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Lighting up Nobel Prize-winning studies with protein intrinsic disorder

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Abstract

Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.

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References

  1. Uversky VN, Gillespie JR, Fink AL (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41(3):415–427

    Article  CAS  PubMed  Google Scholar 

  2. Dunker AK, Lawson JD, Brown CJ et al (2001) Intrinsically disordered protein. J Mol Graph Model 19(1):26–59

    Article  CAS  PubMed  Google Scholar 

  3. Tompa P (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27(10):527–533

    Article  CAS  PubMed  Google Scholar 

  4. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293(2):321–331

    Article  CAS  PubMed  Google Scholar 

  5. Ma B, Kumar S, Tsai CJ et al (1999) Folding funnels and binding mechanisms. Protein Eng 12(9):713–720

    Article  CAS  PubMed  Google Scholar 

  6. Tsai CJ, Kumar S, Ma B et al (1999) Folding funnels, binding funnels, and protein function. Protein Sci 8(6):1181–1190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Tsai CJ, Ma B, Nussinov R (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci USA 96(18):9970–9972

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254(5038):1598–1603

    Article  CAS  PubMed  Google Scholar 

  9. van der Lee R, Buljan M, Lang B et al (2014) Classification of intrinsically disordered regions and proteins. Chem Rev 114(13):6589–6631

    Article  PubMed  PubMed Central  Google Scholar 

  10. Uversky VN (2013) A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci 22(6):693–724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Dunker AK, Oldfield CJ (2015) Back to the future: nuclear magnetic resonance and bioinformatics studies on intrinsically disordered proteins. Adv Exp Med Biol 870:1–34

    Article  CAS  PubMed  Google Scholar 

  12. Dyson HJ, Wright PE (2019) Perspective: the essential role of NMR in the discovery and characterization of intrinsically disordered proteins. J Biomol NMR 73(12):651–659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Uversky VN (2019) Protein intrinsic disorder and structure-function continuum. Prog Mol Biol Transl Sci 166:1–17

    Article  CAS  PubMed  Google Scholar 

  14. Uversky VN (2020) New technologies to analyse protein function: an intrinsic disorder perspective. F1000Res 9:101

    Article  CAS  Google Scholar 

  15. Uversky VN (2021) Per aspera ad chaos: a personal journey to the wonderland of intrinsic disorder. Biochem J 478(15):3015–3024

    Article  CAS  PubMed  Google Scholar 

  16. Uversky VN, Kulkarni P (2021) Intrinsically disordered proteins: Chronology of a discovery. Biophys Chem 279:106694

    Article  CAS  PubMed  Google Scholar 

  17. Dunker AK, Garner E, Guilliot S et al (1998) Protein disorder and the evolution of molecular recognition: theory, predictions and observations. In: Pac Symp Biocomput, pp 473–484

  18. Daughdrill GW, Pielak GJ, Uversky VN et al (2005) Natively disordered proteins. In: Buchner J, Kiefhaber T (eds) Handbook of protein folding. Wiley-VCH, Verlag GmbH & Co. KGaA, Weinheim, pp 271–353

    Google Scholar 

  19. Uversky VN, Dunker AK (2010) Understanding protein non-folding. Biochim Biophys Acta 1804(6):1231–1264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Iakoucheva LM, Brown CJ, Lawson JD et al (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 323(3):573–584

    Article  CAS  PubMed  Google Scholar 

  21. Dunker AK, Cortese MS, Romero P et al (2005) Flexible nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 272(20):5129–5148

    Article  CAS  PubMed  Google Scholar 

  22. Uversky VN, Oldfield CJ, Dunker AK (2005) Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit 18(5):343–384

    Article  CAS  PubMed  Google Scholar 

  23. Dunker AK, Obradovic Z, Romero P et al (2000) Intrinsic protein disorder in complete genomes. Genome Inform Ser Workshop Genome Inform 11:161–171

    CAS  PubMed  Google Scholar 

  24. Ward JJ, Sodhi JS, McGuffin LJ et al (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337(3):635–645

    Article  CAS  PubMed  Google Scholar 

  25. Uversky VN (2010) The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome. J Biomed Biotechnol 2010:568068

    Article  PubMed  Google Scholar 

  26. Uversky VN, Oldfield CJ, Dunker AK (2008) Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 37:215–246

    Article  CAS  PubMed  Google Scholar 

  27. Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269(1):2–12

    Article  CAS  PubMed  Google Scholar 

  28. Williams RM, Obradovi Z, Mathura V et al (2001) The protein non-folding problem: amino acid determinants of intrinsic order and disorder. In: Pac Symp Biocomput, pp 89–100

  29. Romero P, Obradovic Z, Li X et al (2001) Sequence complexity of disordered protein. Proteins 42(1):38–48

    Article  CAS  PubMed  Google Scholar 

  30. Radivojac P, Iakoucheva LM, Oldfield CJ et al (2007) Intrinsic disorder and functional proteomics. Biophys J 92(5):1439–1456

    Article  CAS  PubMed  Google Scholar 

  31. Vacic V, Uversky VN, Dunker AK et al (2007) Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinform 8:211

    Article  Google Scholar 

  32. Garner E, Cannon P, Romero P et al (1998) Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Inform Ser Workshop Genome Inform 9:201–213

    CAS  PubMed  Google Scholar 

  33. He B, Wang K, Liu Y et al (2009) Predicting intrinsic disorder in proteins: an overview. Cell Res 19(8):929–949

    Article  CAS  PubMed  Google Scholar 

  34. Uversky VN (2003) Protein folding revisited. A polypeptide chain at the folding-misfolding-nonfolding cross-roads: which way to go? Cell Mol Life Sci 60(9):1852–1871

    Article  CAS  PubMed  Google Scholar 

  35. Zhang T, Faraggi E, Li Z et al (2013) Intrinsically semi-disordered state and its role in induced folding and protein aggregation. Cell Biochem Biophys 67(3):1193–1205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Dunker AK, Uversky VN (2010) Drugs for “protein clouds”: targeting intrinsically disordered transcription factors. Curr Opin Pharmacol 10(6):782–788

