Protein Folding and Chaperones

Tessa Sinnige, Utrecht University, Utrecht, The Netherlands
G Elif Karagöz, Utrecht University, Utrecht, The Netherlands
Stefan GD Rüdiger, Utrecht University, Utrecht, The Netherlands

Published online: June 2010

DOI: 10.1002/9780470015902.a0005721.pub2

Proteins fold via specific pathways to achieve their native structure. Protein structures are, however, inherently unstable; hence folding and unfolding are in equilibrium. Protein instability is a major concern inside the cell. Specialised proteins called molecular chaperones are, therefore, required to assist proteins in folding and to prevent aggregation of folding intermediates. Many different classes of chaperones exist that are conserved throughout all kingdoms of life, many of which are known as heat-shock proteins. Chaperones typically recognise hydrophobic patches, but the exact functions and mechanisms of action of the various chaperone classes are very different. The main chaperone classes Hsp70, Hsp90, Hsp100 and chaperonins all depend on adenosine triphosphatase (ATPase) cycles, which enable subtle activity control by co-chaperones. The molecular understanding of the mechanism of both chaperones and protein folding are key problems in today's life sciences. The importance is illustrated by the fact that many diseases are associated with these processes.

Key Concepts:

  • Proteins fold via pathways.
  • Protein structures are labile.
  • Protein folding in vivo is assisted by molecular chaperones.
  • Assisted protein folding requires ATP energy.
  • Molecular chaperones are evolutionarily conserved.
  • Chaperone activity is controlled by co-chaperones and cofactors.
  • Chaperone families differ in structure and function.

Keywords: protein folding; protein stability; molecular chaperones; folding pathways; Hsp70; Hsp90; heat-shock response; protein misfolding; intrinsically disordered proteins

Figure 1. Energy landscape describing protein folding and aggregation. The unfolded polypeptide chain moves towards conformations with a lower free energy. In this process the number of available conformations, hence entropy, decreases. The landscape consists of two funnels: one leading to the native state of the protein, the other to an aggregate. Alternatively, the polypeptide may become trapped in a local energy minimum, such as a partially folded state or an oligomer. Not all intermediates are productive for the protein folding process; trapping the protein in a deep local minimum may create an off-pathway intermediate that may frustrate the protein folding process. Inside the cell, such off-pathway intermediates are targeted by molecular chaperones or the cellular degradation machinery.
Figure 2. Chaperones in the bacterial cytosol. The ATP-dependent chaperones of the E. coli cytosol and the nascent chain binding trigger factor are shown as both ribbons and surface charge presentations (blue: positively charged and red: negatively charged). The molecules are shown to scale. GroEL (in complex with GroES 7mer), Hsp60 family, oligomeric state 14mer, pdb file 1aon; ClpB, Hsp100, hexamer, 1qvr; HtpG (ADP-bound), Hsp90, dimer, 2iop; DnaK, Hsp90, monomer, 2kho; trigger factor, no eukaryotic homologues, monomer, 1w26. Nota bene: all chaperones undergo conformational changes on binding nucleotide, cofactors and substrate. All structural pictures and surface charge presentation were done using Pymol. The charge patterns have to be used with care and give only a qualitative impression.
Figure 3. Protein folding in the cytosol, assisted by ATP-driven machines. (a) Protein folding in the cytosol of E. coli. The nascent chain emerges from the ribosome, where it meets its first chaperone, trigger factor (TF). TF is ATP independent but profits from the ATP-driven growth of the polypeptide by the ribosome. Proteins may then either fold on their own, or be assisted by the Hsp70 system DnaK and its cofactors (not shown), or be assisted by the chaperonin, GroEL (shown in complex with its cofactor GroES). Nascent polypeptides may travel between chaperonin and DnaK in case they first bind to a chaperone system that fails in folding them. Proteins may unfold again, in particular under stress conditions, which may lead to aggregation. Even large aggregates can be reversed by concerted action of the DnaK system and the Hsp100 chaperone ClpB. So far, no role could be found for the Hsp90 homologue HtpG. (b) Protein folding in the human cytosol. The processes are similar to those in E. coli, with the following exceptions: (i) The eukaryotic ribosome does not have a TF homologue but the functional analogues nascent chain-associated complex (NAC) and ribosome-associated complex (RAC). (ii) Hsp90 is essential for folding of a subset of substrates, usually following Hsp70 action. (iii) There is no Hsp100 chaperoning activity. All chaperone pictures are based on the pictures in Figure 2; human Hsp90 and Hsp70 are depicted as their E. coli counterparts. Co-chaperones are omitted, except for the GroEL–GroES complex.
Figure 4. The Hsp70 ATPase cycle, as the substrate sees it. Hsp70 consists of an ATPase domain (blue) and a substrate-binding domain that has a substrate holding segment (red) and a lid segment (green). ATP-binding triggers opening of the substrate-binding domain; ATP hydrolysis encloses the substrate. Release of ADP and rebinding of ATP open Hsp70, leading to release of the substrate that subsequently may fold into the native state. It is not known whether the substrate has a different structure after Hsp70 release than before Hsp70 interaction. Hsp70 chaperone activity is tuned by stimulating ATP hydrolysis by J proteins and by triggering nucleotide exchange. Protein folding/unfolding processes that are not assisted by Hsp70 are indicated by grey arrows, all other processes are indicated by black arrows. The pictures are based on pbd file 2kho of DnaK for the closed ADP conformation and on pdb file 2qxl of yeast Hsp70 sse1 for the open ATP conformation.
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Related Sub-Topics:

Basic Cell Biology, Protein, RNA and DNA | Protein Folding, Evolution and Degradation | Biomolecular Interactions | Proteins: Structure, Function, Metabolism
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Article Title: Protein Folding and Chaperones
 
How to Cite close
Sinnige, Tessa, Karagöz, G Elif, and Rüdiger, Stefan GD(Jun 2010) Protein Folding and Chaperones. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005721.pub2]