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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 747))

Abstract

The specific self-association of proteins to form homodimers and higher order oligomers is an extremely common event in biological systems. In this chapter we review the prevalence of protein oligomerization and discuss the likely origins of this phenomenon. We also outline many of the functional advantages conferred by the dimerization or oligomerization of a wide range of different proteins and in a variety of biological roles, that are likely to have placed a selective pressure on biological systems to evolve and maintain homodimerization/oligomerization interfaces.

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References

  1. Marianayagam NJ, Sunde M, Matthews JM. The power of two:protein dimerization in biology. Trends Biochem Sci 2004; 29:618–625.

    Article  CAS  PubMed  Google Scholar 

  2. Krissinel E. Macromolecular complexes in crystals and solutions. Acta Crystallog D, Biol Crystallog 2011; 67:376–385.

    Article  CAS  Google Scholar 

  3. Ispolatov I, Yuryev A, Mazo I et al. Binding properties and evolution of homodimers in protein-protein interaction networks. Nucl Acids Res 2005; 33:3629–3635.

    Article  CAS  PubMed  Google Scholar 

  4. Jacques D, Trewhella J. Small-angle scattering for structural biology—expanding the frontier while avoiding the pitfalls. Protein Sci 2010; 19:642–657.

    Article  CAS  PubMed  Google Scholar 

  5. Lukatsky DB, Shakhnovich BE, Mintseris J et al. Structural similarity enhances interaction propensity of proteins. J Mol Biol 2007; 365:1596–1606.

    Article  CAS  PubMed  Google Scholar 

  6. Dey S, Pal A, Chakrabarti P et al. The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 2010; 398:146–160.

    Article  CAS  PubMed  Google Scholar 

  7. Pearce MJ, Mintseris J, Ferreyra J et al. Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Science 2008; 322:1104–1107.

    Article  CAS  PubMed  Google Scholar 

  8. Darwin KH. Prokaryotic ubiquitin-like protein (Pup), proteasomes and pathogenesis. Nat Rev Microbiol 2009; 7:485–491.

    Article  CAS  PubMed  Google Scholar 

  9. Beckett D. Regulated assembly of transcription factors and control of transcription initiation. J Mol Biol 2001; 314:335–352.

    Article  CAS  PubMed  Google Scholar 

  10. Pereira-Leal JB, Levy ED, Kamp C et al. Evolution of protein complexes by duplication of homomeric interactions. Genome Biol 2007; 8:R51.

    Article  Google Scholar 

  11. Aragues R, Sali A, Bonet J et al. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comp Biol 2007; 3:1761–1771.

    Article  CAS  Google Scholar 

  12. Bahadur RP, Chakrabarti P, Rodier F et al. Dissecting subunit interfaces in homodimeric proteins. Prot Struct Funct Genetics 2003; 53:708–719.

    Article  CAS  Google Scholar 

  13. Yatime L, Hein KL, Nilsson J et al. Structure of the RACK1 dimer from Saccharomyces cerevisiae. J Mol Biol 2011; 411:486–498.

    Article  CAS  PubMed  Google Scholar 

  14. Hopfner KP, Craig L, Moncalian G et al. The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature 2002; 418:562–566.

    Article  CAS  PubMed  Google Scholar 

  15. Cahill D, Carney JP. Dimerization of the Rad50 protein is independent of the conserved hook domain. Mutagenesis 2007; 22:269–274.

    Article  CAS  PubMed  Google Scholar 

  16. Gilmore R, Coffey MC, Leone G et al. Co-translational trimerization of the reovirus cell attachment protein. EMBO J 1996; 15:2651–2658.

    CAS  PubMed  Google Scholar 

  17. Christis C, Lubsen NH, Braakman I. Protein folding includes oligomerization—examples from the endoplasmic reticulum and cytosol. FEBS J 2008; 275:4700–4727.

    Article  CAS  PubMed  Google Scholar 

  18. Yu X, Kong Y, Dore LC et al. An erythroid chaperone that facilitates folding of alpha-globin subunits for hemoglobin synthesis. J Clin Invest 2007; 117:1856–1865.

    Article  CAS  PubMed  Google Scholar 

  19. Zhang X, Beuron F, Freemont PS. Machinery of protein folding and unfolding. Curr Opin Struct Biol 2002; 12:231–238.

    Article  PubMed  Google Scholar 

  20. Yonehara M, Minami Y, Kawata Y et al. Heat-induced chaperone activity of HSP90. J Biol Chem 1996; 271:2641–2645.

    Article  CAS  PubMed  Google Scholar 

  21. Jorgensen CS, Ryder LR, Steino A et al. Dimerization and oligomerization of the chaperone calreticulin. Eur J Biochem 2003; 270:4140–4148.

