Journal of Biomolecular NMR

, Volume 67, Issue 3, pp 179–190 | Cite as

High resolution solid-state NMR spectroscopy of the Yersinia pestis outer membrane protein Ail in lipid membranes

  • Yong Yao
  • Samit Kumar Dutta
  • Sang Ho Park
  • Ratan Rai
  • L. Miya Fujimoto
  • Andrey A. Bobkov
  • Stanley J. Opella
  • Francesca M. Marassi
Article

Abstract

The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail’s biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with 13C or 1H detection, have very narrow line widths (0.40–0.60 ppm for 13C, 0.11–0.15 ppm for 1H, and 0.46–0.64 ppm for 15N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The 1H-detected solid-state NMR 1H/15N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR 1H/15N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.

Keywords

Membrane protein Solid-state NMR Magic angle spinning Ail Yersinia pestis 

References

  1. Akbey U, Rossum BJ, Oschkinat H (2012) Practical aspects of high-sensitivity multidimensional (1)(3)C MAS NMR spectroscopy of perdeuterated proteins. J Magn Reson 217:77–85. doi:10.1016/j.jmr.2012.02.015 ADSCrossRefGoogle Scholar
  2. Andreas LB et al (2015) Structure and mechanism of the influenza A M218-60 dimer of dimers. J Am Chem Soc 137:14877–14886. doi:10.1021/jacs.5b04802 CrossRefGoogle Scholar
  3. Andronesi OC, Becker S, Seidel K, Heise H, Young HS, Baldus M (2005) Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy. J Am Chem Soc 127:12965–12974. doi:10.1021/ja0530164 CrossRefGoogle Scholar
  4. Baker LA, Folkers GE, Sinnige T, Houben K, Kaplan M, van der Cruijsen EA, Baldus M (2015) Magic-angle-spinning solid-state NMR of membrane proteins. Methods Enzymol 557:307–328. doi:10.1016/bs.mie.2014.12.023 CrossRefGoogle Scholar
  5. Baldus M, Petkova A, Herzfield J, Griffin R (1998) Cross polarization in the tilted frame: assignment and spectral simplification in heteronuclear spin systems. Mol Phys 95:1197–1207ADSCrossRefGoogle Scholar
  6. Barbet-Massin E et al (2014) Rapid proton-detected NMR assignment for proteins with fast magic angle spinning. J Am Chem Soc 136:12489–12497. doi:10.1021/ja507382j CrossRefGoogle Scholar
  7. Behlau M, Mills DJ, Quader H, Kuhlbrandt W, Vonck J (2001) Projection structure of the monomeric porin OmpG at 6 A resolution. J Mol Biol 305:71–77. doi:10.1006/jmbi.2000.4284 CrossRefGoogle Scholar
  8. Brown LS, Ladizhansky V (2015) Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 24:1333–1346. doi:10.1002/pro.2700 CrossRefGoogle Scholar
  9. Cross TA, Ekanayake V, Paulino J, Wright A (2014) Solid state NMR: the essential technology for helical membrane protein structural characterization. J Magn Reson 239:100–109. doi:10.1016/j.jmr.2013.12.006 ADSCrossRefGoogle Scholar
  10. Das BB, Nothnagel HJ, Lu GJ, Son WS, Tian Y, Marassi FM, Opella SJ (2012) Structure determination of a membrane protein in proteoliposomes. J Am Chem Soc 134:2047–2056. doi:10.1021/ja209464f CrossRefGoogle Scholar
  11. De Zorzi R, Mi W, Liao M, Walz T (2016) Single-particle electron microscopy in the study of membrane protein structure. Microscopy 65:81–96. doi:10.1093/jmicro/dfv058 CrossRefGoogle Scholar
