Molecule of the Month: Chaperones

Chaperones help new proteins fold into their proper shape

Protein chaperonin GroEL-GroES.
Protein chaperonin GroEL-GroES.
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As you can see when looking through the many structures in the PDB, most active proteins have a stable, globular structure. However, proteins are built as formless chains, pieced together one amino acid at a time by ribosomes. Most protein chains then fold spontaneously into their final structure, driven by the need to shelter their carbon-rich portions from the surrounding water. But some--large proteins or proteins with several domains--need some assistance. As they fold into a compact shape, they might get stuck somewhere along the way.

The Dangers of Misfolding

This is not a trivial problem. Cells cannot merely wait for proteins to fold properly. Misfolded proteins often have carbon-rich amino acids on their surfaces, instead of tucked safely inside. These carbon-rich patches associate strongly with similar patches on other proteins, forming large aggregates. Random aggregates are death to cells: diseases such as sickle cell anemia, mad cow disease, and Alzheimer's disease are caused by unnatural aggregation of proteins into cell-clogging fibrils.

Guides Along the Folding Pathway

Chaperones are proteins that guide proteins along the proper pathways for folding. They protect proteins when they are in the process of folding, shielding them from other proteins that might bind and hinder the process. Many chaperone proteins are termed "heat shock" proteins (with names like HSP-60) because they are made in large amounts when cells are exposed to heat. Heat, in general, destabilizes proteins and makes misfolding more common. So when it gets really hot, cells need some extra help with their proteins.

HSP-60 Chaperones

One impressive type of chaperone forms an enclosed environment for folding proteins which totally protects them as they fold. The GroEL-GroES complex of the bacterium E. coli is shown here, from PDB entry 1aon . It is composed of two stacked rings of GroEL proteins, colored blue and green here, and a cap on one side composed of GroES, colored red and yellow at the bottom. As seen in the top view, seven GroEL proteins form a ring with a protein-sized cavity inside. Unfolded proteins enter this cavity and fold up inside.

HSP-70 chaperonin DnaK (top) and prefoldin (bottom).
HSP-70 chaperonin DnaK (top) and prefoldin (bottom).
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HSP-70 and Prefoldin

Smaller chaperones protect proteins just after they leave the ribosome. At this stage, they may have very little folded structure, so stretches of the chain with lots of exposed carbon atoms are particularly susceptible to aggregation. HSP-70 (shown at the top) finds these stretches and binds to them, shielding them from neighbors. Then, powered by ATP, the chaperone releases the chain when it is ready to fold. HSP-70 is composed of two domains: one that binds ATP and controls the process, shown on the left side of the molecule from PDB entry 1dkg , and one that binds to carbon-rich peptides, shown here on the right side using coordinates from PDB entry 1dkz . A little peptide, colored pink, is bound in the deep protein-binding cleft. The odd jelly-fish shaped prefoldin, shown at the bottom from PDB entry 1fxk , performs a similar job, engulfing protein chains when they are in the process of folding.

Exploring the Structure

GroEL and GroES

The GroEL-GroES complex facilitates the folding of proteins in a sheltered space, shielding them from surrounding unfolded proteins. The upper chamber of the complex features a band of hydrophobic amino acids (shown in white) that stabilize unfolded proteins and coax them inside. As the chamber enlarges and is closed off by GroES, these hydrophobic amino acids become hidden, allowing the protein to fold and conceal its own hydrophobic regions. This process is driven by ATP, which controls a cycle of shape changes in GroEL. PDB entry 1aon has ADP bound to the GroEL subunits shown here at the bottom, which are in an "open" state.

Select the JSmol tab to explore these structures in an interactive view.

This JSmol was designed and illustrated by Ryan Nini.


  1. Hartl, F.U. and Hayer-Hartl, M. (2002) Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein. Science 295, 1852-1858.

August 2002, David Goodsell
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More