CiteULike: cactus chaperonin

Rattling the cage: computational models of chaperonin-mediated protein folding

Jeremy England — 2008-05-26T04:25:38-00:00

Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 163-169.

Chaperonins are known to maintain the stability of the proteome by facilitating the productive folding of numerous misfolded or aggregation-prone proteins and are thus essential for cell viability. Despite their established importance, the mechanism by which chaperonins facilitate protein folding remains unknown. Computer simulation techniques are now being employed to complement experimental ones in order to shed light on this mystery. Here we review previous computational models of chaperonin-mediated protein folding in the context of the two main hypotheses for chaperonin function: iterative annealing and landscape modulation. We then discuss new results pointing to the importance of solvent (a previously neglected factor) in chaperonin activity. We conclude with our views on the future role of simulation in studying chaperonin activity as well as protein folding in other biologically relevant confined contexts.

GroEL stimulates protein folding through forced unfolding

Zong Lin — 2008-03-06T04:15:38-00:00

Nature Structural & Molecular Biology, Vol. 15, No. 3. (02 March 2008), pp. 303-311.

Folding trajectories of human dihydrofolate reductase inside the GroEL GroES chaperonin cavity and free in solution

Reto Horst — 2008-01-11T11:14:54-00:00

Proceedings of the National Academy of Sciences, Vol. 104, No. 52. (26 December 2007), pp. 20788-20792.

The chaperonin GroEL binds non-native polypeptides in an open ring via hydrophobic contacts and then, after ATP and GroES binding to the same ring as polypeptide, mediates productive folding in the now hydrophilic, encapsulated cis chamber. The nature of the folding reaction in the cis cavity remains poorly understood. In particular, it is unclear whether polypeptides take the same route to the native state in this cavity as they do when folding spontaneously free in solution. Here, we have addressed this question by using NMR measurements of the time course of acquisition of amide proton exchange protection of human dihydrofolate reductase (DHFR) during folding in the presence of methotrexate and ATP either free in solution or inside the stable cavity formed between a single ring variant of GroEL, SR1, and GroES. Recovery of DHFR refolded by the SR1/GroES-mediated reaction is 2-fold higher than in the spontaneous reaction. Nevertheless, DHFR folding was found to proceed by the same trajectories inside the cis folding chamber and free in solution. These observations are consistent with the description of the chaperonin chamber as an "Anfinsen cage" where polypeptide folding is determined solely by the amino acid sequence, as it is in solution. However, if misfolding occurs in the confinement of the chaperonin cavity, the polypeptide chain cannot undergo aggregation but rather finds its way back to a productive pathway in a manner that cannot be accomplished in solution, resulting in the observed high overall recovery. 10.1073/pnas.0710042105

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

George Stan — 2007-05-24T07:40:35-00:00

PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8803-8808.

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. 10.1073/pnas.0700607104

Structural Features of the GroEL-GroES Nano-Cage Required for Rapid Folding of Encapsulated Protein

Yun-Chi Tang — 2007-05-16T10:53:12-00:00

Cell, Vol. 125, No. 5. (2 June 2006), pp. 903-914.

Summary GroEL and GroES form a chaperonin nano-cage for proteins up to ~60 kDa to fold in isolation. Here we explored the structural features of the chaperonin cage critical for rapid folding of encapsulated substrates. Modulating the volume of the GroEL central cavity affected folding speed in accordance with confinement theory. Small proteins (~30 kDa) folded more rapidly as the size of the cage was gradually reduced to a point where restriction in space slowed folding dramatically. For larger proteins (~40-50 kDa), either expanding or reducing cage volume decelerated folding. Additionally, interactions with the C-terminal, mildly hydrophobic Gly-Gly-Met repeat sequences of GroEL protruding into the cavity, and repulsion effects from the negatively charged cavity wall were required for rapid folding of some proteins. We suggest that by combining these features, the chaperonin cage provides a physical environment optimized to catalyze the structural annealing of proteins with kinetically complex folding pathways.

Perturbed ATPase activity and not "close confinement" of substrate in the cis cavity affects rates of folding by tail-multiplied GroEL

George Farr — 2007-05-16T10:50:36-00:00

PNAS, Vol. 104, No. 13. (27 March 2007), pp. 5342-5347.

Folding of substrate proteins inside the sequestered and hydrophilic GroEL-GroES cis cavity favors production of the native state. Recent studies of GroEL molecules containing volume-occupying multiplications of the flexible C-terminal tail segments have been interpreted to indicate that close confinement of substrate proteins in the cavity optimizes the rate of folding: the rate of folding of a larger protein, Rubisco (51 kDa), was compromised by multiplication, whereas that of a smaller protein, rhodanese (33 kDa), was increased by tail duplication. Here, we report that this latter effect does not extend to the subunit of malate dehydrogenase (MDH), also 33 kDa. In addition, single-ring versions of tail-duplicated and triplicated molecules, comprising stable cis complexes, did not produce any acceleration of folding of rhodanese or MDH, nor did they show significant retardation of the folding of Rubisco. Tail quadruplication produced major reduction in recovery of native protein with both systems, the result of strongly reduced binding of all three substrates. When steady-state ATPase of the tail-multiplied double-ring GroELs was examined, it scaled directly with the number of tail segments, with more than double the normal ATPase rate upon tail triplication. As previously observed, disturbance of ATPase activity of the cycling double-ring system, and thus of "dwell time" for the folding protein in the cis cavity, produces effects on folding rates. We conclude that, within the limits of the approx10% decrease of cavity volume produced by tail triplication, there does not appear to be an effect of "close confinement" on folding in the cis cavity. 10.1073/pnas.0700820104