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Incorporation of an Azobenzene β-Turn Peptidomimetic into Amyloid-β to Probe Potential Structural Motifs Leading to β-Sheet Self-Assembly

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Peptide Self-Assembly

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1777))

Abstract

Alzheimer’s disease (AD) is characterized by chronic neurodegeneration and the insidious accumulation of senile plaques comprised of the amyloid-β (Aβ) peptide. An important goal in AD research is to characterize the structural basis for how Aβ aggregates exert their noxious effects on neurons. We describe herein synthetic steps to incorporate a light-controlled β-turn mimetic, 3-(3-aminomethylphenylazo)-phenylacetic acid (AMPP), into the backbone of a putative turn region within Aβ. AMPP adopts a rigid β-hairpin turn when azobenzene is in the cis conformation, and can adopt an extended “β-arc” turn in the trans-azobenzene conformation. The long lifetimes of these conformationally stable isomers permit detailed biochemical analyses that help to clarify the controversial role played by these two types of turns during the toxic misfolding pathway of Aβ. Methods to photo-nucleate the cis- or trans-AMPP isomeric turns in aqueous buffer are also described. Finally, we detail selected techniques to characterize the Aβ aggregates derived from these photoisomerized variants.

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References

  1. Braak H, Braak E (1991) Neuropathological stageing if Alzeimer-related changes. Acta Neuropathol 82:239–259

    Article  CAS  Google Scholar 

  2. Qian X, Hamad B, Dias-LAlcaca G (2015) The Alzheimer disease market. Nat Rev Drug Discov 14:675–676

    Article  CAS  Google Scholar 

  3. Jan Bieschke MH, Wiglenda T, Friedrich RP, Boeddrich A, Schiele F, Kleckers D, del Amo JML, Grüning BA, Wang Q, Schmidt MR, Lurz R, Anwyl R, Schnoegl S, Fändrich M, Frank RF, Reif B, Günther S, Walsh DM, Wanker EE (2012) Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils. Nat Chem Biol 8:93–101

    Article  Google Scholar 

  4. Walsh DM, Klyubin I, Fadeeva JV, Cullen WK, Anwyl R, Wolfe MS, Rowan MJ, Selkoe DJ (2002) Naturally secreted oligomers of amyloid-β protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416:535–539

    Article  CAS  Google Scholar 

  5. Walsh DM, Selkoe DJ (2007) Aβ oligomers—a decade of discovery. J Neurochem 101:1172–1184

    Article  CAS  Google Scholar 

  6. Sylvain Lesne ́ MTK, Kotilinek L, Kayed R, Glabe CG, Yang A, Gallagher M, Ashe KH (2006) A specific amyloid-β protein assembly in the brain impairs memory. Nature 440:352–357

    Article  Google Scholar 

  7. Liu P, Reed MN, Kotilinek LA, Grant MK, Forster CL, Qiang W, Shapiro SL, Reichl JH, Chiang AC, Jankowsky JL, Wilmot CM, Cleary JP, Zahs KR, Ashe KH (2015) Quaternary structure defines a large class of amyloid-β oligomers neutralized by sequestration. Cell Rep 11:1760–1771

    Article  CAS  Google Scholar 

  8. Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, Cotman CW, Glabe CG (2003) Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300:486–489

    Article  CAS  Google Scholar 

  9. Brian O’Nuallain DBF, Nicoll AJ, Risse E, Ferguson N, Herron CE, Collinge J, Walsh DM (2010) Amyloid-protein dimers rapidly form stable synaptotoxic protofibrils. J Neurosci 30:14411–14419

    Article  Google Scholar 

  10. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Immunol 75:333–366

    CAS  Google Scholar 

  11. Liang Y, Lynn DG, Berland KM (2010) Direct observation of nucleation and growth in amyloid self-assembly. J Am Chem Soc 132:6306–6308

    Article  CAS  Google Scholar 

  12. Petkova AT, Ishii Y, Balbach JJ, Antzutkin ON, Leapman RD, Delaglio F, Tycko R (2002) A structural model for Alzheimer’s β-amyloid fibrils based on experimental constraints from solid state NMR. Proc Natl Acad Sci U S A 99:16742–16747