    Article  CAS  PubMed  Google Scholar 

  37. Choy WY, Forman-Kay JD (2001) Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J Mol Biol 308(5):1011–1032

    Article  CAS  PubMed  Google Scholar 

  38. Huang A, Stultz CM (2008) The effect of a DeltaK280 mutation on the unfolded state of a microtubule-binding repeat in Tau. PLoS Comput Biol 4(8):e1000155

    Article  PubMed  PubMed Central  Google Scholar 

  39. Strodel B (2021) Energy landscapes of protein aggregation and conformation switching in intrinsically disordered proteins. J Mol Biol 433(20):167182

    Article  CAS  PubMed  Google Scholar 

  40. Oliveira Junior AB, Lin X, Kulkarni P et al (2021) Exploring energy landscapes of intrinsically disordered proteins: insights into functional mechanisms. J Chem Theory Comput 17(5):3178–3187

    Article  CAS  PubMed  Google Scholar 

  41. Chebaro Y, Ballard AJ, Chakraborty D et al (2015) Intrinsically disordered energy landscapes. Sci Rep 5:10386

    Article  PubMed  PubMed Central  Google Scholar 

  42. Jensen MR, Zweckstetter M, Huang JR et al (2014) Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 114(13):6632–6660

    Article  CAS  PubMed  Google Scholar 

  43. Higo J, Umezawa K (2014) Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics. Adv Exp Med Biol 805:331–351

    Article  CAS  PubMed  Google Scholar 

  44. Uversky VN (2013) Unusual biophysics of intrinsically disordered proteins. Biochim Biophys Acta 1834(5):932–951

    Article  CAS  PubMed  Google Scholar 

  45. Uversky VN (2013) Intrinsic disorder-based protein interactions and their modulators. Curr Pharm Des 19(23):4191–4213

    Article  CAS  PubMed  Google Scholar 

  46. Jakob U, Kriwacki R, Uversky VN (2014) Conditionally and transiently disordered proteins: awakening cryptic disorder to regulate protein function. Chem Rev 114(13):6779–6805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Uversky VN (2015) Functional roles of transiently and intrinsically disordered regions within proteins. FEBS J 282(7):1182–1189

    Article  CAS  PubMed  Google Scholar 

  48. Dunker AK, Brown CJ, Lawson JD et al (2002) Intrinsic disorder and protein function. Biochemistry 41(21):6573–6582

    Article  CAS  PubMed  Google Scholar 

  49. Iakoucheva LM, Radivojac P, Brown CJ et al (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32(3):1037–1049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Uversky VN, Kutyshenko VP, Protasova N et al (1996) Circularly permuted dihydrofolate reductase possesses all the properties of the molten globule state, but can resume functional tertiary structure by interaction with its ligands. Protein Sci 5(9):1844–1851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Pervushin K, Vamvaca K, Vogeli B et al (2007) Structure and dynamics of a molten globular enzyme. Nat Struct Mol Biol 14(12):1202–1206

    Article  CAS  PubMed  Google Scholar 

  52. Vamvaca K, Jelesarov I, Hilvert D (2008) Kinetics and thermodynamics of ligand binding to a molten globular enzyme and its native counterpart. J Mol Biol 382(4):971–977

    Article  CAS  PubMed  Google Scholar 

  53. Woycechowsky KJ, Choutko A, Vamvaca K et al (2008) Relative tolerance of an enzymatic molten globule and its thermostable counterpart to point mutation. Biochemistry 47(51):13489–13496

    Article  CAS  PubMed  Google Scholar 

  54. Oldfield CJ, Meng J, Yang JY et al (2008) Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 9(Suppl 1):S1

    Article  PubMed  PubMed Central  Google Scholar 

  55. Nash P, Tang X, Orlicky S et al (2001) Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414(6863):514–521

    Article  CAS  PubMed  Google Scholar 

  56. Mittag T, Orlicky S, Choy WY et al (2008) Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. Proc Natl Acad Sci USA 105(46):17772–17777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Mittag T, Marsh J, Grishaev A et al (2010) Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18(4):494–506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Uversky VN (2011) Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes. Chem Soc Rev 40(3):1623–1634

    Article  CAS  PubMed  Google Scholar 

  59. Dyson HJ, Wright PE (2002) Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12(1):54–60

    Article  CAS  PubMed  Google Scholar 

  60. Oldfield CJ, Cheng Y, Cortese MS et al (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44(37):12454–12470

    Article  CAS  PubMed  Google Scholar 

  61. Tompa P, Fuxreiter M (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci 33(1):2–8

    Article  CAS  PubMed  Google Scholar 

  62. Hazy E, Tompa P (2009) Limitations of induced folding in molecular recognition by intrinsically disordered proteins. ChemPhysChem 10(9–10):1415–1419

    Article  CAS  PubMed  Google Scholar 

  63. Sigalov A, Aivazian D, Stern L (2004) Homooligomerization of the cytoplasmic domain of the T cell receptor zeta chain and of other proteins containing the immunoreceptor tyrosine-based activation motif. Biochemistry 43(7):2049–2061

    Article  CAS  PubMed  Google Scholar 

  64. Sigalov AB, Zhuravleva AV, Orekhov VY (2007) Binding of intrinsically disordered proteins is not necessarily accompanied by a structural transition to a folded form. Biochimie 89(3):419–421

    Article  CAS  PubMed  Google Scholar 

  65. Permyakov SE, Millett IS, Doniach S et al (2003) Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin. Proteins 53(4):855–862

    Article  CAS  PubMed  Google Scholar 

  66. Fuxreiter M (2012) Fuzziness: linking regulation to protein dynamics. Mol Biosyst 8(1):168–177

    Article  CAS  PubMed  Google Scholar 

  67. Fuxreiter M, Tompa P (2012) Fuzzy complexes: a more stochastic view of protein function. Adv Exp Med Biol 725:1–14

    Article  CAS  PubMed  Google Scholar 

  68. Sharma R, Raduly Z, Miskei M et al (2015) Fuzzy complexes: Specific binding without complete folding. FEBS Lett. https://doi.org/10.1016/j.febslet.2015.07.022

    Article  PubMed  Google Scholar 

  69. Uversky VN (2016) p53 proteoforms and intrinsic disorder: an illustration of the protein structure-function continuum concept. Int J Mol Sci 17(11):1874

    Article  PubMed Central  Google Scholar 

  70. Oates ME, Romero P, Ishida T et al (2013) D(2)P(2): database of disordered protein predictions. Nucleic Acids Res 41(Database issue):D508–D516