    Article  CAS  PubMed  Google Scholar 

  22. Ishikawa T, Maurizi MR, Belnap D et al. Docking of components in a bacterial complex. Nature 2000; 408:667–668.

    Article  CAS  PubMed  Google Scholar 

  23. Donaldson LW, Wojtyra U, Houry WA. Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J Biol Chem 2003; 278:48991–48996.

    Article  CAS  PubMed  Google Scholar 

  24. Ogura T, Wilkinson AJ. AAA+ superfamily ATPases: common structure—diverse function. Gene Cell 2001; 6:575–597.

    Article  CAS  Google Scholar 

  25. la Cour T, Kiemer L, Mølgaard A et al. Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel 2004; 17:527–536.

    Article  PubMed  Google Scholar 

  26. Kutay U, Güttinger S. Leucine-rich nuclear-export signals: born to be weak. Trends Cell Biol 2005; 15:121–124.

    Article  CAS  PubMed  Google Scholar 

  27. Dong X, Biswas A, Suel KE et al. Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 2009; 458:1136–1141.

    Article  CAS  PubMed  Google Scholar 

  28. Monecke T, Guttler T, Neumann P et al. Crystal structure of the nuclear export receptor CRM1 in complex with Snurportinl and RanGTP. Science 2009; 324:1087–1091.

    Article  CAS  PubMed  Google Scholar 

  29. Stommel JM, Marchenko ND, Jimenez GS et al. A leucine-rich nuclear export signal in the p53 tetramerization domain: regulation of subcellular localization and p53 activity by NES masking. EMBO J 1999; 18:1660–1672.

    Article  CAS  PubMed  Google Scholar 

  30. Pauling L. The oxygen equilibrium of hemoglobin and its structural interpretation. Proc Natl Acad Sci USA 1935; 21:186–191.

    Article  CAS  PubMed  Google Scholar 

  31. Monod J, Jacob F. Teleonomic mechanisms in cellular metabolism, growth and differentiation. Cold Spring Harb Symp Quant Biol 1961; 26:389–401.

    Article  CAS  PubMed  Google Scholar 

  32. Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Sci 2008; 17:1295–1307.

    Article  CAS  PubMed  Google Scholar 

  33. Wei H, Zhou MM. Dimerization of a viral SET protein endows its function. Proc Natl Acad Sci USA 2010; 107:18433–18438.

    Article  CAS  PubMed  Google Scholar 

  34. Brown RJ, Adams JJ, Pelekanos RA et al. Model for growth hormone receptor activation based on subunit rotation within a receptor dimer. Nat Struct Mol Biol 2005; 12:814–821.

    Article  CAS  PubMed  Google Scholar 

  35. Seubert N, Royer Y, Staerk J et al. Active and inactive orientations of the transmembrane and cytosolic domains of the erythropoietin receptor dimer. Mol Cell 2003; 12:1239–1250.

    Article  CAS  PubMed  Google Scholar 

  36. Woodcock JM, McClure BJ, Stomski FC et al. The human granulocyte-macrophage colony-stimulating factor (GM-CSF ) receptor exists as a preformed receptor complex that can be activated by GM-CSF, interleukin-3, or interleukin-5. Blood 1997; 90:3005–3017.

    CAS  PubMed  Google Scholar 

  37. Lopez AF, Hercus TR, Ekert P et al. Molecular basis of cytokine receptor activation. IUBMB Life 2010; 62:509–518.

    Article  CAS  PubMed  Google Scholar 

  38. Boulanger MJ, Chow D-c, Brevnova EE et al. Hexameric structure and assembly of the interleukin-6/il-6 α-receptor/gp130 complex. Science 2003; 300:2101–2104.

    Article  CAS  PubMed  Google Scholar 

  39. Hansen G, Hercus TR, McClure BJ et al. The structure of the GM-CSF receptor complex reveals a distinct mode of cytokine receptor activation. Cell 2008; 134:496–507.

    Article  CAS  PubMed  Google Scholar 

  40. Yu X, Sharma KD, Takahashi T et al. Ligand-independent dimer formation of epidermal growth factor receptor (EGFR) is a step separable from ligand-induced EGFR signaling. Mol Biol Cell 2002; 13:2547–2557.

    Google Scholar 

  41. Mukai Y, Nakamura T, Yoshikawa M et al. Solution of the structure of the TNF-TNFR2 complex. Sci Signal 2010; 3:ra83-.