  12. Devaux PF, Seigneuret M (1985) Specificity of lipid-protein interactions as determined by spectroscopic techniques. Biochim Biophys Acta 822:63–125CrossRefGoogle Scholar
  13. Ding Y, Yao Y, Marassi FM (2013) Membrane protein structure determination in membrana. Acc Chem Res 46:2182–2190. doi:10.1021/ar400041a CrossRefGoogle Scholar
  14. Ding Y, Fujimoto LM, Yao Y, Plano GV, Marassi FM (2015) Influence of the lipid membrane environment on structure and activity of the outer membrane protein Ail from Yersinia pestis. Biochim Biophys Acta 1848:712–720. doi:10.1016/j.bbamem.2014.11.021 CrossRefGoogle Scholar
  15. Dolder M, Zeth K, Tittmann P, Gross H, Welte W, Wallimann T (1999) Crystallization of the human, mitochondrial voltage-dependent anion-selective channel in the presence of phospholipids. J Struct Biol 127:64–71. doi:10.1006/jsbi.1999.4141 CrossRefGoogle Scholar
  16. Eddy MT et al (2012) Lipid dynamics and protein-lipid interactions in 2D crystals formed with the beta-barrel integral membrane protein VDAC1. J Am Chem Soc 134:6375–6387. doi:10.1021/ja300347v CrossRefGoogle Scholar
  17. Eddy MT et al (2015) Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR. J Biomol NMR 61:299–310. doi:10.1007/s10858-015-9903-1 CrossRefGoogle Scholar
  18. Ernst M, Samoson A, Meier BH (2003) Low-power XiX decoupling in MAS NMR experiments. J Magn Reson 163:332–339ADSCrossRefGoogle Scholar
  19. Findlay EJ, Barton PG (1978) Phase behavior of synthetic phosphatidylglycerols and binary mixtures with phosphatidylcholines in the presence and absence of calcium ions. BioChemistry 17:2400–2405CrossRefGoogle Scholar
  20. Fung BM, Khitrin AK, Ermolaev K (2000) An improved broadband decoupling sequence for liquid crystals and solids. J Magn Reson 142:97–101ADSCrossRefGoogle Scholar
  21. Gennis RB (1989) Biomembranes : molecular structure and function. springer advanced texts in chemistry. Springer, New YorkCrossRefGoogle Scholar
  22. Hagn F, Etzkorn M, Raschle T, Wagner G (2013) Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins. J Am Chem Soc 135:1919–1925. doi:10.1021/ja310901f CrossRefGoogle Scholar
  23. Hiller M, Krabben L, Vinothkumar KR, Castellani F, van Rossum BJ, Kuhlbrandt W, Oschkinat H (2005) Solid-state magic-angle spinning NMR of outer-membrane protein G from Escherichia coli. Chembiochem 6:1679–1684CrossRefGoogle Scholar
  24. Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH (2012) A supplementary coil for (2)H decoupling with commercial HCN MAS probes. J Magn Reson 214:76–80. doi:10.1016/j.jmr.2011.10.010 ADSCrossRefGoogle Scholar
  25. Janiak MJ, Small DM, Shipley GG (1976) Nature of the Thermal pretransition of synthetic phospholipids: dimyristolyl- and dipalmitoyllecithin. BioChemistry 15:4575–4580CrossRefGoogle Scholar
  26. Lee AG (2003) Lipid-protein interactions in biological membranes: a structural perspective. Biochim Biophys Acta 1612:1–40CrossRefGoogle Scholar
  27. Lee AG (2011) Biological membranes: the importance of molecular detail. Trends Biochem Sci 36:493–500. doi:10.1016/j.tibs.2011.06.007 CrossRefGoogle Scholar
  28. Lee J, Patel DS, Kucharska I, Tamm LK, Im W (2017) Refinement of OprH-LPS interactions by molecular simulations. Biophys J 112:346–355. doi:10.1016/j.bpj.2016.12.006 CrossRefGoogle Scholar
