Abstract
Solid-state NMR (ssNMR) is a versatile technique that can provide high-resolution (sub-angstrom) structural data for integral membrane proteins embedded in native and model membrane environments. The methodologies for a priori structure determination have for the most part been developed using samples with crystalline and fibrous morphologies. However, the techniques are now being applied to large, polytopic membrane proteins including receptors, ion channels, and porins. ssNMR data may be used to annotate and refine existing structures in regions of the protein not fully resolved by crystallography (including ligand-binding sites and mobile solvent accessible loop regions). This review describes the spectroscopic experiments and data analysis methods (including assignment) used to generate high-resolution structural data for membrane proteins. We also consider the range of sample morphologies that are appropriate for study by this method.
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References
Wallin E, von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7:1029–1038
Boyd D, Schierle C, Beckwith J (1998) How many membrane proteins are there? Protein Sci 7:201–205
Russell RB, Eggleston DS (2000) New roles for structure in biology and drug discovery. Nat Struct Biol 7(Suppl):928–930
Watts A (2005) Solid-state NMR in drug design and discovery for membrane-embedded targets. Nat Rev Drug Discov 4:555–568
Judge PJ, Watts A (2011) Recent contributions from solid-state NMR to the understanding of membrane protein structure and function. Curr Opin Chem Biol 15:690–695
Kamihira M, Vosegaard T, Mason AJS (2005) Structural and orientational constraints of bacteriorhodopsin in purple membranes determined by oriented-sample solid-state NMR spectroscopy. J Struct Biol 149:7–16
Zhou DH, Shah G, Mullen C et al (2009) Proton-detected solid-state NMR spectroscopy of natural-abundance peptide and protein pharmaceuticals. Angew Chem 48:1253–1256
Chevelkov V, Rehbein K, Diehl A, Reif B (2006) Ultrahigh resolution in proton solid-state NMR spectroscopy at high levels of deuteration. Angew Chem 45:3878–3881
Linser R, Fink U, Reif B (2008) Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins. J Magn Reson 193:89–93
Akbey U, Lange S, Trent Franks W (2010) Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy. J Biomol NMR 46:67–73
Hong M, Jakes K (1999) Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations. J Biomol NMR 14:71–74
Castellani F, van Rossum B, Diehl A et al (2002) Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Nature 420:98–102
Becker J, Ferguson N, Flinders J et al (2008) A sequential assignment procedure for proteins that have intermediate line widths in MAS NMR spectra: Amyloid fibrils of human CA150. Chembiochem 9:1946–1952
Cross TA, Sharma M, Yi M, Zhou HX (2011) Influence of solubilizing environments on membrane protein structures. Trends Biochem Sci 36:117–125
Murray DT, Das N, Cross TA (2013) Solid State NMR strategy for characterizing native membrane protein structures. Acc Chem Res 46:2172–2181
Judge PJ, Taylor GF, Vermeer LS, Watts A (2014) Structural insights from solid-state NMR into the function of the bacteriorhodopsin photoreceptor protein. In: Separovic F, Naito A (eds) Advances in biological solid-state NMR: proteins and membrane-active peptides. The Royal Society of Chemistry, Cambridge, UK
Warschawski DE, Arnold AA, Beaugrand M et al (2011) Choosing membrane mimetics for NMR structural studies of transmembrane proteins. Biochim Biophys Acta 1808:1957–1974
Rigaud JL, Levy D (2003) Reconstitution of membrane proteins into liposomes. Meth Enzymol 372:65–86
Das N, Murray DT, Cross TA (2013) Lipid bilayer preparations of membrane proteins for oriented and magic-angle spinning solid-state NMR samples. Nat Protoc 8:2256–2270
Abdine A, Park KH, Warschawski DE (2012) Cell-free membrane protein expression for solid-state NMR. Meth Mol Biol 831:85–109
Abdine A, Verhoeven MA, Warschawski DE (2011) Cell-free expression and labeling strategies for a new decade in solid-state NMR. New Biotechnol 28:272–276
Prosser RS, Evanics F, Kitevski JL, Al-Abdul-Wahid MS (2006) Current applications of bicelles in NMR studies of membrane-associated amphiphiles and proteins. Biochemistry 45:8453–8465
Diller A, Loudet C, Aussenac F et al (2009) Bicelles: a natural “molecular goniometer” for structural, dynamical and topological studies of molecules in membranes. Biochimie 91:744–751
Cho HS, Dominick JL, Spence MM (2010) Lipid domains in bicelles containing unsaturated lipids and cholesterol. J Phys Chem B 114:9238–9245
Park SH, Opella SJ (2010) Triton X-100 as the “short chain lipid” improves the magnetic alignment and stability of membrane proteins in phosphatidylcholine bilayers for oriented sample (OS) solid-state NMR Spectroscopy. J Am Chem Soc 132:12552–12553
Marcotte I, Belanger A, Auger M (2006) The orientation effect of gramicidin A on bicelles and Eu3+ -doped bicelles as studied by solid-state NMR and FT-IR spectroscopy. Chem Phys Lipids 139:137–149
Grobner G, Taylor A, Williamson PT et al (1997) Macroscopic orientation of natural and model membranes for structural studies. Anal Biochem 254:132–138
Varga K, Watts A (2007) Introduction to solid state NMR and its application to membrane protein-ligand binding studies. In: Pebay-Peyroula E (ed) Biophysical analysis of membrane proteins. Investigating structure and function. Wiley-VCH, Weinheim, pp 55–87
Bertini I, Engelke F, Luchinat C et al (2012) NMR properties of sedimented solutes. Phys Chem Chem Phys 14:439–447
