Abstract
Alpha-synuclein, the principal protein involved in the pathogenesis of Parkinson’s disease, has been shown to exchange between multiple conformational states, with hitherto unclear physiological role of such conformational changes. Due to its ability to provide rich structural information for proteins in their near-native environment, nuclear magnetic resonance (NMR) spectroscopy has been a valuable tool to study these conformational states. In this review we describe the application of model systems and NMR methods to the study of membrane-bound states of alpha-synuclein. We provide a detailed description, primarily meant for someone new to the field, of how to prepare the necessary samples, perform the basic experiments, and obtain an initial interpretation of the results.
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References
Bussell R, Eliezer D (2003) A structural and functional role for 11-mer repeats in alpha-synuclein and other exchangeable lipid binding proteins. J Mol Biol 329(4):763–778
Chandra S, Chen X, Rizo J, Jahn R, Südhof TC (2003) A broken α-helix in folded α-synuclein. J Biol Chem 278(17):15313–15318
Dominguez A, Fernandez A, Gonzalez N, Iglesias E, Montenegro L (1997) Determination of critical micelle concentration of some surfactants by three techniques. J Chem Educ 74(10):1227
Fuguet E, Ràfols C, Rosés M, Bosch E (2005) Critical micelle concentration of surfactants in aqueous buffered and unbuffered systems. Anal Chim Acta 548(1–2):95–100
Mazer NA, Benedek GB, Carey MC (1976) An investigation of the micellar phase of sodium dodecyl sulfate in aqueous sodium chloride solutions using quasielastic light scattering spectroscopy. J Phys Chem 80(10):1075–1085
Duplatre G, MR FM (1996) Size of sodium dodecyl sulfate micelles in aqueous solutions as studied by positron annihilation lifetime spectroscopy. J Phys Chem 3654(96):16608–16612
Georgieva ER, Ramlall TF, Borbat PP, Freed JH, Eliezer D (2010) The lipid-binding domain of wild type and mutant alpha-synuclein: compactness and interconversion between the broken and extended helix forms. J Biol Chem 285(36):28261–28274
Eliezer D, Kutluay E, Bussell R, Browne G (2001) Conformational properties of alpha-synuclein in its free and lipid-associated states. J Mol Biol 307(4):1061–1073
Bodner CR, Dobson CM, Bax A (2009) Multiple tight phospholipid-binding modes of α-Synuclein revealed by solution NMR spectroscopy. J Mol Biol 390(4):775–790
Bussell R, Eliezer D (2004) Effects of Parkinson’s disease-linked mutations on the structure of lipid-associated alpha-synuclein. Biochemistry 43(16):4810–4818
Breckenridge WC, Morgan IG, Zanetta JP, Vincendon G (1973) Adult rat brain synaptic vesicles II. Lipid composition. Biochim Biophys Acta Gen Subj 320(3):681–686
Deutsch JW, Kelly RB (1981) Lipids of synaptic vesicles: relevance to the mechanism of membrane fusion. Biochemistry 20(2):378–385
Takamori S, Holt M, Stenius K, Lemke EA, Grønborg M, Riedel D et al (2006) Molecular anatomy of a trafficking organelle. Cell 127(4):831–846
Barenholz Y, Gibbes D, Litman BJ, Goll J, Thompson TE, Carlson RD (1977) A simple method for the preparation of homogeneous phospholipid vesicles. Biochemistry 16(12):2806–2810
Middleton ER, Rhoades E (2010) Effects of curvature and composition on α-synuclein binding to lipid vesicles. Biophys J 99(7):2279–2288
Dürr UHN, Soong R, Ramamoorthy A (2013) When detergent meets bilayer: birth and coming of age of lipid bicelles. Prog Nucl Magn Reson Spectrosc 69:1–22
Bayburt TH, Grinkova YV, Sligar SG (2002) Self-assembly of discoidal phospholipid bilayer nanoparticles with membrane scaffold proteins. Nano Lett 2(8):853–856
Yusuf Y, Massiot J, Chang Y-T, Wu P-H, Yeh V, Kuo P-C et al (2018) Optimization of the production of covalently circularized nanodiscs and their characterization in physiological conditions. Langmuir 34(11):3525–3532
Nasr ML, Baptista D, Strauss M, Sun ZYJ, Grigoriu S, Huser S et al (2016) Covalently circularized nanodiscs for studying membrane proteins and viral entry. Nat Methods 14(1):49–52
Nasr ML, Wagner G (2018) Covalently circularized nanodiscs; challenges and applications. Curr Opin Struct Biol 51:129–134