  29. Leftin A, Brown MF (2011) An NMR database for simulations of membrane dynamics. Biochim Biophys Acta 1808:818–839. doi:10.1016/j.bbamem.2010.11.027 CrossRefGoogle Scholar
  30. Li Y, Berthold DA, Frericks HL, Gennis RB, Rienstra CM (2007) Partial (13)C and (15)N chemical-shift assignments of the disulfide-bond-forming enzyme DsbB by 3D magic-angle spinning NMR spectroscopy. Chembiochem 8:434–442. doi:10.1002/cbic.200600484 CrossRefGoogle Scholar
  31. Linser R et al (2011) Proton-detected solid-state NMR spectroscopy of fibrillar and membrane proteins. Angew Chem Int Ed Engl 50:4508–4512. doi:10.1002/anie.201008244 CrossRefGoogle Scholar
  32. Mahalakshmi R, Marassi FM (2008) Orientation of the Escherichia coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-state NMR. BioChemistry 47:6531–6538. doi:10.1021/bi800362b CrossRefGoogle Scholar
  33. Mahalakshmi R, Franzin CM, Choi J, Marassi FM (2007) NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. Biochim Biophys Acta 1768:3216–3224. doi:10.1016/j.bbamem.2007.08.008 CrossRefGoogle Scholar
  34. Marassi FM, Ding Y, Schwieters CD, Tian Y, Yao Y (2015) Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. J Biomol NMR 63:59–65. doi:10.1007/s10858-015-9963-2 CrossRefGoogle Scholar
  35. Maslennikov I, Choe S (2013) Advances in NMR structures of integral membrane proteins. Curr Opin Struct Biol 23:555–562. doi:10.1016/j.sbi.2013.05.002 CrossRefGoogle Scholar
  36. Moraes I, Evans G, Sanchez-Weatherby J, Newstead S, Stewart PD (2014) Membrane protein structure determination—the next generation. Biochim Biophys Acta 1838:78–87. doi:10.1016/j.bbamem.2013.07.010 CrossRefGoogle Scholar
  37. Morris GA, Freeman R (1979) Enhancement of nuclear magnetic resonance signals by polarization transfer. J Am Chem Soc 101:760–762. doi:10.1021/ja00497a058 CrossRefGoogle Scholar
  38. Pauli J, Baldus M, van Rossum B, de Groot H, Oschkinat H (2001) Backbone and side-chain 13 C and 15 N signal assignments of the alpha-spectrin SH3 domain by magic angle spinning solid-state NMR at 17.6 T. Chembiochem 2:272–281. doi:10.1002/1439-7633(20010401)2:4<272::AID-CBIC272>3.0.CO;2-2 CrossRefGoogle Scholar
  39. Pines A, Gibby MG, Waugh JS (1973) Proton-enhanced NMR of dilute spins in solids. J Chem Phys 59:569–590. doi:10.1063/1.1680061 ADSCrossRefGoogle Scholar
  40. Plesniak LA, Mahalakshmi R, Rypien C, Yang Y, Racic J, Marassi FM (2011) Expression, refolding, and initial structural characterization of the Y. pestis Ail outer membrane protein in lipids. Biochim Biophys Acta 1808:482–489. doi:10.1016/j.bbamem.2010.09.017 CrossRefGoogle Scholar
  41. Rand RP, Chapman D, Larsson K (1975) Tilted hydrocarbon chains of dipalmitoyl lecithin become perpendicular to the bilayer before melting. Biophys J 15:1117–1124. doi:10.1016/S0006-3495(75)85888-7 CrossRefGoogle Scholar
  42. Renault M, Tommassen-van Boxtel R, Bos MP, Post JA, Tommassen J, Baldus M (2012) Cellular solid-state nuclear magnetic resonance spectroscopy. Proc Natl Acad Sci USA 109:4863–4868. doi:10.1073/pnas.1116478109 ADSCrossRefGoogle Scholar
  43. Saurel O et al (2017) Local and global dynamics in klebsiella pneumoniae outer membrane protein a in lipid bilayers probed at atomic resolution. J Am Chem Soc. doi:10.1021/jacs.6b11565 Google Scholar
