The GroEL–GroES Chaperonin Machine: A Nano-Cage for Protein Folding

doi:10.1016/j.tibs.2015.07.009

Trends in Biochemical Sciences

Volume 41, Issue 1, January 2016, Pages 62-76

https://doi.org/10.1016/j.tibs.2015.07.009 Get rights and content

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The group I chaperonin GroEL and its cofactor GroES are essential components of the cellular machinery of protein folding in bacteria. Homologous chaperonins occur in mitochondria and chloroplast, while more distantly related group II chaperonins are found in archaea and the eukaryotic cytosol.

GroEL is a double-ring complex with ATPase activity that binds non-native SP in the ring opening. Binding of the lid-shaped GroES to GroEL results in the displacement of SP into an enclosed nano-cage for folding to occur unimpaired by aggregation.

GroEL, non-native protein, and GroES undergo ATP-regulated binding and release cycles.

Recent advances indicate that the physical environment of the GroEL–GroES cage can accelerate the folding of some SPs. An effect of steric confinement of SP in the cage may contribute to the rate enhancement of folding.

The bacterial chaperonin GroEL and its cofactor GroES constitute the paradigmatic molecular machine of protein folding. GroEL is a large double-ring cylinder with ATPase activity that binds non-native substrate protein (SP) via hydrophobic residues exposed towards the ring center. Binding of the lid-shaped GroES to GroEL displaces the bound protein into an enlarged chamber, allowing folding to occur unimpaired by aggregation. GroES and SP undergo cycles of binding and release, regulated allosterically by the GroEL ATPase. Recent structural and functional studies are providing insights into how the physical environment of the chaperonin cage actively promotes protein folding, in addition to preventing aggregation. Here, we review different models of chaperonin action and discuss issues of current debate.

Section snippets

The Molecular Chaperone Concept

Proteins are involved in essentially all cellular processes. Following their synthesis on ribosomes as linear chains of amino acids, to become functionally active proteins generally must fold to unique 3D structures. Fundamental insight into the protein folding process was provided by Anfinsen's pioneering experiments, which showed that small proteins can refold spontaneously on removal from denaturant [1]. This finding not only demonstrated that the amino acid sequence dictates the native

Structural Architecture of GroEL and GroES

Early negative-stain electron microscopic (EM) images of GroEL alone, and with bound GroES, followed by detailed structural characterization by crystallography and cryo-EM have provided a solid foundation for understanding the GroEL/ES functional cycle 8, 19. Like all group I chaperonins, GroEL of Escherichia coli is a cylindrical complex of two heptameric rings of ∼57 kDa subunits. The subunits are composed of three domains formed by discontinuous sequence elements: an equatorial ATP-binding

The GroEL/ES Protein Folding Cycle

The interactions of GroEL with SP, nucleotide, and GroES that underlie chaperonin-assisted protein folding have been investigated extensively, but several aspects of the mechanism remain to be firmly established 10, 25, 26, 27, 28, 29, 30, 31.

In Vivo Substrates of GroEL

GroEL/ES is required for E. coli growth under all conditions [14], indicating the existence of essential proteins that depend on the chaperonin for folding. While GroEL interacts with a wide range of denatured proteins in vitro, only a limited set of ∼250 proteins was shown to bind stably to GroEL upon translation in vivo, corresponding to ∼10% of total E. coli cytosolic proteins and including 67 essential proteins [58] (Figure 3A). A wider range of newly synthesized proteins aggregated upon

GroEL–GroES: More Than an Infinite Dilution Box?

The exact mechanism by which the chaperonin system assists in protein folding is still a matter of debate. Three models have been proposed, which differ in whether GroEL/ES solely acts passively by preventing aggregation (passive cage) or additionally promotes the folding process by an active mechanism (active cage and iterative annealing) [30] (Figure 4).

Role of Chaperonin in Evolution

Protein evolution is based on the Darwinian selection of mutant proteins. However, most mutations either structurally destabilize the native state of a protein or result in the formation of kinetically trapped folding intermediates 95, 96. It has been suggested that GroEL/ES facilitates the structural evolution of proteins by buffering deleterious effects of mutations on foldability and stability 70, 97, 98, 99, 100, 101, 102. For example, overexpression of GroEL/ES allowed previously

Concluding Remarks

The GroEL/ES chaperonin system has been widely studied as a paradigm macromolecular machine for more than 25 years. It has been a source of inspiration and controversy to the present day. There is (almost) general agreement that the most significant feature of the chaperonin is to provide a compartment in which a single protein molecule is transiently enclosed and allowed to fold in isolation, thereby avoiding aberrant interactions that would otherwise lead to aggregation (Figure 7, Key

Acknowledgments

We are grateful to D. Balchin and A.J. Gupta for critically reading the manuscript. We apologize to our colleagues that with a few exceptions original work prior to 2000 could not be cited owing to space limitations.

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Trends in Biochemical Sciences

ReviewSpecial Issue: 40 Years of TIBSThe GroEL–GroES Chaperonin Machine: A Nano-Cage for Protein Folding

Trends

Section snippets

The Molecular Chaperone Concept

Structural Architecture of GroEL and GroES

The GroEL/ES Protein Folding Cycle

In Vivo Substrates of GroEL

GroEL–GroES: More Than an Infinite Dilution Box?

Role of Chaperonin in Evolution

Concluding Remarks

Acknowledgments

Curr. Opin. Struct. Biol.

Curr. Opin. Struct. Biol.

Mol. Cell

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J. Mol. Biol.

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J. Biol. Chem.

Cell

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Mol. Cell

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Prog. Biophys. Mol. Biol.

J. Struct. Biol.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Mol. Biol.

J. Struct. Biol.

Cell

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Cell Rep.

Cell

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Cell Rep.

FEBS Lett.

Cell

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J. Biol. Chem.

Cell

J. Biol. Chem.

FEBS Lett.

J. Mol. Biol.

J. Mol. Biol.

J. Mol. Biol.

Biophys J.

Chem. Eng. Sci.

J. Mol. Biol.

Principles that govern the folding of protein chains

Science

Protein folding – a perspective from theory and experiment

Angew. Chem. Int. Ed. Engl.

Protein misfolding, functional amyloid, and human disease

Annu. Rev. Biochem.

An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms

Nat. Struct. Mol. Biol.

Protein aggregation in crowded environments

Biol. Chem.

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

PLoS Comput. Biol.

Converging concepts of protein folding in vitro and in vivo

Nat. Struct. Mol. Biol.

Review
Special Issue: 40 Years of TIBS
The GroEL–GroES Chaperonin Machine: A Nano-Cage for Protein Folding