Bockmann A, Gardiennet C, Verel R et al (2009) Characterization of different water pools in solid-state NMR protein samples. J Biomol NMR 45:319–327
Watts A, Straus SK, Grage S et al (2004) Membrane protein structure determination using solid state NMR. In: Downing K (ed) Methods in molecular biology – techniques in protein NMR, vol 278. Humana Press, Totowa, NJ, pp 403–474
Takegoshi K, Nakamura S, Terao T (2001) C-13-H-1 dipolar-assisted rotational resonance in magic-angle spinning NMR. Chem Phys Lett 344:631–637
Bayro MJ, Ramachandran R, Caporini MA et al (2008) Radio frequency-driven recoupling at high magic-angle spinning frequencies: homonuclear recoupling sans heteronuclear decoupling. J Chem Phys 128:052321
Fung BM, Khitrin AK, Ermolaev K (2000) An improved broadband decoupling sequence for liquid crystals and solids. J Magn Reson 142:97–101
Baldus M, Geurts DG, Hediger S, Meier BH (1996) Efficient 15N–13C polarization transfer by adiabatic-passage Hartmann–Hahn cross polarization. J Magn Reson A 118:140–144
Baldus M, Petkova A, Herzfeld J, Griffin R (1998) Cross polarization in the tilted frame: assignment and spectral simplification in heteronuclear spin systems. Mol Phys 95:1197–1207
Pauli J, Baldus M, van Rossum B, de Groot H et al (2001) Backbone and side-chain 13C and 15N signal assignments of the alpha-spectrin SH3 domain by magic angle spinning solid-state NMR at 17.6 Tesla. Chembiochem 2:272–281
Higman VA (2013) Proteins in solution and at interfaces. In: Pineiro A, Ruso J (eds) Methods and applications in biotechnology and materials science. Wiley-Blackwell, New York, pp 23–48
Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171–180
Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647–1651
Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS plus: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223
Higman VA, Varga K, Aslimovska L et al (2011) The conformation of bacteriorhodopsin loops in purple membranes resolved by solid-state MAS NMR spectroscopy. Angew Chem 50:8432–8435
Yao L, Grishaev A, Cornilescu G, Bax A (2010) Site-specific backbone amide (15)N chemical shift anisotropy tensors in a small protein from liquid crystal and cross-correlated relaxation measurements. J Am Chem Soc 132:4295–4309
Bechinger B, Sizun C (2003) Alignment and structural analysis of membrane polypeptides by 15N and 31P solid-state NMR spectroscopy. Concepts Magn Reson 18A:130–145
Vosegaard T, Nielsen NC (2002) Towards high-resolution solid-state NMR on large uniformly 15N- and [13C,15N]-labeled membrane proteins in oriented lipid bilayers. J Biomol NMR 22:225–247
Marassi FM, Ma C, Gesell JJ, Opella SJ (2000) Three-dimensional solid-state NMR spectroscopy is essential for resolution of resonances from in-plane residues in uniformly (15)N-labeled helical membrane proteins in oriented lipid bilayers. J Magn Reson 144:156–161
Gor’kov PL, Witter R, Chekmenev EY et al (2007) Low-E probe for 19F–1H NMR of dilute biological solids. J Magn Reson 189:182–189
Seelig J (1977) Deuterium magnetic resonance: theory and application to lipid membranes. Q Rev Biophys 10:353–418
Ulrich AS, Wallat I, Heyn MP, Watts A (1995) Re-orientation of retinal in the M-photointermediate of bacteriorhodopsin. Nat Struct Biol 12:190–192
Vostrikov VV, Daily AE, Greathouse DV, Koeppe RE II (2010) Charged or aromatic anchor residue dependence of transmembrane peptide tilt. J Biol Chem 285:31723–31730
Salgado GF, Struts AV, Tanaka K et al (2004) Deuterium NMR structure of retinal in the ground state of rhodopsin. Biochemistry 43:12819–12828
Ulrich AS, Watts A, Wallat I, Heyn MP (1994) Distorted structure of the retinal chromophore in bacteriorhodopsin resolved by 2H-NMR. Biochemistry 33:5370–5375
Glaubitz C, Burnett IJ, Grobner G et al (1999) Deuterium MAS NMR spectroscopy on oriented membrane proteins: applications to photointermediates of bacteriorhodopsin. J Am Chem Soc 121:5787–5794
Vijayan V, Demers JP, Biernat J et al (2009) Low-power solid-state NMR experiments for resonance assignment under fast magic-angle spinning. Chemphyschem 10:2205–2208
Dvinskikh SV, Castro V, Sandstrom D (2004) Heating caused by radiofrequency irradiation and sample rotation in 13C magic angle spinning NMR studies of lipid membranes. Magn Reson Chem 42:875–881
Thurber KR, Tycko R (2009) Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder. J Magn Reson 196:84–87
Bielecki A, Burum DP (1995) Temperature dependence of 207Pb MAS spectra of solid lead nitrate. An accurate, sensitive thermoMETER for variable-temperature MAS. J Magn Reson A 116:215–220
Langer B, Schnell II, Spiess HW, Grimmer AR (1999) Temperature calibration under ultrafast MAS conditions. J Magn Reson 138:182–186
Acknowledgements
The authors acknowledge funding from the Medical Research Council (UK), the Biotechnology and Biological Sciences Research Council (UK), the European Metrology Research Programme, and the National Physical Laboratory (London, UK).
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Judge, P.J., Taylor, G.F., Dannatt, H.R.W., Watts, A. (2015). Solid-State Nuclear Magnetic Resonance Spectroscopy for Membrane Protein Structure Determination. In: Owens, R. (eds) Structural Proteomics. Methods in Molecular Biology, vol 1261. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2230-7_17
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DOI: https://doi.org/10.1007/978-1-4939-2230-7_17
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