    CAS  PubMed  Google Scholar 

  71. Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596(7873):583–589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Mirdita M, Schütze K, Moriwaki Y et al (2022) ColabFold: making protein folding accessible to all. Nat Methods 19(6):679–682. https://doi.org/10.1038/s41592-022-01488-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Oldfield CJ, Cheng Y, Cortese MS et al (2005) Comparing and combining predictors of mostly disordered proteins. Biochemistry 44(6):1989–2000

    Article  CAS  PubMed  Google Scholar 

  74. Xue B, Oldfield CJ, Dunker AK et al (2009) CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions. FEBS Lett 583(9):1469–1474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Huang F, Oldfield CJ, Xue B et al (2014) Improving protein order-disorder classification using charge-hydropathy plots. BMC Bioinform 15(Suppl 17):S4

    Article  Google Scholar 

  76. Mohan A, Sullivan WJ Jr, Radivojac P et al (2008) Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes. Mol Biosyst 4(4):328–340

    Article  CAS  PubMed  Google Scholar 

  77. Huang F, Oldfield C, Meng J et al (2012) Subclassifying disordered proteins by the CH-CDF plot method. In: Pac Symp Biocomput, pp 128–39

  78. Rajagopalan K, Mooney SM, Parekh N et al (2011) A majority of the cancer/testis antigens are intrinsically disordered proteins. J Cell Biochem 112(11):3256–3267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Obradovic Z, Peng K, Vucetic S et al (2005) Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 61(S7):176–182

    Article  CAS  PubMed  Google Scholar 

  80. Peng K, Radivojac P, Vucetic S et al (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinform 7:208

    Article  Google Scholar 

  81. Necci M, Piovesan D, Predictors C et al (2021) Critical assessment of protein intrinsic disorder prediction. Nat Methods 18(5):472–481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Peng K, Vucetic S, Radivojac P et al (2005) Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol 3(01):35–60

    Article  CAS  PubMed  Google Scholar 

  83. Xue B, Dunbrack RL, Williams RW et al (2010) PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1804(4):996–1010

    Article  CAS  Google Scholar 

  84. Meszaros B, Erdos G, Dosztanyi Z (2018) IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res 46(W1):W329–W337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. The Nobel Prize in Physiology or Medicine 1965 (2022) https://www.nobelprize.org/prizes/medicine/1965/summary/

  86. Liu J, Perumal NB, Oldfield CJ et al (2006) Intrinsic disorder in transcription factors. Biochemistry 45(22):6873–6888

    Article  CAS  PubMed  Google Scholar 

  87. Tarczewska A, Greb-Markiewicz B (2019) The significance of the intrinsically disordered regions for the functions of the bHLH transcription factors. Int J Mol Sci 20(21):5306

    Article  CAS  PubMed Central  Google Scholar 

  88. Gowers DM, Halford SE (2003) Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling. EMBO J 22(6):1410–1418

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Kalodimos CG, Biris N, Bonvin AM et al (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305(5682):386–389

    Article  CAS  PubMed  Google Scholar 

  90. Gitlin L, Hagai T, LaBarbera A et al (2014) Rapid evolution of virus sequences in intrinsically disordered protein regions. PLoS Pathog 10(12):e1004529

    Article  PubMed  PubMed Central  Google Scholar 

  91. The Nobel Prize in Physiology or Medicine 1977 (2022) https://www.nobelprize.org/prizes/medicine/1977/summary/

  92. Harris GW (1955) Neural control of the pituitary gland, vol 3. Eward Arnold, London

    Google Scholar 

  93. Spiess J, Rivier J, Rivier C et al (1981) Primary structure of corticotropin-releasing factor from ovine hypothalamus. Proc Natl Acad Sci USA 78(10):6517–6521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Whitfeld PL, Seeburg PH, Shine J (1982) The human pro-opiomelanocortin gene: organization, sequence, and interspersion with repetitive DNA. DNA 1(2):133–143

    Article  CAS  PubMed  Google Scholar 

  95. Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276(5688):565–570

    Article  CAS  PubMed  Google Scholar 

  96. Nusslein-Volhard C, Wieschaus E (1980) Mutations affecting segment number and polarity in Drosophila. Nature 287(5785):795–801

    Article  CAS  PubMed  Google Scholar 

  97. Frasch M, Hoey T, Rushlow C et al (1987) Characterization and localization of the even-skipped protein of Drosophila. EMBO J 6(3):749–759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Hirsch JA, Aggarwal AK (1995) Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J 14(24):6280–6291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Harding K, Rushlow C, Doyle HJ et al (1986) Cross-regulatory interactions among pair-rule genes in Drosophila. Science 233(4767):953–959

    Article  CAS  PubMed  Google Scholar 

  100. Macdonald PM, Ingham P, Struhl G (1986) Isolation, structure, and expression of even-skipped: a second pair-rule gene of Drosophila containing a homeo box. Cell 47(5):721–734

    Article  CAS  PubMed  Google Scholar 

  101. Kotra LP (2008) Infectious diseases. xPharm Compr Pharmacol Ref 2007:1-2. https://doi.org/10.1016/B978-008055232-3.60849-9

    Article  Google Scholar 

  102. Colby DW, Prusiner SB (2011) Prions. Cold Spring Harb Perspect Biol 3(1):a006833

    Article  PubMed  PubMed Central  Google Scholar 

  103. Cohen FE, Pan KM, Huang Z et al (1994) Structural clues to prion replication. Science 264(5158):530–531

    Article  CAS  PubMed  Google Scholar 

  104. Linden R, Martins VR, Prado MA et al (2008) Physiology of the prion protein. Physiol Rev 88(2):673–728

    Article  CAS  PubMed  Google Scholar 

  105. Guillot-Sestier MV, Sunyach C, Druon C et al (2009) The alpha-secretase-derived N-terminal product of cellular prion, N1, displays neuroprotective function in vitro and in vivo. J Biol Chem 284(51):35973–35986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Resenberger UK, Harmeier A, Woerner AC et al (2011) The cellular prion protein mediates neurotoxic signalling of beta-sheet-rich conformers independent of prion replication. EMBO J 30(10):2057–2070

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Brown DR, Qin K, Herms JW et al (1997) The cellular prion protein binds copper in vivo. Nature 390(6661):684–687

