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X-Ray Structural Study of Amyloid-Like Fibrils of Tau Peptides Bound to Small-Molecule Ligands

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Tau Protein

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1523))

Abstract

Atomic structures of Tau involved in Alzheimer’s disease complexed with small molecule binders are the first step to define the Tau pharmacophore, leading the way to a structure-based design of improved diagnostics and therapeutics. Yet the partially disordered and polymorphic nature of Tau hinders structural analyses. Fortunately, short segments from amyloid proteins, which exhibit similar biophysical properties to the full-length proteins, also form fibrils and oligomers, and their atomic structures can be determined using X-ray microcrystallography. Such structures were successfully used to design amyloid inhibitors. This chapter describes experimental procedures used to determine crystal structures of Tau peptide segments in complex with small-molecule binders.

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References

  1. Anand K, Sabbagh M (2015) Early investigational drugs targeting tau protein for the treatment of Alzheimer’s disease. Expert Opin Investig Drugs 24(10):1355–1360

    Article  CAS  PubMed  Google Scholar 

  2. Brunden KR, Ballatore C, Crowe A et al (2010) Tau-directed drug discovery for Alzheimer’s disease and related tauopathies: a focus on tau assembly inhibitors. Exp Neurol 223:304–310

    Article  CAS  PubMed  Google Scholar 

  3. Bulic B, Pickhardt M, Khlistunova I et al (2007) Rhodanine-based tau aggregation inhibitors in cell models of tauopathy. Angew Chem Int Ed Engl 119:9375–9379

    Article  Google Scholar 

  4. Bulic B, Pickhardt M, Mandelkow E-M et al (2010) Tau protein and tau aggregation inhibitors. Neuropharmacology 59:276–289

    Article  CAS  PubMed  Google Scholar 

  5. Bulic B, Pickhardt M, Schmidt B et al (2009) Development of tau aggregation inhibitors for Alzheimer’s disease. Angew Chem Int Ed Engl 48:1740–1752

    Article  CAS  PubMed  Google Scholar 

  6. Crowe A, Ballatore C, Hyde E et al (2007) High throughput screening for small molecule inhibitors of heparin-induced tau fibril formation. Biochem Biophys Res Commun 358:1–6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Fuse S, Matsumura K, Fujita Y et al (2014) Development of dual targeting inhibitors against aggregations of amyloid-β and tau protein. Eur J Med Chem 85:228–234

    Article  CAS  PubMed  Google Scholar 

  8. Larbig G, Pickhardt M, Lloyd DG, Schmidt B, Mandelkow E (2007) Screening for inhibitors of tau protein aggregation into Alzheimer paired helical filaments: a ligand based approach results in successful scaffold hopping. Curr Alzheimer Res 4(3):315–323

    Article  CAS  PubMed  Google Scholar 

  9. Harrington CR, Storey JMD, Clunas S et al (2015) Cellular models of aggregation-dependent template-directed proteolysis to characterize tau aggregation inhibitors for treatment of Alzheimer disease. J Biol Chem 290:10862–10875

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Karakani AM, Riazi G, Mahmood GS et al (2015) Inhibitory effect of corcin on aggregation of 1N/4R human tau protein in vitro. Iran J Basic Med Sci 18:485–492

    PubMed  PubMed Central  Google Scholar 

  11. Paranjape SR, Riley AP, Somoza AD et al (2015) Azaphilones inhibit tau aggregation and dissolve tau aggregates in vitro. ACS Chem Neurosci 6:751–760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wobst HJ, Sharma A, Diamond MI et al (2015) The green tea polyphenol (−)-epigallocatechin gallate prevents the aggregation of tau protein into toxic oligomers at substoichiometric ratios. FEBS Lett 589:77–83

    Article  CAS  PubMed  Google Scholar 

  13. Balbirnie M, Grothe R, Eisenberg DS (2001) An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid. Proc Natl Acad Sci U S A 98:2375–2380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Nelson R, Sawaya MR, Balbirnie M et al (2005) Structure of the cross-beta spine of amyloid-like fibrils. Nature 435:773–778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ivanova MI, Thompson MJ, Eisenberg D (2006) A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments. Proc Natl Acad Sci U S A 103:4079–4082

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Sawaya MR, Sambashivan S, Nelson R et al (2007) Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447:453–457

    Article  CAS  PubMed  Google Scholar 

  17. Wiltzius JJ, Sievers SA, Sawaya MR et al (2008) Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin). Protein Sci 17:1467–1474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ivanova MI, Sievers SA, Sawaya MR et al (2009) Molecular basis for insulin fibril assembly. Proc Natl Acad Sci U S A 106:18990–18995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Wiltzius JJ, Landau M, Nelson R et al (2009) Molecular mechanisms for protein-encoded inheritance. Nat Struct Mol Biol 16:973–978

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wiltzius JJ, Sievers SA, Sawaya MR et al (2009) Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process. Protein Sci 18:1521–1530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Laganowsky A, Benesch JL, Landau M et al (2010) Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function. Protein Sci 19:1031–1043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Apostol MI, Wiltzius JJ, Sawaya MR et al (2011) Atomic structures suggest determinants of transmission barriers in mammalian prion disease. Biochemistry 50:2456–2463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Colletier JP, Laganowsky A, Landau M et al (2011) Molecular basis for amyloid-beta polymorphism. Proc Natl Acad Sci U S A 108:16938–16943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Liu C, Zhao M, Jiang L et al (2012) Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates. Proc Natl Acad Sci U S A 109:20913–20918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Sievers SA, Karanicolas J, Chang HW et al (2011) Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature 475:96–100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Jiang L, Liu C, Leibly D et al (2013) Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta. Elife 2:e00857

