Protein Folding in Vivo

Abstract

Proteins are composed of linear chains of amino acids. Upon synthesis in the cell, most proteins must rapidly acquire a specific three‐dimensional structure, a process known as folding, before they can perform their various biological functions. Productive folding is often competed by aggregation, owing to the high macromolecular crowding of the cellular environment. Moreover, the process of translation increases the danger of misfolding, as incomplete nascent polypeptides are not yet able to fold into stable structures in many cases. To avoid these off‐pathway reactions, a class of proteins called molecular chaperones has evolved in all organisms. They interact with nascent or stress‐denatured polypeptides, prevent their aggregation and assist in folding and assembly processes, often in an ATP‐regulated manner. These functions are especially important in conditions of cell stress, and their failure is linked with the manifestation of numerous age‐dependent degenerative diseases.

Key Concepts

  • Molecular chaperones are proteins that mediate folding and assembly of other proteins, without being components of the final folded or assembled structures.
  • Molecular chaperones prevent the potentially toxic aggregation of newly synthesised polypeptides during translation and when mature proteins unfold during stress conditions or ageing.
  • Hsp70 chaperones act as a hub in the proteostasis network by assisting protein folding and conformational maintenance and by distributing client proteins to other chaperones for correct folding.
  • The chaperonins mediate the folding of proteins with complex topologies and kinetically frustrated folding pathways.

Keywords: protein folding; molecular chaperones; chaperonins; Hsp70; Hsp90; protein aggregation

Figure 1. Structure and functional cycle of Hsp70. (a) Structure of Hsp70. Hsp70 consists of two domains, the nucleotide‐binding domain (NBD) and the substrate‐binding domain (SBD), connected by a conserved linker. The closed state of DnaK (left; PDB 2KHO) was solved using a combination of solution nuclear magnetic resonance spectroscopy and crystal structures of the individual domains. The structure illustrates the ADP‐bound NBD separated by a linker from the SBD. The α‐helical lid of the SBD is closed over the substrate peptide (amino acid sequence NRLLLTG) bound in the pocket of the β‐sandwich domain. The open state is illustrated by the crystal structure of ATP‐bound Sse1 (yeast Hsp110; right; PDB 2QXL). The β‐sandwich domain contacts sub‐domain IA of the NBD, whereas the α‐helical lid contacts sub‐domains IA and IB. (b) Reaction cycle. ATP binding to the NBD stabilises the open state of Hsp70, facilitating the binding of substrate protein recruited to Hsp70 by Hsp40 co‐chaperone. The open state has fast on and off rates for substrate peptide. Hsp40 stimulates ATP hydrolysis on Hsp70, resulting in the closing of the SBD α‐helical lid over the bound substrate peptide. The closed state has slow on and off rates for substrate peptide. NEFs stimulate the release of ADP from the NBD, and ATP binding causes substrate release. Reproduced from Kim YE, Hipp MS, Bracher A, Hayer‐Hartl M, Hartl FU (2013) © Annual Reviews.
Figure 2. Structure and function of the GroEL‐GroES chaperonin. (a) Left: view of the asymmetric GroEL–GroES‐(ADP)7 complex generated with the co‐ordinates 1AON and program Weblab ViewLite 4.0 (Molecular Simulations). The equatorial, intermediate and apical domains of one subunit each in the ‐ and ‐rings of GroEL are coloured pink, yellow and dark blue, respectively, and one subunit of GroES is coloured red. Right: the accessible surface of the central cavity of the GroEL–GroES complex. Polar and charged side‐chain atoms, blue; hydrophobic side‐chain atoms, yellow; backbone atoms, white and solvent‐excluded surfaces at subunit interfaces, grey. Reproduced from Hartl, FU and Hayer‐Hartl, M (2002) © American Association for the Advancement of Science (AAAS). (b) Model of the GroEL/ES mechanism of assisted protein folding. Reproduced from Kim YE, Hipp MS, Bracher A, Hayer‐Hartl M, Hartl FU (2013) © Annual Reviews.
Figure 3. Organisation of chaperone pathways in the cytosol. In (a) bacteria, (b) archaea and (c) eukarya, ribosome‐bound chaperones (TF in bacteria, NAC in archaea and eukarya) aid folding co‐translationally by binding to hydrophobic segments on the emerging nascent chains. For longer nascent chains, members of the Hsp70 family (DnaK in bacteria and Hsp70 in eukarya) together with Hsp40 mediate co‐ and post‐translational folding. In archaea lacking the Hsp70 system, prefoldin assists in folding downstream of NAC. Partially folded substrates may be transferred to the chaperonins (GroEL–GroES in bacteria, thermosome in archaea and TRiC/CCT in eukarya). In addition to the chaperonin system, eukarya are equipped with the Hsp90 system which receives its substrates from Hsc70 and mediates folding together with additional co‐factors. Insert in (c) shows the ribosome‐binding chaperone system, RAC, in fungi. RAC is composed of Ssz1 (a specialised Hsp70) and zuotin (Hsp40) and assists nascent chain folding together with the Hsp70 isoform, Ssb. Percentages indicate the approximate protein flux through the various chaperones. Reproduced from Kim YE, Hipp MS, Bracher A, Hayer‐Hartl M, Hartl FU (2013) © Annual Reviews.
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Further Reading

Chiti F and Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annual Review of Biochemistry 75: 333–366.

Fersht A (1999) Structure and Mechanism in Protein Science. New York: Freeman.

Hipp MS, Park SH and Hartl FU (2014) Proteostasis impairment in protein‐misfolding and ‐aggregation diseases. Trends in Cell Biology 24: 506–514.

Pain RH (ed) (2000) Mechanisms of Protein Folding. Oxford: University Press.

Prodromou C (2012) The ‘active life’ of Hsp90 complexes. Biochimica et Biophysica Acta 1823: 614–623.

Ramirez‐Alvarado M, Kelly JW and Dobson CM (eds) (2010) Protein Misfolding Diseases: Current and Emerging Principles and Therapies. Hoboken: John Wiley & Sons, Inc.

Taipale M, Jarosz DF and Lindquist S (2010) Hsp90 at the hub of protein homeostasis: emerging mechanistic insights. Nature Reviews Molecular Cell Biology 11: 515–528.

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Georgescauld, Florian, and Hartl, Franz‐Ulrich(Apr 2015) Protein Folding in Vivo. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000552.pub3]