    Article  CAS  PubMed  Google Scholar 

  108. Taylor DR, Watt NT, Perera WS et al (2005) Assigning functions to distinct regions of the N-terminus of the prion protein that are involved in its copper-stimulated, clathrin-dependent endocytosis. J Cell Sci 118(Pt 21):5141–5153

    Article  CAS  PubMed  Google Scholar 

  109. Younan ND, Klewpatinond M, Davies P et al (2011) Copper(II)-induced secondary structure changes and reduced folding stability of the prion protein. J Mol Biol 410(3):369–382

    Article  CAS  PubMed  Google Scholar 

  110. Carlsson A (1959) The occurrence, distribution and physiological role of catecholamines in the nervous system. Pharmacol Rev 11(2, Part 2):490–493

    CAS  PubMed  Google Scholar 

  111. Greengard P, Valtorta F, Czernik AJ et al (1993) Synaptic vesicle phosphoproteins and regulation of synaptic function. Science 259(5096):780–785

    Article  CAS  PubMed  Google Scholar 

  112. Martin KC, Casadio A, Zhu H et al (1997) Synapse-specific, long-term facilitation of aplysia sensory to motor synapses: a function for local protein synthesis in memory storage. Cell 91(7):927–938

    Article  CAS  PubMed  Google Scholar 

  113. Scheggi S, De Montis MG, Gambarana C (2018) DARPP-32 in the orchestration of responses to positive natural stimuli. J Neurochem 147(4):439–453

    Article  CAS  PubMed  Google Scholar 

  114. Walaas SI, Greengard P (1984) DARPP-32, a dopamine- and adenosine 3’:5’-monophosphate-regulated phosphoprotein enriched in dopamine-innervated brain regions. I. Regional and cellular distribution in the rat brain. J Neurosci 4(1):84–98

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Halpain S, Girault JA, Greengard P (1990) Activation of NMDA receptors induces dephosphorylation of DARPP-32 in rat striatal slices. Nature 343(6256):369–372

    Article  CAS  PubMed  Google Scholar 

  116. Fernandez E, Schiappa R, Girault JA et al (2006) DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2(12):e176

    Article  PubMed  PubMed Central  Google Scholar 

  117. Lin TH, Huang YC, Chin ML et al (2004) 1H, 15N, and 13C resonance assignments of DARPP-32 (dopamine and cAMP-regulated phosphoprotein, Mr. 32,000)–a protein inhibitor of protein phosphatase-1. J Biomol NMR 28(4):413–414

    Article  CAS  PubMed  Google Scholar 

  118. Marsh JA, Dancheck B, Ragusa MJ et al (2010) Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators. Structure 18(9):1094–1103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Montminy M (1997) Transcriptional regulation by cyclic AMP. Annu Rev Biochem 66:807–822

    Article  CAS  PubMed  Google Scholar 

  120. Dash PK, Hochner B, Kandel ER (1990) Injection of the cAMP-responsive element into the nucleus of Aplysia sensory neurons blocks long-term facilitation. Nature 345(6277):718–721

    Article  CAS  PubMed  Google Scholar 

  121. Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447(7147):1021–1025

    Article  CAS  PubMed  Google Scholar 

  122. Huang Y, Liu Z (2010) Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins. PLoS ONE 5(11):e15375

    Article  PubMed  PubMed Central  Google Scholar 

  123. Dahal L, Kwan TOC, Shammas SL et al (2017) pKID binds to KIX via an unstructured transition state with nonnative interactions. Biophys J 113(12):2713–2722

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Dahal L, Shammas SL, Clarke J (2017) Phosphorylation of the IDP KID modulates affinity for KIX by increasing the lifetime of the complex. Biophys J 113(12):2706–2712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Kelly C, Kuravsky M, Redfield C, Shammas SL (2020) The dynamic search mode of a disordered transcription factor. Biophys J 118(3):6a

    Article  Google Scholar 

  126. Thelander L (2020) Ubiquitin-mediated proteolysis. Advanced information on the Nobel Prize in Chemistry 2004. https://www.nobelprize.org/uploads/2018/06/advanced-chemistryprize2004-1.pdf

  127. Catic A, Collins C, Church GM et al (2004) Preferred in vivo ubiquitination sites. Bioinformatics 20(18):3302–3307

    Article  CAS  PubMed  Google Scholar 

  128. Hagai T, Azia A, Toth-Petroczy A et al (2011) Intrinsic disorder in ubiquitination substrates. J Mol Biol 412(3):319–324

    Article  CAS  PubMed  Google Scholar 

  129. Guharoy M, Bhowmick P, Sallam M et al (2016) Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system. Nat Commun 7(1):10239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Tomita T, Matouschek A (2019) Substrate selection by the proteasome through initiation regions. Protein Sci 28(7):1222–1232

    CAS  PubMed  PubMed Central  Google Scholar 

  131. Fishbain S, Inobe T, Israeli E et al (2015) Sequence composition of disordered regions fine-tunes protein half-life. Nat Struct Mol Biol 22(3):214–221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Bhowmick P, Pancsa R, Guharoy M et al (2013) Functional diversity and structural disorder in the human ubiquitination pathway. PLoS ONE 8(5):e65443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Stewart MD, Ritterhoff T, Klevit RE et al (2016) E2 enzymes: more than just middle men. Cell Res 26(4):423–440

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Vittal V, Shi L, Wenzel DM et al (2015) Intrinsic disorder drives N-terminal ubiquitination by Ube2w. Nat Chem Biol 11(1):83–89

    Article  CAS  PubMed  Google Scholar 

  135. Service RF (2006) Nobel Prize in chemistry. Solo winner detailed path from DNA to RNA. Science 314(5797):236

    Article  PubMed  Google Scholar 

  136. Cramer P, Bushnell DA, Fu J et al (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288(5466):640–649

    Article  CAS  PubMed  Google Scholar 

  137. Cramer P, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292(5523):1863–1876

    Article  CAS  PubMed  Google Scholar 

  138. Piovesan D, Tabaro F, Paladin L et al (2018) MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res 46(D1):D471–D476

    Article  CAS  PubMed  Google Scholar 

  139. Suh H, Hazelbaker DZ, Soares LM et al (2013) The C-terminal domain of Rpb1 functions on other RNA polymerase II subunits. Mol Cell 51(6):850–858

