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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Whitesides GM, Boncheva M (2002) Beyond molecules: self-assembly of mesoscopic and macroscopic components. Proc Natl Acad Sci U S A 99:4769–4774
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
Whitesides G, Mathias J, Seto C (1991) Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. Science 80:1312–1319
De Santis E, Ryadnov MG (2015) Peptide self-assembly for nanomaterials: the old new kid on the block. Chem Soc Rev 44:8288–8300
Hay EH (2013) Cell biology of extracellular matrix, 2nd edn. Springer Science & Business Media, Dordrecht
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
Mienaltowski MJ, Birk DE (2014) Structure, physiology, and biochemistry of collagens. Adv Exp Med Biol 802:5–29
Ross CA, Poirier MA (2004) Protein aggregation and neurodegenerative disease. Nat Med 10:S10–S17
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
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
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
Scheibel T, Kowal AS, Bloom JD, Lindquist SL (2001) Bidirectional amyloid fiber growth for a yeast prion determinant. Curr Biol 11:366–369
Woolfson DN, Ryadnov MG (2006) Peptide-based fibrous biomaterials: some things old, new and borrowed. Curr Opin Chem Biol 10:559–567
De Santis E, Faruqui N, Noble JE, Ryadnov MG (2014) Exploitable length correlations in peptide nanofibres. Nanoscale 6:11425–11430
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
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
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
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
Shaw M, Zajiczek L, O’Holleran K (2015) High speed structured illumination microscopy in optically thick samples. Methods 88:11–19
Chernyatina AA, Hess JF, Guzenko D, Voss JC, Strelkov SV (2016) How to study intermediate filaments in atomic detail. Methods Enzymol 568:3–33
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
Starborg T, Lu Y, Meadows RS, Kadler KE, Holmes DF (2008) Electron microscopy in cell-matrix research. Methods 45:53–64
Bella A, Shaw M, Ray S, Ryadnov MG (2014) Filming protein fibrillogenesis in real time. Sci Rep 4:7529
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
Hartmann MD, Mendler CT, Bassler J, Karamichali I, Ridderbusch O, Lupas AN, Avarez BH (2016) α/β coiled coils. elife 5:11861
Ryadnov MG (2007) Peptide alpha-helices for synthetic nanostructures. Biochem Soc Trans 35:487–491
Ryadnov MG, Bella A, Timson S, Woolfson DN (2009) Modular design of peptide fibrillar nano- to microstructures. J Am Chem Soc 131:13240–13241
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
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
De Santis E, Castelletto V, Ryadnov MG (2015) Interfacial zippering-up of coiled-coil protein filaments. Phys Chem Chem Phys 17:31055–31060
Ryadnov MG, Woolfson DN (2003) Engineering the morphology of a self-assembling protein fibre. Nat Mater 2:329–332
Ryadnov MG, Woolfson DN (2005) MaP peptides: programming the self-assembly of peptide-based mesoscopic matrices. J Am Chem Soc 127:12407–12415
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
Makin OS, Serpell LC (2005) X-ray diffraction studies of amyloid structure. Methods Mol Biol 299:67–80
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
Gustafsson MG (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198:82–87
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
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
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
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
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7811-3_4
Published:
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