Popp M, Antos JM, Ploegh HL (2009) Current protocols in protein science. Curr Protoc Protein Sci Chapter 15:Unit 15.3
Viennet T, Wördehoff MM, Uluca B, Poojari C, Hoyer W, Etzkorn M et al (2017) A structural and kinetic link between membrane association and amyloid fibril formation of α-Synuclein. BioRxiv 1:1–31
Coelho-Cerqueira E, Carmo-Gonçalves P, Sá Pinheiro A, Cortines J, Follmer C (2013) α-Synuclein as an intrinsically disordered monomer—Fact or artefact? FEBS J 280(19):4915–4927
Kaiser J, Schafer R (1980) On the use of the I0-sinh window for spectrum analysis. IEEE Trans Acoust 28(1):105–107
Cavanagh J, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2007) Experimental aspects of NMR spectroscopy. In: Protein NMR spectroscopy. Elsevier, New York, pp 114–270
Kjaergaard M, Brander S, Poulsen FM (2011) Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH. J Biomol NMR 49(2):139–149
Kjaergaard M, Poulsen FM (2011) Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J Biomol NMR 50(2):157–165
Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ (2001) Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc 123(13):2970–2978
Bax A (1989) Two-dimensional NMR and protein structure. Annu Rev Biochem 58:223–256
Georgieva ER, Ramlall TF, Borbat PP, Freed JH, Eliezer D (2008) Membrane-bound alpha-synuclein forms an extended helix: long-distance pulsed ESR measurements using vesicles, bicelles, and rodlike micelles. J Am Chem Soc 130(39):12856–12857
Anderson VL, Ramlall TF, Rospigliosi CC, Webb WW, Eliezer D (2010) Identification of a helical intermediate in trifluoroethanol-induced alpha-synuclein aggregation. Proc Natl Acad Sci U S A 107(44):18850–18855
Dikiy I, Eliezer D (2012) Folding and misfolding of alpha-synuclein on membranes. Biochim Biophys Acta 1818(4):1013–1018
Dikiy I, Fauvet B, Jovičić A, Mahul-Mellier AL, Desobry C, El-Turk F et al (2016) Semisynthetic and in vitro phosphorylation of alpha-Synuclein at Y39 promotes functional partly helical membrane-bound states resembling those induced by PD mutations. ACS Chem Biol 11(9):2428–2437
Sung Y-H, Eliezer D (2018) Structure and dynamics of the extended-helix state of alpha-synuclein: intrinsic lability of the linker region. Protein Sci 22(6):1–50
Rovere M, Sanderson JB, Fonseca-Ornelas L, Patel DS, Bartels T (2018) Refolding of helical soluble α-synuclein through transient interaction with lipid interfaces. FEBS Lett 592:1464
Eliezer D (2006) Characterizing residual structure in disordered protein states using nuclear magnetic resonance. In: Bai Y, Nussinov R (eds) Protein folding protocols. Humana Press, Totowa, pp 49–68
Wishart DS, Bigam CG, Yao J, Abildgaard F, Dyson HJ, Oldfield E et al (1995) 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6(2):135–140
Eliezer D (2012) Distance information for disordered proteins from NMR and ESR measurements using paramagnetic spin labels. Methods Mol Biol 895(1):127–138
Anthis NJ, Clore GM (2015) Visualizing transient dark states by NMR spectroscopy. Q Rev Biophys 48(1):35–116
Fawzi NL, Ying J, Torchia DA, Clore GM (2010) Kinetics of amyloid β monomer-to-oligomer exchange by NMR relaxation. J Am Chem Soc 132(29):9948–9951
Fawzi NL, Ying J, Ghirlando R, Torchia DA, Clore GM (2011) Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR. Nature 480(7376):268–272
Fusco G, Pape T, Stephens AD, Mahou P, Costa AR, Kaminski CF et al (2016) Structural basis of synaptic vesicle assembly promoted by α-synuclein. Nat Commun 7:1–11
Fusco G, De Simone A, Gopinath T, Vostrikov V, Vendruscolo M, Dobson CM et al (2014) Direct observation of the three regions in α-synuclein that determine its membrane-bound behaviour. Nat Commun 5(May):1–8
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Das, T., Eliezer, D. (2019). Probing Structural Changes in Alpha-Synuclein by Nuclear Magnetic Resonance Spectroscopy. In: Bartels, T. (eds) Alpha-Synuclein. Methods in Molecular Biology, vol 1948. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9124-2_13
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DOI: https://doi.org/10.1007/978-1-4939-9124-2_13
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