    Article  CAS  PubMed  Google Scholar 

  140. Harlen KM, Churchman LS (2017) The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol 18(4):263–273

    Article  CAS  PubMed  Google Scholar 

  141. Hahn S (2004) Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol 11(5):394–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Ishiguro A, Nogi Y, Hisatake K et al (2000) The Rpb6 subunit of fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol Cell Biol 20(4):1263–1270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Tan Q, Prysak MH, Woychik NA (2003) Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol Cell Biol 23(9):3329–3338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Armache KJ, Kettenberger H, Cramer P (2003) Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci USA 100(12):6964–6968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Ramakrishnan V (2002) Ribosome structure and the mechanism of translation. Cell 108(4):557–572

    Article  CAS  PubMed  Google Scholar 

  146. Nissen P, Hansen J, Ban N et al (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289(5481):920–930

    Article  CAS  PubMed  Google Scholar 

  147. Glotz C, Mussig J, Gewitz HS et al (1987) Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria. Biochem Int 15(5):953–960

    CAS  PubMed  Google Scholar 

  148. Schuwirth BS, Borovinskaya MA, Hau CW et al (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science 310(5749):827–834

    Article  CAS  PubMed  Google Scholar 

  149. Peng Z, Oldfield CJ, Xue B et al (2014) A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome. Cell Mol Life Sci 71(8):1477–1504

    Article  CAS  PubMed  Google Scholar 

  150. Semrad K, Green R, Schroeder R (2004) RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli. RNA 10(12):1855–1860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Muller EC, Wittmann-Liebold B (1997) Phylogenetic relationship of organisms obtained by ribosomal protein comparison. Cell Mol Life Sci 53(1):34–50

    Article  CAS  PubMed  Google Scholar 

  152. Diedrich G, Spahn CM, Stelzl U et al (2000) Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transfer. EMBO J 19(19):5241–5250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Kaltschmidt E (1971) Ribosomal proteins. XIV. Isoelectric points of ribosomal proteins of E. coli as determined by two-dimensional polyacrylamide gel electrophoresis. Anal Biochem 43(1):25–31

    Article  CAS  PubMed  Google Scholar 

  154. Wilson DN, Nierhaus KH (2005) Ribosomal proteins in the spotlight. Crit Rev Biochem Mol Biol 40(5):243–267

    Article  CAS  PubMed  Google Scholar 

  155. Khaitovich P, Tenson T, Mankin AS et al (1999) Peptidyl transferase activity catalyzed by protein-free 23S ribosomal RNA remains elusive. RNA 5(5):605–608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Polacek N, Mankin AS (2005) The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit Rev Biochem Mol Biol 40(5):285–311

    Article  CAS  PubMed  Google Scholar 

  157. Chen JW, Romero P, Uversky VN et al (2006) Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. J Proteome Res 5(4):879–887

    Article  PubMed  PubMed Central  Google Scholar 

  158. Chen JW, Romero P, Uversky VN et al (2006) Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder. J Proteome Res 5(4):888–898

    Article  PubMed  PubMed Central  Google Scholar 

  159. Timsit Y, Acosta Z, Allemand F et al (2009) The role of disordered ribosomal protein extensions in the early steps of eubacterial 50 S ribosomal subunit assembly. Int J Mol Sci 10(3):817–834

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Nierhaus KH (1991) The assembly of prokaryotic ribosomes. Biochimie 73(6):739–755

    Article  CAS  PubMed  Google Scholar 

  161. Spillmann S, Dohme F, Nierhaus KH (1977) Assembly in vitro of the 50 S subunit from Escherichia coli ribosomes: proteins essential for the first heat-dependent conformational change. J Mol Biol 115(3):513–523

    Article  CAS  PubMed  Google Scholar 

  162. Vassilatis DK, Hohmann JG, Zeng H et al (2003) The G protein-coupled receptor repertoires of human and mouse. Proc Natl Acad Sci 100(8):4903–4908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Billington CK, Penn RB, Hall IP (2016) β 2 agonists. Pharmacology and therapeutics of asthma and COPD. Springer, Cham, pp 23–40

    Chapter  Google Scholar 

  164. Rasmussen SG, Choi H-J, Rosenbaum DM et al (2007) Crystal structure of the human β 2 adrenergic G-protein-coupled receptor. Nature 450(7168):383–387

    Article  CAS  PubMed  Google Scholar 

  165. Rasmussen SG, DeVree BT, Zou Y et al (2011) Crystal structure of the β 2 adrenergic receptor–Gs protein complex. Nature 477(7366):549–555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Butcher AJ, Prihandoko R, Kong KC et al (2011) Differential G-protein-coupled receptor phosphorylation provides evidence for a signaling bar code. J Biol Chem 286(13):11506–11518

    Article  CAS  PubMed  Google Scholar 

  167. Furness SG, Wootten D, Christopoulos A et al (2012) Consequences of splice variation on Secretin family G protein-coupled receptor function. Br J Pharmacol 166(1):98–109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Ozgur C, Doruker P, Akten ED (2016) Investigation of allosteric coupling in human β 2-adrenergic receptor in the presence of intracellular loop 3. BMC Struct Biol 16(1):9

    Article  PubMed  PubMed Central  Google Scholar 

  169. Boguth CA, Singh P, Huang CC et al (2010) Molecular basis for activation of G protein-coupled receptor kinases. EMBO J 29(19):3249–3259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Krasel C, Zabel U, Lorenz K et al (2008) Dual role of the β2-adrenergic receptor C terminus for the binding of β-arrestin and receptor internalization. J Biol Chem 283(46):31840–31848

    Article  CAS  PubMed  Google Scholar 

  171. Xiao K, Shenoy SK (2011) β2-adrenergic receptor lysosomal trafficking is regulated by ubiquitination of lysyl residues in two distinct receptor domains. J Biol Chem 286(14):12785–12795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Gurevich VV, Gurevich EV, Uversky VN (2018) Arrestins: structural disorder creates rich functionality. Protein Cell 9(12):986–1003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Fonin AV, Darling AL, Kuznetsova IM et al (2019) Multi-functionality of proteins involved in GPCR and G protein signaling: making sense of structure-function continuum with intrinsic disorder-based proteoforms. Cell Mol Life Sci 76(22):4461–4492

