Skip to main content
Log in

Studying heat shock proteins through single-molecule mechanical manipulation

  • PERSPECTIVES ON sHSPs
  • Published:
Cell Stress and Chaperones Aims and scope

Abstract

Imbalances of cellular proteostasis are linked to ageing and human diseases, including neurodegenerative and neuromuscular diseases. Heat shock proteins (HSPs) and small heat shock proteins (sHSPs) together form a crucial core of the molecular chaperone family that plays a vital role in maintaining cellular proteostasis by shielding client proteins against aggregation and misfolding. sHSPs are thought to act as the first line of defence against protein unfolding/misfolding and have been suggested to act as “sponges” that rapidly sequester these aberrant species for further processing, refolding, or degradation, with the assistance of the HSP70 chaperone system. Understanding how these chaperones work at the molecular level will offer unprecedented insights for their manipulation as therapeutic avenues for the treatment of ageing and human disease. The evolution in single-molecule force spectroscopy techniques, such as optical tweezers (OT) and atomic force microscopy (AFM), over the last few decades have made it possible to explore at the single-molecule level the structural dynamics of HSPs and sHSPs and to examine the key molecular mechanisms underlying their chaperone activities. In this paper, we describe the working principles of OT and AFM and the experimental strategies used to employ these techniques to study molecular chaperones. We then describe the results of some of the most relevant single-molecule manipulation studies on HSPs and sHSPs and discuss how these findings suggest a more complex physiological role for these chaperones than previously assumed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Alderson TR, Roche J, Gastall HY, Dias DM, Pritišanac I, Ying J, Bax A, Benesch JL, Baldwin AJ (2019) Local unfolding of the HSP27 monomer regulates chaperone activity. Nat Commun 10(1):1068

    PubMed  PubMed Central  Google Scholar 

  • Ali MM, Roe SM, Vaughan CK, Meyer P, Panaretou B, Piper PW, Prodromou C, Pearl LH (2006) Crystal structure of an Hsp90–nucleotide–p23/Sba1 closed chaperone complex. Nature 440(7087):1013

    CAS  PubMed  PubMed Central  Google Scholar 

  • Balchin D, Hayer-Hartl M, Hartl FU (2016) In vivo aspects of protein folding and quality control. Science 353(6294):aac4354

    PubMed  Google Scholar 

  • Bauer D, Merz DR, Pelz B, Theisen KE, Yacyshyn G, Mokranjac D, Dima RI, Rief M, Žoldák G (2015) Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK. Proc Natl Acad Sci 112(33):10389–10394

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bauer D, Meinhold S, Jakob RP, Stigler J, Merkel U, Maier T, Rief M, Žoldák G (2018) A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy. Proc Natl Acad Sci 115(18):4666–4671

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bechtluft P, Van Leeuwen RG, Tyreman M, Tomkiewicz D, Nouwen N, Tepper HL, Driessen AJ, Tans SJ (2007) Direct observation of chaperone-induced changes in a protein folding pathway. Science 318(5855):1458–1461

    CAS  PubMed  Google Scholar 

  • Benndorf R, Martin JL, Pond SLK, Wertheim JO (2014) Neuropathy-and myopathy-associated mutations in human small heat shock proteins: characteristics and evolutionary history of the mutation sites. Mutat Res Rev Mutat Res 761:15–30

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bertz M, Rief M (2008) Mechanical unfoldons as building blocks of maltose-binding protein. J Mol Biol 378(2):447–458

    CAS  PubMed  Google Scholar 

  • Bertz M, Kunfermann A, Rief M (2008) Navigating the folding energy landscape of green fluorescent protein. Angew Chem Int Ed 47(43):8192–8195

    CAS  Google Scholar 

  • Bertz M, Chen J, Feige MJ, Franzmann TM, Buchner J, Rief M (2010) Structural and mechanical hierarchies in the α-crystallin domain dimer of the hyperthermophilic small heat shock protein Hsp16. 5. J Mol Biol 400(5):1046–1056