    Article  Google Scholar 

  42. Chan FK, Chun HJ, Zheng L et al. A domain in TNF receptors that mediates ligand-independent receptor assembly and signaling. Science 2000; 288:2351–2354.

    Article  CAS  PubMed  Google Scholar 

  43. Clancy L, Mruk K, Archer K et al. Preligand assembly domain-mediated ligand-independent association between TRAIL receptor 4 (TR4) and TR2 regulates TRAIL-induced apoptosis. Proc Natl Acad Sci USA 2005; 102:18099–18104.

    Article  CAS  PubMed  Google Scholar 

  44. Wassenaar TA, Quax WJ, Mark AE. The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study. Proteins 2008; 70:333–343.

    Article  CAS  PubMed  Google Scholar 

  45. Woolf PJ, Linderman JJ. Self organization of membrane proteins via dimerization. Biophys Chem 2003; 104:217–227.

    Article  CAS  PubMed  Google Scholar 

  46. Chabre M, Deterre P, Antonny B. The apparent cooperativity of some GPCRs does not necessarily imply dimerization. Trends Pharmacol Sci 2009; 30:182–187.

    Article  CAS  PubMed  Google Scholar 

  47. Milligan G. The role of dimerisation in the cellular trafficking of G-protein-coupled receptors. Curr Opin Pharmacol 2010; 10:23–29.

    Article  CAS  PubMed  Google Scholar 

  48. Whorton MR, Bokoch MP, Rasmussen SG et al. A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein. Proc Natl Acad Sci USA 2007; 104:7682–7687.

    Article  CAS  PubMed  Google Scholar 

  49. Maurel D, Comps-Agrar L, Brock C et al. Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies: application to GPCR oligomerization. Nat Methods 2008; 5:561–567.

    Article  CAS  PubMed  Google Scholar 

  50. Wilson S, Wilkinson G, Milligan G. The CXCR1 and CXCR2 receptors form constitutive homo-and heterodimers selectively and with equal apparent affinities. J Biol Chem 2005; 280:28663–28674.

    Article  CAS  PubMed  Google Scholar 

  51. Gurevich VV, Gurevich EV. GPCR monomers and oligomers: it takes all kinds. Trends Neurosci 2008; 31:74–81.

    Article  CAS  PubMed  Google Scholar 

  52. Gonen T, Walz T. The structure of aquaporins. Q Rev Biophys 2006; 39:361–396.

    Article  CAS  PubMed  Google Scholar 

  53. Raja M. Diverse gating in K(+) channels: Differential role of the pore-helix glutamate in stabilizing the channel pore. Biochem Biophys Res Comm 2011.

    Google Scholar 

  54. Singh H. Two decades with dimorphic Chloride Intracellular Channels (CLICs). FEBS Lett 2010; 584:2112–2121.

    Article  CAS  PubMed  Google Scholar 

  55. Cockerill PN. Structure and function of active chromatin and DNase I hypersensitive sites. FEBS Journal 2011; 278:2182–2210.

    Article  CAS  PubMed  Google Scholar 

  56. Matthews JM, Visvader JE. LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins. EMBO Rep 2003; 4:1132–1137.

    Article  CAS  PubMed  Google Scholar 

  57. Cross AJ, Jeffries CM, Trewhella J et al. LIM Domain Binding Proteins 1 and 2 Have Different Oligomeric States. J Mol Biol 2010; 399:133–144.

    Article  CAS  PubMed  Google Scholar 

  58. Breen JJ, Agulnick AD, Westphal H et al. Interactions between LIM domains and the LIM domain-binding protein Ldb1. J Biol Chem 1998; 273:4712–4717.

    Article  CAS  PubMed  Google Scholar 

  59. Song SH, Hou C, Dean A. A positive role for NLI/Ldb1 in long-range beta-globin locus control region function. Mol Cell 2007; 28:810–822.

    Article  CAS  PubMed  Google Scholar 

  60. Soler E, Andrieu-Soler C, de Boer E et al. The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes Dev 2010; 24:277–289.

    Article  CAS  PubMed  Google Scholar 

  61. Jurata LW, Pfaff SL, Gill GN. The nuclear LIM domain interactor NLI mediates homo-and heterodimerization of LIM domain transcription factors. J Biol Chem 1998; 273:3152–3157.

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Jacqueline M. Matthews .

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Matthews, J.M., Sunde, M. (2012). Dimers, Oligomers, Everywhere. In: Matthews, J.M. (eds) Protein Dimerization and Oligomerization in Biology. Advances in Experimental Medicine and Biology, vol 747. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3229-6_1

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