body fraction contained the collective of abundant proteins of the bacterial cytoplasm as determined by SDS͞PAGE and proteolysis͞MS analyses. Pulse-chase experiments revealed that newly made proteins, but not preexistent ones, were recruited to this insoluble fraction. Although aggregation of ''stringent'' GroEL͞GroES-dependent substrates may secondarily produce an ''avalanche'' of aggregation, the observations raise the possibility, supported by in vitro refolding experiments, that the widespread aggregation reflects that GroEL function supports the proper folding of a majority of newly translated polypeptides, not just the limited number indicated by interaction studies and in vitro experiments.chaperone ͉ misfolding ͉ protein folding

“…This ''smoothing of the energy landscape'' model was suggested by Hartl (16) to explain chaperoninmediated folding-rate increases that could not be attributed to multiple rounds of binding and release of the substrate protein in accordance with the IAM described above. In particular, Hartl noted that RuBisCo, a stringent GroEL substrate folds faster when trapped inside SR-1 (a mutant of GroEL that cannot unbind from GroES) than it does in a dilute bulk environment (16). It has been proposed that this scenario can be reconciled within a noncycling limit of the IAM (10,12,15), in which a single binding event [n ϭ 1 (15)] would be sufficient to lead to accelerated folding events.…”

mentioning

confidence: 99%

Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: Creation of an alternate fast folding pathway

Jewett

Baumketner

Shea

2004

112

158

Recent experiments suggest that the folding of certain proteins can take place entirely within a chaperonin-like cavity. These substrate proteins experience folding rate enhancements without undergoing multiple rounds of ATP-induced binding and release from the chaperonin. Rather, they undergo only a single binding event, followed by sequestration into the chaperonin cage. The present work uses molecular dynamics simulations to investigate the folding of a highly frustrated protein within this chaperonin cavity. The chaperonin interior is modeled by a sphere with a lining of tunable degree of hydrophobicity. We demonstrate that a moderately hydrophobic environment, similar to the interior of the GroEL cavity upon complexion with ATP and GroES, is sufficient to accelerate the folding of a frustrated protein by more than an order of magnitude. Our simulations support a mechanism by which the moderately hydrophobic chaperonin environment provides an alternate pathway to the native state through a transiently bound intermediate state.