  44. Shahid SA, Markovic S, Linke D, van Rossum BJ (2012) Assignment and secondary structure of the YadA membrane protein by solid-state MAS NMR. Sci Rep 2:803. doi:10.1038/srep00803 ADSCrossRefGoogle Scholar
  45. Shaka AJ, Keeler J, Frenkiel T, Freeman R (1983) An improved sequence for broadband decoupling: WALTZ-16. J Magn Reson 52:335–338. doi:10.1016/0022-2364(83)90207-X ADSGoogle Scholar
  46. Szeverenyi NM, Sullivan MJ, Maciel GE (1982) Observation of spin exchange by two-dimensional fourier transform 13 C cross polarization-magic-angle spinning. J Magn Reson 47:462–475. doi:10.1016/0022-2364(82)90213-X ADSGoogle Scholar
  47. Takamori S et al (2006) Molecular anatomy of a trafficking organelle. Cell 127:831–846. doi:10.1016/j.cell.2006.10.030 CrossRefGoogle Scholar
  48. Takegoshi K, Nakamura S, Terao T (2001) 13 C-1H dipolar-assisted rotational resonance in magic-angle spinning NMR. Chem Phys Lett 344:631–637ADSCrossRefGoogle Scholar
  49. Takegoshi K, Nakamura S, Terao T (2003) 13C–1 H dipolar-driven 13C–13 C recoupling without 13 C rf irradiation in nuclear magnetic resonance of rotating solids. J Chem Phys 118:2325–2341. doi:10.1063/1.1534105 ADSCrossRefGoogle Scholar
  50. Takeuchi K, Arthanari H, Shimada I, Wagner G (2015) Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR. J Biomol NMR 63:323–331. doi:10.1007/s10858-015-9991-y CrossRefGoogle Scholar
  51. Tang M, Comellas G, Mueller LJ, Rienstra CM (2010) High resolution (1)(3)C-detected solid-state NMR spectroscopy of a deuterated protein. J Biomol NMR 48:103–111. doi:10.1007/s10858-010-9442-8 CrossRefGoogle Scholar
  52. Tardieu A, Luzzati V, Reman FC (1973) Structure and polymorphism of the hydrocarbon chains of lipids: a study of lecithin-water phases. J Mol Biol 75:711–733CrossRefGoogle Scholar
  53. Warschawski DE, Devaux PF (2005) 1 H-13C polarization transfer in membranes: a tool for probing lipid dynamics and the effect of cholesterol. J Magn Reson 177:166–171. doi:10.1016/j.jmr.2005.07.011 ADSCrossRefGoogle Scholar
  54. Yamashita S et al (2011) Structural insights into Ail-mediated adhesion in Yersinia pestis. Structure 19:1672–1682. doi:10.1016/j.str.2011.08.010 CrossRefGoogle Scholar
  55. Yao Y, Ding Y, Tian Y, Opella SJ, Marassi FM (2013) Membrane protein structure determination: back to the membrane. Methods Mol Biol 1063:145–158. doi:10.1007/978-1-62703-583-5_8 CrossRefGoogle Scholar
  56. Zhou HX, Cross TA (2013) Influences of membrane mimetic environments on membrane protein structures. Annu Rev Biophys 42:361–392. doi:10.1146/annurev-biophys-083012-130326 CrossRefGoogle Scholar
  57. Zhou DH, Rienstra CM (2008) High-performance solvent suppression for proton detected solid-state NMR. J Magn Reson 192:167–172. doi:10.1016/j.jmr.2008.01.012 ADSCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Yong Yao
    • 1
  • Samit Kumar Dutta
    • 1
  • Sang Ho Park
    • 2
  • Ratan Rai
    • 2
  • L. Miya Fujimoto
    • 1
  • Andrey A. Bobkov
    • 1
  • Stanley J. Opella
    • 2
  • Francesca M. Marassi
    • 1
  1. 1.Sanford Burnham Prebys Medical Discovery InstituteLa JollaUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaUSA

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