    Article  CAS  PubMed  Google Scholar 

  174. Gurdon JB, Uehlinger V (1966) “Fertile” intestine nuclei. Nature 210(5042):1240–1241

    Article  CAS  PubMed  Google Scholar 

  175. Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126(4):663–676

    Article  CAS  PubMed  Google Scholar 

  176. Yu J, Vodyanik MA, Smuga-Otto K et al (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318(5858):1917–1920

    Article  CAS  PubMed  Google Scholar 

  177. Xue B, Oldfield CJ, Van YY et al (2012) Protein intrinsic disorder and induced pluripotent stem cells. Mol Biosyst 8(1):134–150

    Article  CAS  PubMed  Google Scholar 

  178. Goodfellow PN, Lovell-Badge R (1993) SRY and sex determination in mammals. Annu Rev Genet 27:71–92

    Article  CAS  PubMed  Google Scholar 

  179. Remenyi A, Lins K, Nissen LJ et al (2003) Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev 17(16):2048–2059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Weiss MA (2001) Floppy SOX: mutual induced fit in hmg (high-mobility group) box-DNA recognition. Mol Endocrinol 15(3):353–362

    Article  CAS  PubMed  Google Scholar 

  181. Li J, Pan G, Cui K et al (2007) A dominant-negative form of mouse SOX2 induces trophectoderm differentiation and progressive polyploidy in mouse embryonic stem cells. J Biol Chem 282(27):19481–19492

    Article  CAS  PubMed  Google Scholar 

  182. Schaefer T, Lengerke C (2020) SOX2 protein biochemistry in stemness, reprogramming, and cancer: the PI3K/AKT/SOX2 axis and beyond. Oncogene 39(2):278–292

    Article  CAS  PubMed  Google Scholar 

  183. Wilson M, Koopman P (2002) Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators. Curr Opin Genet Dev 12(4):441–446

    Article  CAS  PubMed  Google Scholar 

  184. Schekman RW (2013) Nobel lecture: genes and proteins that control the secretory pathway. https://www.nobelprize.org/prizes/medicine/2013/schekman/lecture/

  185. Rothman JE (2013) Nobel lecture: the principle of membrane fusion in the cell. https://www.nobelprize.org/prizes/medicine/2013/rothman/lecture/

  186. Südhof TC (2013) Nobel lecture: the molecular machine of neurotransmitter release. https://www.nobelprize.org/prizes/medicine/2013/sudhof/lecture/?utm_source=twitter&utm_medium=social&utm_campaign=twitter_tweet

  187. Chua JJ, Kindler S, Boyken J et al (2010) The architecture of an excitatory synapse. J Cell Sci 123(Pt 6):819–823

    Article  CAS  PubMed  Google Scholar 

  188. Snead D, Eliezer D (2019) Intrinsically disordered proteins in synaptic vesicle trafficking and release. J Biol Chem 294(10):3325–3342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Jahn R, Scheller RH (2006) SNAREs–engines for membrane fusion. Nat Rev Mol Cell Biol 7(9):631–643

    Article  CAS  PubMed  Google Scholar 

  190. Mohrmann R, Dhara M, Bruns D (2015) Complexins: small but capable. Cell Mol Life Sci 72(22):4221–4235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Pabst S, Hazzard JW, Antonin W et al (2000) Selective interaction of complexin with the neuronal SNARE complex. Determination of the binding regions. J Biol Chem 275(26):19808–19818

    Article  CAS  PubMed  Google Scholar 

  192. Choi UB, Zhao M, Zhang Y et al (2016) Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex. Elife. https://doi.org/10.7554/eLife.16886

    Article  PubMed  PubMed Central  Google Scholar 

  193. Weninger K, Bowen ME, Choi UB et al (2008) Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex. Structure 16(2):308–320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Lai Y, Choi UB, Zhang Y et al (2016) N-terminal domain of complexin independently activates calcium-triggered fusion. Proc Natl Acad Sci USA 113(32):E4698–E4707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Maximov A, Tang J, Yang X et al (2009) Complexin controls the force transfer from SNARE complexes to membranes in fusion. Science 323(5913):516–521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Rizo J (2018) Mechanism of neurotransmitter release coming into focus. Protein Sci 27(8):1364–1391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Snead D, Lai AL, Wragg RT et al (2017) Unique structural features of membrane-bound C-terminal domain motifs modulate complexin inhibitory function. Front Mol Neurosci 10:154

    Article  PubMed  PubMed Central  Google Scholar 

  198. Lindahl T, Modrich P, Sancar A (2016) The 2015 Nobel Prize in chemistry the discovery of essential mechanisms that repair DNA damage. J Assoc Genet Technol 42(1):37–41

    PubMed  Google Scholar 

  199. Sakumi K, Sekiguchi M (1990) Structures and functions of DNA glycosylases. Mutat Res 236(2–3):161–172

    Article  CAS  PubMed  Google Scholar 

  200. Hossain MA, Lin Y, Yan S (2018) Single-strand break end resection in genome integrity: mechanism and regulation by APE2. Int J Mol Sci 19(8):2389

    Article  PubMed Central  Google Scholar 

  201. Krokan HE, Bjoras M (2013) Base excision repair. Cold Spring Harb Perspect Biol 5(4):a012583

    Article  PubMed  PubMed Central  Google Scholar 

  202. Krokan HE, Drablos F, Slupphaug G (2002) Uracil in DNA–occurrence, consequences and repair. Oncogene 21(58):8935–8948

    Article  CAS  PubMed  Google Scholar 

  203. Hegde ML, Hazra TK, Mitra S (2010) Functions of disordered regions in mammalian early base excision repair proteins. Cell Mol Life Sci 67(21):3573–3587

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Rodriguez G, Esadze A, Weiser BP et al (2017) Disordered N-terminal domain of human uracil DNA glycosylase (hUNG2) enhances DNA translocation. ACS Chem Biol 12(9):2260–2263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  205. Otterlei M, Warbrick E, Nagelhus TA et al (1999) Post-replicative base excision repair in replication foci. EMBO J 18(13):3834–3844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Weiser BP, Rodriguez G, Cole PA et al (2018) N-terminal domain of human uracil DNA glycosylase (hUNG2) promotes targeting to uracil sites adjacent to ssDNA-dsDNA junctions. Nucleic Acids Res 46(14):7169–7178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Hagen L, Kavli B, Sousa MM et al (2008) Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J 27(1):51–61