    Article  CAS  Google Scholar 

  13. Paravastu AK, Leapman RD, Yau W-M, Tycko R (2008) Molecular structural basis for polymorphism in Alzheimer’s β-amyloid fibrils. Proc Natl Acad Sci U S A 105:18349–18354

    Article  CAS  Google Scholar 

  14. Lührs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Döbeli H, Schubert D, Riek R (2005) 3D structure of Alzheimer’s amyloid-β(1–42) fibrils. Proc Natl Acad Sci U S A 102:17342–17347

    Article  Google Scholar 

  15. Yiling Xiao BM, McElheny D, Parthasarathy S, Long F, Hoshi M, Nussinov R, Ishii Y (2015) Aβ(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer’s disease. Nat Struct Mol Biol 22:499–505

    Article  Google Scholar 

  16. Petkova AT, Yau W-M, Tycko R (2006) Experimental constraints on quaternary structure in Alzheimer’s β-amyloid fibrils. Biochemistry 45:498–512

    Article  CAS  Google Scholar 

  17. Hoyer W, Grönwall C, Jonsson A, Ståhl S, Härd T (2008) Stabilization of a β-hairpin in monomeric Alzheimer’s amyloid-β peptide inhibits amyloid formation. Proc Natl Acad Sci U S A 105:5099–5104

    Article  CAS  Google Scholar 

  18. Lazo ND, Grant MA, Condron MC, Rigby AC, Teplow DB (2005) On the nucleation of amyloid β-protein monomer folding. Protein Sci 14:1581–1596

    Article  CAS  Google Scholar 

  19. Tomaselli S, Esposito V, Vangone P, NAJv N, Bonvin AMJJ, Guerrini R, Tancredi T, Temussi PA, Picone D (2006) The α-to-β conformational transition of Alzheimer’s Aβ-(1–42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of β conformation seeding. Chembiochem 7:257–267

    Article  CAS  Google Scholar 

  20. Kajava AV, Baxa U, Steven AC (2010) β arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils. FASEB J 24:1311–1319

    Article  CAS  Google Scholar 

  21. Cerf E, Sarroukh R, Tamamizu-Kato S, Breydo L, Derclaye S, Dufrene YF, Narayanaswami V, Goormaghtigh E, Ruysschaert J-M, Raussens V (2009) Antiparallel β-sheet: a signature structure of the oligomeric amyloid β-peptide. Biochem J 421:415–423

    Article  CAS  Google Scholar 

  22. Zimmerman DHI, Martin PK, Nix AJ, Rosenberry TL, Paravastu AK (2015) Antiparallel β-sheet structure within the C-terminal region of 42-residue Alzheimer’s amyloid-β peptides when they form 150-kDa oligomers. J Mol Biol 427:2319–2328

    Article  Google Scholar 

  23. Ahmed M, Davis J, Aucoin D, Sato T, Ahuja S, Aimoto S, Elliott JI, Sostrand WEV, Smith SO (2010) Structural conversion of neurotoxic amyloid-β(1-42) oligomers to fibrils. Nat Struct Mol Biol 17:561–567

    Article  CAS  Google Scholar 

  24. Sandberg A, Luheshi LM, Söllvander S, TPd B, Macao B, Knowles TPJ, Biverstål H, Lendel C, Ekholm-Petterson F, Dubnovitsky A, Lannfelt L, Dobson CM, Härd T (2010) Stabilization of neurotoxic Alzheimer amyloid-β oligomers by protein engineering. Proc Natl Acad Sci U S A 107:15595–15600

    Article  CAS  Google Scholar 

  25. Sciarretta KL, Gordon DJ, Petkova AT, Tycko R, Meredith SC (2005) Aβ40-Lactam (D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry 44:6003–6014

    Article  CAS  Google Scholar 

  26. Doran TM, Anderson EA, Latchney SE, Opanashuk LA, Nilsson BL (2012) Turn nucleation perturbs amyloid β self-assembly and cytotoxicity. J Mol Biol 421:315–328