    CAS  PubMed  Google Scholar 

  • Boncoraglio A, Minoia M, Carra S (2012) The family of mammalian small heat shock proteins (HSPBs): implications in protein deposit diseases and motor neuropathies. Int J Biochem Cell Biol 44(10):1657–1669

    CAS  PubMed  Google Scholar 

  • Bonorino C, Sistonen L, Eriksson J, Mezger V, Santoro G, Hightower LE (2018). The VIII international congress on stress proteins in biology and medicine: täynnä henkeä. Cell Stress Chaperones 23(2): 171–177

  • Borgia MB, Borgia A, Best RB, Steward A, Nettels D, Wunderlich B, Schuler B, Clarke J (2011) Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature 474(7353):662

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bukau B, Weissman J, Horwich A (2006) Molecular chaperones and protein quality control. Cell 125(3):443–451

    CAS  PubMed  Google Scholar 

  • Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273(5278):1058–1073

    CAS  PubMed  Google Scholar 

  • Bustamante C, Macosko JC, Wuite GJ (2000) Grabbing the cat by the tail: manipulating molecules one by one. Nat Rev Mol Cell Biol 1(2):130–136

    CAS  PubMed  Google Scholar 

  • Caldarini M, Sonar P, Valpapuram I, Tavella D, Volonté C, Pandini V, Vanoni M, Aliverti A, Broglia R, Tiana G (2014) The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations. Biophys Chem 195:32–42

    CAS  PubMed  Google Scholar 

  • Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM (1999) Mechanical and chemical unfolding of a single protein: a comparison. Proc Natl Acad Sci 96(7):3694–3699

    CAS  PubMed  PubMed Central  Google Scholar 

  • Caspers G-J, Leunissen JA, de Jong WW (1995) The expanding small heat-shock protein family, and structure predictions of the conserved “α-crystallin domain”. J Mol Evol 40(3):238–248

    CAS  PubMed  Google Scholar 

  • Cecconi C, Shank EA, Bustamante C, Marqusee S (2005) Direct observation of the three-state folding of a single protein molecule. Science 309(5743):2057–2060

    CAS  PubMed  Google Scholar 

  • Cecconi C, Shank EA, Dahlquist FW, Marqusee S, Bustamante C (2008) Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers. Eur Biophys J 37(6):729–738

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cecconi C, Shank EA, Marqusee S, Bustamante C (2011) DNA molecular handles for single-molecule protein-folding studies by optical tweezers. DNA Nanotechnology, Springer 255–271

  • Chen B, Retzlaff M, Roos T, Frydman J (2011) Cellular strategies of protein quality control. Cold Spring Harb Perspect Biol 3(8):a004374

    PubMed  PubMed Central  Google Scholar 

  • Choudhary D, Mossa A, Jadhav M, Cecconi C (2019) Bio-molecular applications of recent developments in optical tweezers. Biomolecules 9(1):23

    PubMed Central  Google Scholar 

  • Dame RT, Noom MC, Wuite GJ (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444(7117):387–390

    CAS  PubMed  Google Scholar 

  • de Jong WW, Leunissen JA, Voorter C (1993) Evolution of the alpha-crystallin/small heat-shock protein family. Mol Biol Evol 10(1):103–126

    PubMed  Google Scholar 

  • Delbecq SP, Klevit RE (2013) One size does not fit all: the oligomeric states of αB crystallin. FEBS Lett 587(8):1073–1080

    CAS  PubMed  Google Scholar 

  • Dierick I, Irobi J, De Jonghe P, Timmerman V (2005) Small heat shock proteins in inherited peripheral neuropathies. Ann Med 37(6):413–422

    CAS  PubMed  Google Scholar 

  • Dietz H, Rief M (2004) Exploring the energy landscape of GFP by single-molecule mechanical experiments. Proc Natl Acad Sci 101(46):16192–16197