    Article  CAS  PubMed  Google Scholar 

  208. Gowers DM, Wilson GG, Halford SE (2005) Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc Natl Acad Sci USA 102(44):15883–15888

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Takeshige K, Baba M, Tsuboi S et al (1992) Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. J Cell Biol 119(2):301–311

    Article  CAS  PubMed  Google Scholar 

  210. Levine B, Klionsky DJ (2004) Development by self-digestion: molecular mechanisms and biological functions of autophagy. Dev Cell 6(4):463–477

    Article  CAS  PubMed  Google Scholar 

  211. Gatica D, Lahiri V, Klionsky DJ (2018) Cargo recognition and degradation by selective autophagy. Nat Cell Biol 20(3):233–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Mizushima N (2005) The pleiotropic role of autophagy: from protein metabolism to bactericide. Cell Death Differ 12(Suppl 2):1535–1541

    Article  CAS  PubMed  Google Scholar 

  213. Yang Y, Klionsky DJ (2020) Autophagy and disease: unanswered questions. Cell Death Differ 27(3):858–871

    Article  PubMed  PubMed Central  Google Scholar 

  214. Yin Z, Pascual C, Klionsky DJ (2016) Autophagy: machinery and regulation. Microb Cell 3(12):588–596

    Article  PubMed  PubMed Central  Google Scholar 

  215. Mizushima N, Yoshimori T, Ohsumi Y (2011) The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 27:107–132

    Article  CAS  PubMed  Google Scholar 

  216. Fujioka Y, Suzuki SW, Yamamoto H et al (2014) Structural basis of starvation-induced assembly of the autophagy initiation complex. Nat Struct Mol Biol 21(6):513–521

    Article  CAS  PubMed  Google Scholar 

  217. Yamamoto H, Fujioka Y, Suzuki SW et al (2016) The Intrinsically disordered protein Atg13 mediates supramolecular assembly of autophagy initiation complexes. Dev Cell 38(1):86–99

    Article  CAS  PubMed  Google Scholar 

  218. Stjepanovic G, Davies CW, Stanley RE et al (2014) Assembly and dynamics of the autophagy-initiating Atg1 complex. Proc Natl Acad Sci USA 111(35):12793–12798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Kofinger J, Ragusa MJ, Lee IH et al (2015) Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site. Structure 23(5):809–818

    Article  PubMed  PubMed Central  Google Scholar 

  220. Mao K, Chew LH, Inoue-Aono Y et al (2013) Atg29 phosphorylation regulates coordination of the Atg17-Atg31-Atg29 complex with the Atg11 scaffold during autophagy initiation. Proc Natl Acad Sci USA 110(31):E2875–E2884

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Jung CH, Jun CB, Ro SH et al (2009) ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell 20(7):1992–2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. Mei Y, Su M, Soni G et al (2014) Intrinsically disordered regions in autophagy proteins. Proteins 82(4):565–578

    Article  CAS  PubMed  Google Scholar 

  223. Gustafson CL, Parsley NC, Asimgil H et al (2017) A slow conformational switch in the bmal1 transactivation domain modulates circadian rhythms. Mol Cell 66(4):447-457 e7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Chang DC, Reppert SM (2003) A novel C-terminal domain of drosophila PERIOD inhibits dCLOCK:CYCLE-mediated transcription. Curr Biol 13(9):758–762

    Article  CAS  PubMed  Google Scholar 

  225. King HA, Hoelz A, Crane BR et al (2011) Structure of an enclosed dimer formed by the Drosophila period protein. J Mol Biol 413(3):561–572

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Jackson FR, Bargiello TA, Yun SH et al (1986) Product of per locus of Drosophila shares homology with proteoglycans. Nature 320(6058):185–188

    Article  CAS  PubMed  Google Scholar 

  227. Kucera N, Schmalen I, Hennig S et al (2012) Unwinding the differences of the mammalian PERIOD clock proteins from crystal structure to cellular function. Proc Natl Acad Sci USA 109(9):3311–3316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Xu H, Gustafson CL, Sammons PJ et al (2015) Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C terminus. Nat Struct Mol Biol 22(6):476–484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  229. Hennig S, Strauss HM, Vanselow K et al (2009) Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2. PLoS Biol 7(4):e94

    Article  PubMed  Google Scholar 

  230. Price JL, Blau J, Rothenfluh A et al (1998) double-time is a novel Drosophila clock gene that regulates PERIOD protein accumulation. Cell 94(1):83–95

    Article  CAS  PubMed  Google Scholar 

  231. Zhang Q, Yan Q, Yang H et al (2019) Oxygen sensing and adaptability won the 2019 Nobel Prize in Physiology or medicine. Genes Dis 6(4):328–332

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  232. Wang GL, Semenza GL (1996) Oxygen sensing and response to hypoxia by mammalian cells. Redox Rep 2(2):89–96

    Article  CAS  PubMed  Google Scholar 

  233. Vatrinet R, Leone G, De Luise M et al (2017) The alpha-ketoglutarate dehydrogenase complex in cancer metabolic plasticity. Cancer Metab 5:3

    Article  PubMed  PubMed Central  Google Scholar 

  234. Mole DR, Maxwell PH, Pugh CW et al (2001) Regulation of HIF by the von Hippel-Lindau tumour suppressor: implications for cellular oxygen sensing. IUBMB Life 52(1–2):43–47

    CAS  PubMed  Google Scholar 

  235. Semenza GL (2000) Hypoxia, clonal selection, and the role of HIF-1 in tumor progression. Crit Rev Biochem Mol Biol 35(2):71–103

    Article  CAS  PubMed  Google Scholar 

  236. Hwang SH, Bang S, Kim W et al (2020) Von Hippel-Lindau tumor suppressor (VHL) stimulates TOR signaling by interacting with phosphoinositide 3-kinase (PI3K). J Biol Chem 295(8):2336–2347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  237. Tabaro F, Minervini G, Sundus F et al (2016) VHLdb: a database of von Hippel-Lindau protein interactors and mutations. Sci Rep 6:31128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  238. Cargill KR, Sims-Lucas S (2020) Von Hippel-Lindau: implications in development and disease-response. Ann Transl Med 8(4):142