    PubMed  PubMed Central  Google Scholar 

  27. Landau M, Sawaya MR, Faull KF et al (2011) Towards a pharmacophore for amyloid. PLoS Biol 9:e1001080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. von Bergen M, Friedhoff P, Biernat J et al (2000) Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure. Proc Natl Acad Sci U S A 97:5129–5134

    Article  Google Scholar 

  29. Yang F, Lim GP, Begum AN et al (2005) Curcumin inhibits formation of amyloid beta oligomers and fibrils, binds plaques, and reduces amyloid in vivo. J Biol Chem 280:5892–5901

    Article  CAS  PubMed  Google Scholar 

  30. Jacobson A, Petric A, Hogenkamp D et al (1996) 1,1-Dicyano-2-[6-(dimethylamino)naphthalen-2-yl]propene (DDNP): a solvent polarity and viscosity sensitive fluorophore for fluorescence microscopy. J Am Chem Soc 118:5572–5579

    Article  CAS  Google Scholar 

  31. Krebs MR, Bromley EH, Donald AM (2005) The binding of thioflavin-T to amyloid fibrils: localisation and implications. J Struct Biol 149:30–37

    Article  CAS  PubMed  Google Scholar 

  32. Wolfe LS, Calabrese MF, Nath A et al (2010) Protein-induced photophysical changes to the amyloid indicator dye thioflavin T. Proc Natl Acad Sci U S A 107:16863–16868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Childers WS, Mehta AK, Lu K et al (2009) Templating molecular arrays in Amyloid’s cross-{beta} grooves. J Am Chem Soc 131:10165–10172

    Article  CAS  PubMed  Google Scholar 

  34. Schutz AK, Soragni A, Hornemann S et al (2011) The amyloid-Congo red interface at atomic resolution. Angew Chem Int Ed Engl 50:5956–5960

    Article  PubMed  Google Scholar 

  35. Goldschmidt L, Teng PK, Riek R et al (2010) Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc Natl Acad Sci U S A 107:3487–3492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J et al (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22:1302–1306

    Article  CAS  PubMed  Google Scholar 

  37. Maurer-Stroh S, Debulpaep M, Kuemmerer N et al (2010) Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods 7:237–242

    Article  CAS  PubMed  Google Scholar 

  38. Tartaglia GG, Pawar AP, Campioni S et al (2008) Prediction of aggregation-prone regions in structured proteins. J Mol Biol 380:425–436

    Article  CAS  PubMed  Google Scholar 

  39. Moshe A, Landau M, Eisenberg D (2016) Preparation of crystalline samples of amyloid fibrils and oligomers. In: Eliezer D (ed) Protein amyloid aggregation, vol 1345, Methods and protocols, methods in molecular biology. Springer, New York, pp 201–210. doi:10.1007/978-1-4939-2978-8_13

    Chapter  Google Scholar 

  40. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallogr 26:795–800

    Article  CAS  Google Scholar 

  41. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. In: Carter CW Jr, Sweet RM (eds) Macromolecular crystallography, part A, vol 276. Academic, New York

    Chapter  Google Scholar 

  42. Read RJ (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D Biol Crystallogr 57:1373–1382

    Article  CAS  PubMed  Google Scholar 

  43. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240–255

    Article  CAS  PubMed  Google Scholar 

  44. Adams PD, Afonine PV, Bunkoczi G et al (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Bricogne G, Blanc E, Brandl M et al (2009) BUSTER, Version 2.8.0. Global Phasing Ltd., Cambridge, UK

    Google Scholar 

  46. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132

    Article  PubMed  Google Scholar 

  47. Ivanova MI, Sievers SA, Guenther EL et al (2014) Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS. Proc Natl Acad Sci U S A 111:197–201

    Article  CAS  PubMed  Google Scholar 

  48. Bostrom J, Greenwood JR, Gottfries J (2003) Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model 21:449–462

    Article  CAS  PubMed  Google Scholar 

  49. Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol 385:381–392

    Article  CAS  PubMed  Google Scholar 

  50. Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65:538–548

    Article  CAS  PubMed  Google Scholar 

  51. Brunger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

ML thanks the U.S.-Israel Binational Science Foundation (BSF), Alon Fellowship from the Israeli Council for Higher Education, David and Inez Mayers Career Advancement Chair in Life Sciences, the J. and A. Tau Biological Research Fund, the I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation, Center of Excellence in Integrated Structural Cell Biology; Grant No 1775/12, and the Support for training and career development of researchers (Marie Curie) CIG, Seventh framework program, Single Beneficiary.

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Authors and Affiliations

  1. Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel

    Einav Tayeb-Fligelman & Meytal Landau

Authors
  1. Einav Tayeb-Fligelman
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  2. Meytal Landau
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Correspondence to Meytal Landau .

Editor information

Editors and Affiliations

  1. UMR CNRS 8576, Villeneuve d’Ascq, France

    Caroline Smet-Nocca

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Tayeb-Fligelman, E., Landau, M. (2017). X-Ray Structural Study of Amyloid-Like Fibrils of Tau Peptides Bound to Small-Molecule Ligands. In: Smet-Nocca, C. (eds) Tau Protein. Methods in Molecular Biology, vol 1523. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6598-4_5

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  • DOI: https://doi.org/10.1007/978-1-4939-6598-4_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6596-0

  • Online ISBN: 978-1-4939-6598-4

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