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Imaging Protein Fibers at the Nanoscale and In Situ

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Peptide Self-Assembly

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

Abstract

Protein self-assembly offers a rich repertoire of tools and technologies. However, despite significant progress in this area, a deterministic measure of the phenomenon, which might lead to predictable relationships between protein components, assembly mechanisms, and ultimately function, is lacking. Often the challenge relates to the choice of the most informative and precise measurements that can link the chemistry of the building blocks with the resulting assembly, ideally in situ and in real time. Using the example of protein fibrillogenesis—a self-assembly process fundamental to nearly every aspect of biological organization, from viral assembly to tissue restoration—this chapter demonstrates how protein self-assembly can be visually and precisely measured while providing measurement protocols applicable to other self-assembly systems.

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References

  1. Whitesides GM, Boncheva M (2002) Beyond molecules: self-assembly of mesoscopic and macroscopic components. Proc Natl Acad Sci U S A 99:4769–4774

    Article  CAS  Google Scholar 

  2. Adler-Abramovich L, Gazit E (2014) The physical properties of supramolecular peptide assemblies: from building block association to technological applications. Chem Soc Rev 43:6881–9683

    Article  CAS  Google Scholar 

  3. Whitesides G, Mathias J, Seto C (1991) Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. Science 80:1312–1319

    Article  Google Scholar 

  4. De Santis E, Ryadnov MG (2015) Peptide self-assembly for nanomaterials: the old new kid on the block. Chem Soc Rev 44:8288–8300

    Article  Google Scholar 

  5. Hay EH (2013) Cell biology of extracellular matrix, 2nd edn. Springer Science & Business Media, Dordrecht

    Google Scholar 

  6. Grosse R, Vartiainen MK (2013) To be or not to be assembled: progressing into nuclear actin filaments. Nat Rev Mol Cell Biol 14:693–697

    Article  CAS  Google Scholar 

  7. Mienaltowski MJ, Birk DE (2014) Structure, physiology, and biochemistry of collagens. Adv Exp Med Biol 802:5–29

    Article  CAS  Google Scholar 

  8. Ross CA, Poirier MA (2004) Protein aggregation and neurodegenerative disease. Nat Med 10:S10–S17

    Article  Google Scholar 

  9. Van Raaij MJ, Mitraki A, Lavigne G, Cusack S (1999) A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein. Nature 401:935–938

    Article  Google Scholar 

  10. Papapostolou D, Smith AM, Atkins EDT, Oliver SJ, Ryadnov MG, Serpell LC, Woolfson DN (2007) Engineering nanoscale order into a designed protein fiber. Proc Natl Acad Sci U S A 104:10853–10858

    Article  CAS  Google Scholar 

  11. Smith AM, Acquah SFA, Bone NK, Harold W, Ryadnov MG, Stevens MSP, Walton DRM, Woolfson DN (2004) Polar assembly in a designed protein fiber. Angew Chem Int Ed Engl 44:325–328

    Article  Google Scholar 

  12. Scheibel T, Kowal AS, Bloom JD, Lindquist SL (2001) Bidirectional amyloid fiber growth for a yeast prion determinant. Curr Biol 11:366–369

    Article  CAS  Google Scholar 

  13. Woolfson DN, Ryadnov MG (2006) Peptide-based fibrous biomaterials: some things old, new and borrowed. Curr Opin Chem Biol 10:559–567

    Article  CAS  Google Scholar 

  14. De Santis E, Faruqui N, Noble JE, Ryadnov MG (2014) Exploitable length correlations in peptide nanofibres. Nanoscale 6:11425–11430

    Article  Google Scholar 

  15. Jaroniec CP, MacPhee CE, Astrof NS, Dobson CM, Griffin RG (2002) Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril. Proc Natl Acad Sci U S A 99:16748–16753

    Article  CAS  Google Scholar 

  16. Rong J, Oberbeck F, Wang X, Li X, Oxsher J, Niu Z, Wang Q (2009) Tobacco mosaic virus templated synthesis of one dimensional inorganic–polymer hybrid fibres. J Mater Chem 19:2841

    Article  CAS  Google Scholar 

  17. Poincloux R, Lizárraga F, Chavrier P (2009) Matrix invasion by tumour cells: a focus on MT1-MMP trafficking to invadopodia. J Cell Sci 122:3015–3024

    Article  CAS  Google Scholar 

  18. O'Holleran K, Shaw M (2014) Optimized approaches for optical sectioning and resolution enhancement in 2D structured illumination microscopy. Biomed Opt Express 5:2580–2590

    Article  Google Scholar 

  19. Shaw M, Zajiczek L, O’Holleran K (2015) High speed structured illumination microscopy in optically thick samples. Methods 88:11–19

    Article  CAS  Google Scholar 

  20. Chernyatina AA, Hess JF, Guzenko D, Voss JC, Strelkov SV (2016) How to study intermediate filaments in atomic detail. Methods Enzymol 568:3–33