    Article  PubMed  PubMed Central  Google Scholar 

  239. Minervini G, Mazzotta GM, Masiero A et al (2015) Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. Sci Rep 5:12605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  240. Westermann L, Neubauer B, Kottgen M (2021) Nobel Prize 2020 in Chemistry honors CRISPR: a tool for rewriting the code of life. Pflugers Arch 473(1):1–2

    Article  CAS  PubMed  Google Scholar 

  241. Doudna JA, Charpentier E (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096

    Article  PubMed  Google Scholar 

  242. Doudna JA (2020) The promise and challenge of therapeutic genome editing. Nature 578(7794):229–236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  243. Karginov FV, Hannon GJ (2010) The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 37(1):7–19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  244. Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482(7385):331–338

    Article  CAS  PubMed  Google Scholar 

  245. Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  246. Deltcheva E, Chylinski K, Sharma CM et al (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471(7340):602–607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  247. Jiang W, Bikard D, Cox D et al (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31(3):233–239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  248. Mali P, Esvelt KM, Church GM (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10(10):957–963

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  249. Jinek M, Jiang F, Taylor DW et al (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343(6176):1247997

    Article  PubMed  PubMed Central  Google Scholar 

  250. Zuo Z, Zolekar A, Babu K et al (2019) Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. Elife. https://doi.org/10.7554/eLife.46500

    Article  PubMed  PubMed Central  Google Scholar 

  251. Du Z, Uversky VN (2017) Functional roles of intrinsic disorder in CRISPR-associated protein Cas9. Mol Biosyst 13(9):1770–1780

    Article  CAS  PubMed  Google Scholar 

  252. Caterina MJ, Schumacher MA, Tominaga M et al (1997) The capsaicin receptor: a heat-activated ion channel in the pain pathway. Nature 389(6653):816–824

    Article  CAS  PubMed  Google Scholar 

  253. Clapham DE, Julius D, Montell C et al (2005) International Union of Pharmacology. XLIX. Nomenclature and structure-function relationships of transient receptor potential channels. Pharmacol Rev 57(4):427–450

    Article  CAS  PubMed  Google Scholar 

  254. Colburn RW, Lubin ML, Stone DJ Jr et al (2007) Attenuated cold sensitivity in TRPM8 null mice. Neuron 54(3):379–386

    Article  CAS  PubMed  Google Scholar 

  255. Coste B, Mathur J, Schmidt M et al (2010) Piezo1 and Piezo2 are essential components of distinct mechanically activated cation channels. Science 330(6000):55–60

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  256. Yu FH, Catterall WA (2004) The VGL-chanome: a protein superfamily specialized for electrical signaling and ionic homeostasis. Sci STKE 2004(253):re15

    Article  PubMed  Google Scholar 

  257. Lishko PV, Procko E, Jin X et al (2007) The ankyrin repeats of TRPV1 bind multiple ligands and modulate channel sensitivity. Neuron 54(6):905–918

    Article  CAS  PubMed  Google Scholar 

  258. Liao M, Cao E, Julius D et al (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504(7478):107–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  259. Venkatachalam K, Montell C (2007) TRP channels. Annu Rev Biochem 76:387–417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  260. Wood JN, Winter J, James IF et al (1988) Capsaicin-induced ion fluxes in dorsal root ganglion cells in culture. J Neurosci 8(9):3208–3220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  261. Tominaga M, Caterina MJ, Malmberg AB et al (1998) The cloned capsaicin receptor integrates multiple pain-producing stimuli. Neuron 21(3):531–543

    Article  CAS  PubMed  Google Scholar 

  262. Chu Y, Cohen BE, Chuang HH (2020) A single TRPV1 amino acid controls species sensitivity to capsaicin. Sci Rep 10(1):8038

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  263. Goretzki B, Guhl C, Tebbe F et al (2021) Unstructural biology of TRP ion channels: the role of intrinsically disordered regions in channel function and regulation. J Mol Biol 433(17):166931

    Article  CAS  PubMed  Google Scholar 

  264. Loukin SH, Teng J, Kung C (2015) A channelopathy mechanism revealed by direct calmodulin activation of TrpV4. Proc Natl Acad Sci USA 112(30):9400–9405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  265. Arbabian A, Iftinca M, Altier C et al (2020) Mutations in calmodulin-binding domains of TRPV4/6 channels confer invasive properties to colon adenocarcinoma cells. Channels (Austin) 14(1):101–109

    Article  Google Scholar 

  266. Coste B, Xiao B, Santos JS et al (2012) Piezo proteins are pore-forming subunits of mechanically activated channels. Nature 483(7388):176–181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  267. Wu J, Lewis AH, Grandl J (2017) Touch, tension, and transduction—the function and regulation of Piezo Ion channels. Trends Biochem Sci 42(1):57–71

    Article  PubMed  Google Scholar 

  268. Woo SH, Lukacs V, de Nooij JC et al (2015) Piezo2 is the principal mechanotransduction channel for proprioception. Nat Neurosci 18(12):1756–1762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  269. Florez-Paz D, Bali KK, Kuner R et al (2016) A critical role for Piezo2 channels in the mechanotransduction of mouse proprioceptive neurons. Sci Rep 6:25923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  270. Verkest C, Schaefer I, Jegelka JM et al (2022) Intrinsically disordered intracellular domains control key features of the mechanically-gated ion channel PIEZO2. Nat Commun 13(1):1365–1378. https://doi.org/10.1038/s41467-022-28974-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding

All authors acknowledge financial support by the DFG (RTG 2467, project number 391498659 ‘Intrinsically Disordered Proteins—Molecular Principles, Cellular Functions, and Diseases’).

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AKD conceived the idea. LP, MK, AS, and VNU wrote and assembled the manuscript. LP and VNU designed figures. All involved students of the RTG 2467 contributed specific parts to the final manuscript. All authors give their consent for submission and publication of this manuscript.

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Correspondence to Marcel Köhn, Andrea Sinz or Vladimir N. Uversky.

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Piersimoni, L., Abd el Malek, M., Bhatia, T. et al. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell. Mol. Life Sci. 79, 449 (2022). https://doi.org/10.1007/s00018-022-04468-y

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