    CAS  PubMed  PubMed Central  Google Scholar 

  • Elms PJ, Chodera JD, Bustamante C, Marqusee S (2012) The molten globule state is unusually deformable under mechanical force. Proc Natl Acad Sci 109(10):3796–3801

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gao Y, Sirinakis G, Zhang Y (2011) Highly anisotropic stability and folding kinetics of a single coiled coil protein under mechanical tension. J Am Chem Soc 133(32):12749–12757

    CAS  PubMed  PubMed Central  Google Scholar 

  • Genest O, Hoskins JR, Kravats AN, Doyle SM, Wickner S (2015) Hsp70 and Hsp90 of E. coli directly interact for collaboration in protein remodeling. J Mol Biol 427(24):3877–3889

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hainzl O, Lapina MC, Buchner J, Richter K (2009) The charged linker region is an important regulator of Hsp90 function. J Biol Chem 284(34):22559–22567

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475(7356):324–332

    CAS  PubMed  Google Scholar 

  • Haslbeck M, Weinkauf S, Buchner J (2019) Small heat shock proteins: simplicity meets complexity. J Biol Chem 294(6):2121–2132

    CAS  PubMed  Google Scholar 

  • Heidarsson PTO, Valpapuram I, Camilloni C, Imparato A, Tiana G, Poulsen FM, Kragelund BB, Cecconi C (2012) A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway. J Am Chem Soc 134(41):17068–17075

    CAS  PubMed  Google Scholar 

  • Heidarsson PO, Otazo MR, Bellucci L, Mossa A, Imparato A, Paci E, Corni S, Di Felice R, Kragelund BB, Cecconi C (2013) Single-molecule folding mechanism of an EF-hand neuronal calcium sensor. Structure 21(10):1812–1821

    CAS  PubMed  Google Scholar 

  • Hessling M, Richter K, Buchner J (2009) Dissection of the ATP-induced conformational cycle of the molecular chaperone Hsp90. Nat Struct Mol Biol 16(3):287–293

    CAS  PubMed  Google Scholar 

  • Hipp MS, Kasturi P, Hartl FU (2019) The proteostasis network and its decline in ageing. Nat Rev Mol Cell Biol 1

  • Ito H, Okamoto K, Nakayama H, Isobe T, Kato K (1997) Phosphorylation of αB-crystallin in response to various types of stress. J Biol Chem 272(47):29934–29941

    CAS  PubMed  Google Scholar 

  • Jahn M, Rehn A, Pelz B, Hellenkamp B, Richter K, Rief M, Buchner J, Hugel T (2014) The charged linker of the molecular chaperone Hsp90 modulates domain contacts and biological function. Proc Natl Acad Sci 111(50):17881–17886

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jahn M, Buchner J, Hugel T, Rief M (2016) Folding and assembly of the large molecular machine Hsp90 studied in single-molecule experiments. Proc Natl Acad Sci 113(5):1232–1237

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jahn M, Tych K, Girstmair H, Steinmaßl M, Hugel T, Buchner J, Rief M (2018) Folding and domain interactions of three orthologs of Hsp90 studied by single-molecule force spectroscopy. Structure 26(1):96–105 e104

    CAS  PubMed  Google Scholar 

  • Kappé G, Franck E, Verschuure P, Boelens WC, Leunissen JA, de Jong WW (2003) The human genome encodes 10 α-crystallin–related small heat shock proteins: HspB1–10. Cell Stress Chaperones 8(1):53–61

    PubMed  PubMed Central  Google Scholar 

  • Kapur M, Ackerman SL (2018) mRNA translation gone awry: translation fidelity and neurological disease. Trends Genet 34(3):218–231

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kityk R, Kopp J, Sinning I, Mayer MP (2012) Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. Mol Cell 48(6):863–874

    CAS  PubMed  Google Scholar 

  • Klaips CL, Jayaraj GG, Hartl FU (2018) Pathways of cellular proteostasis in aging and disease. J Cell Biol 217(1):51–63