    Article  Google Scholar 

  21. Liu C, Zhao M, Jiang L, Cheng PN, Park J, Sawaya MR, Pensalfini A, Gou D, Berk AJ, Glabe CG, Nowick J, Eisenberg D (2012) Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates. Proc Natl Acad Sci U S A 109:20913–20918

    Article  CAS  Google Scholar 

  22. Starborg T, Lu Y, Meadows RS, Kadler KE, Holmes DF (2008) Electron microscopy in cell-matrix research. Methods 45:53–64

    Article  CAS  Google Scholar 

  23. Bella A, Shaw M, Ray S, Ryadnov MG (2014) Filming protein fibrillogenesis in real time. Sci Rep 4:7529

    Article  CAS  Google Scholar 

  24. Bella A, Ray S, Shaw M, Ryadnov MG (2012) Arbitrary self-assembly of peptide extracellular microscopic matrices. Angew Chem Int Ed Engl 51:428–431

    Article  CAS  Google Scholar 

  25. Hartmann MD, Mendler CT, Bassler J, Karamichali I, Ridderbusch O, Lupas AN, Avarez BH (2016) α/β coiled coils. elife 5:11861

    Google Scholar 

  26. Ryadnov MG (2007) Peptide alpha-helices for synthetic nanostructures. Biochem Soc Trans 35:487–491

    Article  CAS  Google Scholar 

  27. Ryadnov MG, Bella A, Timson S, Woolfson DN (2009) Modular design of peptide fibrillar nano- to microstructures. J Am Chem Soc 131:13240–13241

    Article  CAS  Google Scholar 

  28. Anzini P, Xu C, Hughes S, Magnotti E, Jiang T, Hemmingsen L, Demeler B, Conticello VP (2013) Controlling self-assembly of a peptide-based material via metal-ion induced registry shift. J Am Chem Soc 135:10278–10281

    Article  CAS  Google Scholar 

  29. Potekhin SA, Melnik TN, Popov V, Lanina NF, Vazina AA, Rigler P, Verdini AS, Corradin G, Kajava AV (2001) De novo design of fibrils made of short α-helical coiled coil peptides. Chem Biol 8:1025–1032

    Article  CAS  Google Scholar 

  30. De Santis E, Castelletto V, Ryadnov MG (2015) Interfacial zippering-up of coiled-coil protein filaments. Phys Chem Chem Phys 17:31055–31060

    Article  CAS  Google Scholar 

  31. Ryadnov MG, Woolfson DN (2003) Engineering the morphology of a self-assembling protein fibre. Nat Mater 2:329–332

    Article  CAS  Google Scholar 

  32. Ryadnov MG, Woolfson DN (2005) MaP peptides: programming the self-assembly of peptide-based mesoscopic matrices. J Am Chem Soc 127:12407–12415

    Article  CAS  Google Scholar 

  33. Faruqui N, Bella A, Ravi J, Ray S, Lamarre B, Ryadnov MG (2014) Differentially instructive extracellular protein micro-nets. J Am Chem Soc 136:7889–7898

    Article  CAS  Google Scholar 

  34. Makin OS, Serpell LC (2005) X-ray diffraction studies of amyloid structure. Methods Mol Biol 299:67–80

    CAS  PubMed  Google Scholar 

  35. Kner P, Chhun BB, Griffis ER, Winoto L, Gustafsson MG (2009) Super-resolution video microscopy of live cells by structured illumination. Nat Methods 6:339–342

    Article  CAS  Google Scholar 

  36. Gustafsson MG (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198:82–87

    Article  CAS  Google Scholar 

  37. Gustafsson MG, Shao L, Carlton PM, Wang CJ, Golubovskaya IN, Cande WZ, Agard DA, Sedat JW (2008) Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 94:4957–4970

    Article  CAS  Google Scholar 

  38. Pinotsi D, Buell AK, Galvagnion C, Dobson CM, Kaminski-Schierle GS, Kaminski CF (2014) Direct observation of heterogeneous amyloid fibril growth kinetics via two-color super-resolution microscopy. Nano Lett 14:339–345

    Article  CAS  Google Scholar 

  39. Kuipers BJH, Gruppen H (2007) Prediction of molar extinction coefficients of proteins and peptides using UV absorption of the constituent amino acids at 214 nm to enable quantitative reverse phase high-performance liquid chromatography-mass spectrometry analysis. J Agric Food Chem 55:5445–5451

    Article  CAS  Google Scholar 

  40. Smith MB, Li H, Shen T, Huang X, Yusuf E, Vavylonis D (2010) Segmentation and tracking of cytoskeletal filaments using open active contours. Cytoskeleton 67:693–705

    Article  Google Scholar 

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Correspondence to Maxim G. Ryadnov .

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Bella, A., Shaw, M., De Santis, E., Ryadnov, M.G. (2018). Imaging Protein Fibers at the Nanoscale and In Situ. 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_4

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  • DOI: https://doi.org/10.1007/978-1-4939-7811-3_4

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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

  • eBook Packages: Springer Protocols

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