    Article  CAS  Google Scholar 

  27. Doran TM, Anderson EA, Latchney SE, Opanashuk LA, Nilsson BL (2012) An azobenzene photoswitch sheds light on turn nucleation in amyloid-β self-assembly. ACS Chem Neurosci 3:211–220

    Article  CAS  Google Scholar 

  28. Aemissegger A, Kräutler V, Gunsteren WFV, Hilvert D (2005) A Photoinducible β-Hairpin. J Am Chem Soc 127:2929–2936

    Article  CAS  Google Scholar 

  29. Aemissegger A, Hilvert D (2007) Synthesis and application of an azobenzene amino acid as a light-switchable turn element in polypeptides. Nat Protoc 2:161–167

    Article  CAS  Google Scholar 

  30. Kräutler V, Aemissegger A, Hünenberger PH, Hilvert D, Hansson T, Gunsteren WFV (2005) Use of molecular dynamics in the design and structure DETERMINATION of a photoinducible β-hairpin. J Am Chem Soc 127:4935–4942

    Article  Google Scholar 

  31. Dong S-L, Loweneck M, Schrader TE, Schreier WJ, Moroder L, Renner C (2006) A photocontrolled β-hairpin peptide. Chem Eur J 12:1114–1120

    Article  CAS  Google Scholar 

  32. O’Nuallain B, Thakur AK, Williams AD, Bhattacharyya AM, Chen S, Thiagarajan G, Wetzel R (2006) Kinetics and thermodynamics of amyloid assembly using a high-performance liquid chromatography-based sedimentation assay. Methods Enzymol 413:34–74

    Article  Google Scholar 

  33. O’Nuallain B, Shivaprasad S, Kheterpal I, Wetzel R (2005) Thermodynamics of Aβ(1–40) amyloid fibril formation. Biochemistry 44:12709–12718

    Article  Google Scholar 

  34. Ulysse L, Cubillos J, Chmielewski J (1995) Photoregulation of cyclic peptide conformation. J Am Chem Soc 117:8466–8467

    Article  CAS  Google Scholar 

  35. Behrendt R, Renner C, Schenk M, Wang F, Wachtveitl J, Oesterhelt D, Moroder L (1999) Photomodulation of the conformation of cyclic peptides with azobenzene moieties in the peptide backbone. Angew Chem Int Ed 38:2771–2774

    Article  CAS  Google Scholar 

  36. Donald A, Wellings EA (1997) Standard Fmoc protocols. Methods Enzymol 289:44–67

    Article  Google Scholar 

  37. Chi L, Sadovski O, Woolley GA (2006) A blue-green absorbing cross-linker for rapid photoswitching of peptide helix content. Bioconjug Chem 17:670–676

    Article  CAS  Google Scholar 

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Acknowledgments

This work was made possible by a grant from the Alzheimer’s Association (NIRG-08-90797). We thank Professor Joseph P. Dinnocenzo for helpful discussions regarding photoisomerization methods and Karen Bentley of the University of Rochester Medical Center Electron Microscopy Core for assistance with transmission electron microscopy.

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Author notes

  1. Todd M. Doran

    Present address: Department of Medicinal Chemistry, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA

Authors and Affiliations

  1. Department of Chemistry, University of Rochester, Rochester, NY, USA

    Bradley L. Nilsson

Authors
  1. Todd M. Doran
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  2. Bradley L. Nilsson
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Corresponding author

Correspondence to Bradley L. Nilsson .

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Editors and Affiliations

  1. Department of Chemistry, University of Rochester, Rochester, New York, USA

    Bradley L. Nilsson

  2. Department of Medicinal Chemistry, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA

    Todd M. Doran

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Doran, T.M., Nilsson, B.L. (2018). Incorporation of an Azobenzene β-Turn Peptidomimetic into Amyloid-β to Probe Potential Structural Motifs Leading to β-Sheet Self-Assembly. In: Nilsson, B., Doran, T. (eds) Peptide Self-Assembly. Methods in Molecular Biology, vol 1777. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7811-3_25

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  • DOI: https://doi.org/10.1007/978-1-4939-7811-3_25

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7809-0

  • Online ISBN: 978-1-4939-7811-3

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