    CAS  PubMed  PubMed Central  Google Scholar 

  • Labbadia J, Morimoto RI (2015) The biology of proteostasis in aging and disease. Annu Rev Biochem 84:435–464

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee S, Hohng S (2013) An optical trap combined with three-color FRET. J Am Chem Soc 135(49):18260–18263

    CAS  PubMed  Google Scholar 

  • Li H, Linke WA, Oberhauser AF, Carrion-Vazquez M, Kerkvliet JG, Lu H, Marszalek PE, Fernandez JM (2002) Reverse engineering of the giant muscle protein titin. Nature 418(6901):998–1002

    CAS  PubMed  Google Scholar 

  • Mandal SS, Merz DR, Buchsteiner M, Dima RI, Rief M, Žoldák G (2017) Nanomechanics of the substrate binding domain of Hsp70 determine its allosteric ATP-induced conformational change. Proc Natl Acad Sci 114(23):6040–6045

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mashaghi A, Kramer G, Bechtluft P, Zachmann-Brand B, Driessen AJ, Bukau B, Tans SJ (2013) Reshaping of the conformational search of a protein by the chaperone trigger factor. Nature 500(7460):98

    CAS  PubMed  Google Scholar 

  • Mashaghi A, Bezrukavnikov S, Minde DP, Wentink AS, Kityk R, Zachmann-Brand B, Mayer MP, Kramer G, Bukau B, Tans SJ (2016) Alternative modes of client binding enable functional plasticity of Hsp70. Nature 539(7629):448–451

    CAS  PubMed  Google Scholar 

  • Mayer MP, Schröder H, Rüdiger S, Paal K, Laufen T, Bukau B (2000) Multistep mechanism of substrate binding determines chaperone activity of Hsp70. Nat Struct Mol Biol 7(7):586

    CAS  Google Scholar 

  • Neupane K, Foster DA, Dee DR, Yu H, Wang F, Woodside MT (2016) Direct observation of transition paths during the folding of proteins and nucleic acids. Science 352(6282):239–242

    CAS  PubMed  Google Scholar 

  • Nunes JM, Mayer-Hartl M, Hartl FU, Müller DJ (2015) Action of the Hsp70 chaperone system observed with single proteins. Nat Commun 6:6307

    CAS  PubMed  Google Scholar 

  • Perales-Calvo J, Giganti D, Stirnemann G, Garcia-Manyes S (2018) The force-dependent mechanism of DnaK-mediated mechanical folding. Sci Adv 4(2):eaaq0243

    PubMed  PubMed Central  Google Scholar 

  • Peschek J, Braun N, Rohrberg J, Back KC, Kriehuber T, Kastenmüller A, Weinkauf S, Buchner J (2013) Regulated structural transitions unleash the chaperone activity of αB-crystallin. Proc Natl Acad Sci 110(40):E3780–E3789

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pfitzner E, Wachauf C, Kilchherr F, Pelz B, Shih WM, Rief M, Dietz H (2013) Rigid DNA beams for high-resolution single-molecule mechanics. Angew Chem Int Ed 52(30):7766–7771

    CAS  Google Scholar 

  • Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276(5315):1109–1112

    CAS  PubMed  Google Scholar 

  • Ritchie DB, Woodside MT (2015) Probing the structural dynamics of proteins and nucleic acids with optical tweezers. Curr Opin Struct Biol 34:43–51

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sandal M, Valle F, Tessari I, Mammi S, Bergantino E, Musiani F, Brucale M, Bubacco L, Samorì B (2008) Conformational equilibria in monomeric α-synuclein at the single-molecule level. PLoS Biol 6(1):e6

    PubMed  PubMed Central  Google Scholar 

  • Scholz C, Zarnt T, Kern G, Lang K, Burtscher H, Fischer G, Schmid FX (1996) Autocatalytic folding of the folding catalyst FKBP12. J Biol Chem 271(22):12703–12707

    CAS  PubMed  Google Scholar 

  • Schopf FH, Biebl MM, Buchner J (2017) The HSP90 chaperone machinery. Nat Rev Mol Cell Biol 18(6):345–360

    CAS  PubMed  Google Scholar 

  • Schröder H, Langer T, Hartl F, Bukau B (1993) DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage. EMBO J 12(11):4137–4144

    PubMed  PubMed Central  Google Scholar 

  • Schwaiger I, Kardinal A, Schleicher M, Noegel AA, Rief M (2004) A mechanical unfolding intermediate in an actin-crosslinking protein. Nat Struct Mol Biol 11(1):81–85

    CAS  PubMed  Google Scholar 

  • Shank EA, Cecconi C, Dill JW, Marqusee S, Bustamante C (2010) The folding cooperativity of a protein is controlled by its chain topology. Nature 465(7298):637–640

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shibata Y, Morimoto RI (2014) How the nucleus copes with proteotoxic stress. Curr Biol 24(10):R463–R474

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sirinakis G, Ren Y, Gao Y, Xi Z, Zhang Y (2012) Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy. Rev Sci Instrum 83(9):093708

    PubMed  PubMed Central  Google Scholar 

  • Skowyra D, Georgopoulos C, Zylicz M (1990) The E. coli dnaK gene product, the hsp70 homolog, can reactivate heat-inactivated RNA polymerase in an ATP hydrolysis-dependent manner. Cell 62(5):939–944

    CAS  PubMed  Google Scholar 

  • Stigler J, Ziegler F, Gieseke A, Gebhardt JCM, Rief M (2011) The complex folding network of single calmodulin molecules. Science 334(6055):512–516

    CAS  PubMed  Google Scholar 

  • Szabo A, Langer T, Schröder H, Flanagan J, Bukau B, Hartl FU (1994) The ATP hydrolysis-dependent reaction cycle of the Escherichia coli Hsp70 system DnaK, DnaJ, and GrpE. Proc Natl Acad Sci 91(22):10345–10349

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tissiéres A, Mitchell HK, Tracy UM (1974) Protein synthesis in salivary glands of Drosophila melanogaster: relation to chromosome puffs. J Mol Biol 84(3):389–398

    PubMed  Google Scholar 

  • Ungelenk S, Moayed F, Ho C-T, Grousl T, Scharf A, Mashaghi A, Tans S, Mayer MP, Mogk A, Bukau B (2016) Small heat shock proteins sequester misfolding proteins in near-native conformation for cellular protection and efficient refolding. Nat Commun 7:13673

    PubMed  PubMed Central  Google Scholar 

  • van Montfort RL, Basha E, Friedrich KL, Slingsby C, Vierling E (2001) Crystal structure and assembly of a eukaryotic small heat shock protein. Nat Struct Mol Biol 8(12):1025

    Google Scholar 

  • Wen J-D, Manosas M, Li PT, Smith SB, Bustamante C, Ritort F, Tinoco I Jr (2007) Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys J 92(9):2996–3009

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wright CF, Teichmann SA, Clarke J, Dobson CM (2005) The importance of sequence diversity in the aggregation and evolution of proteins. Nature 438(7069):878–881

    CAS  PubMed  Google Scholar 

  • Yang G, Cecconi C, Baase WA, Vetter IR, Breyer WA, Haack JA, Matthews BW, Dahlquist FW, Bustamante C (2000) Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. Proc Natl Acad Sci 97(1):139–144

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

S.C and C.C. acknowledge funding by Italian Ministry of University and Research (MIUR), Departments of excellence 2018–2022; E91I18001480001, PRIN—Progetti di Ricerca di Interesse Nazionale (2017 EX_ALS) and University of Modena and Reggio Emilia (FAR 2016).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Serena Carra or Ciro Cecconi.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Choudhary, D., Mediani, L., Carra, S. et al. Studying heat shock proteins through single-molecule mechanical manipulation. Cell Stress and Chaperones 25, 615–628 (2020). https://doi.org/10.1007/s12192-020-01096-y

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12192-020-01096-y

Keywords

Navigation