Skip to main content
Log in

High resolution observed in 800 MHz DNP spectra of extremely rigid type III secretion needles

  • Communication
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800 MHz, the resolution of DNP spectra of type III secretion needles (T3SS) could be improved by 22 %, indicating that inhomogeneous broadening is not the dominant effect that limits the resolution of T3SS needles under DNP conditions. The outstanding spectral resolution of this system under DNP conditions can be attributed to its low overall flexibility.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

References

  • Barnes AB, Paepe GD, van der Wel PC, Hu KN, Joo CG, Bajaj VS, Mak-Jurkauskas ML, Sirigiri JR, Herzfeld J, Temkin RJ, Griffin RG (2008) High-field dynamic nuclear polarization for solid and solution biological NMR. Appl Magn Reson 34:237–263. doi:10.1007/s00723-008-0129-1

    Article  Google Scholar 

  • Becker-Baldus J, Bamann C, Saxena K, Gustmann H, Brown LJ, Brown RC, Reiter C, Bamberg E, Wachtveitl J, Schwalbe H, Glaubitz C (2015) Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy. Proc Natl Acad Sci USA 112:9896–9901. doi:10.1073/pnas.1507713112

    Article  ADS  Google Scholar 

  • Can TV, Ni QZ, Griffin RG (2015) Mechanisms of dynamic nuclear polarization in insulating solids. J Magn Reson 253:23–35. doi:10.1016/j.jmr.2015.02.005

    Article  ADS  Google Scholar 

  • Chevelkov V, Zhuravleva AV, Xue Y, Reif B, Skrynnikov NR (2007) Combined analysis of (15)N relaxation data from solid- and solution-state NMR spectroscopy. J Am Chem Soc 129:12594–12595. doi:10.1021/ja073234s

    Article  Google Scholar 

  • Debelouchina GT, Bayro MJ, Fitzpatrick AW, Ladizhansky V, Colvin MT, Caporini MA, Jaroniec CP, Bajaj VS, Rosay M, Macphee CE, Vendruscolo M, Maas WE, Dobson CM, Griffin RG (2013) Higher order amyloid fibril structure by MAS NMR and DNP spectroscopy. J Am Chem Soc 135:19237–19247. doi:10.1021/ja409050a

    Article  Google Scholar 

  • Del Amo JML, Schneider D, Loquet A, Lange A, Reif B (2013) Cryogenic solid state NMR studies of fibrils of the Alzheimer’s disease amyloid-beta peptide: perspectives for DNP. J Biomol NMR 56:359–363. doi:10.1007/s10858-013-9755-5

    Article  Google Scholar 

  • Demers JP, Sgourakis NG, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A (2013) The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles. PLoS Pathog 9:e1003245. doi:10.1371/journal.ppat.1003245

    Article  Google Scholar 

  • Demers JP, Habenstein B, Loquet A, Vasa SK, Giller K, Becker S, Baker D, Lange A, Sgourakis NG (2014) High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy. Nat Commun 5:4976. doi:10.1038/ncomms5976

    Article  ADS  Google Scholar 

  • Fasshuber HK, Lakomek NA, Habenstein B, Loquet A, Shi C, Giller K, Wolff S, Becker S, Lange A (2015) Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR. Protein Sci 24:592–598. doi:10.1002/pro.2654

    Article  Google Scholar 

  • Fricke P, Demers JP, Becker S, Lange A (2014) Studies on the MxiH protein in T3SS needles using DNP-enhanced ssNMR spectroscopy. Chem Phys Chem 15:57–60. doi:10.1002/cphc.201300994

    Google Scholar 

  • Fricke P, Chevelkov V, Shi C, Lange A (2015) Strategies for solid-state NMR investigations of supramolecular assemblies with large subunit sizes. J Magn Reson 253:2–9. doi:10.1016/j.jmr.2014.10.018

    Article  ADS  Google Scholar 

  • Gupta R, Lu M, Hou G, Caporini MA, Rosay M, Maas W, Struppe J, Suiter C, Ahn J, Byeon IJ, Franks WT, Orwick-Rydmark M, Bertarello A, Oschkinat H, Lesage A, Pintacuda G, Gronenborn AM, Polenova T (2016) Dynamic nuclear polarization enhanced MAS NMR spectroscopy for structural analysis of HIV-1 protein assemblies. J Phys Chem B 120:329–339. doi:10.1021/acs.jpcb.5b12134

    Article  Google Scholar 

  • Hohwy M, Rienstra CM, Jaroniec CP, Griffin RG (1999) Fivefold symmetric homonuclear dipolar recoupling in rotating solids: application to double quantum spectroscopy. J Chem Phys 110:7983–7992. doi:10.1063/1.478702

    Article  ADS  Google Scholar 

  • Ivanir-Dabora H, Nimerovsky E, Madhu PK, Goldbourt A (2015) Site-resolved backbone and side-chain intermediate dynamics in a carbohydrate-binding module protein studied by magic-angle spinning NMR spectroscopy. Chemistry 21:10778–10785. doi:10.1002/chem.201500856

    Article  Google Scholar 

  • Kaplan M, Cukkemane A, van Zundert GC, Narasimhan S, Daniels M, Mance D, Waksman G, Bonvin AM, Fronzes R, Folkers GE, Baldus M (2015) Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nat Methods 12:649–652. doi:10.1038/nmeth.3406

    Article  Google Scholar 

  • Koers EJ, van der Cruijsen EA, Rosay M, Weingarth M, Prokofyev A, Sauvee C, Ouari O, van der Zwan J, Pongs O, Tordo P, Maas WE, Baldus M (2014) NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. J Biomol NMR 60:157–168. doi:10.1007/s10858-014-9865-8

    Article  Google Scholar 

  • Lamley JM, Oster C, Stevens RA, Lewandowski JR (2015) Intermolecular interactions and protein dynamics by solid-state NMR spectroscopy. Angew Chem Int Ed 54:15374–15378. doi:10.1002/anie.201509168

    Article  Google Scholar 

  • Lee D, Hediger S, De Paepe G (2015) Is solid-state NMR enhanced by dynamic nuclear polarization? Solid State Nucl Magn Reson 66–67:6–20. doi:10.1016/j.ssnmr.2015.01.003

    Article  Google Scholar 

  • Lelli M, Chaudhari SR, Gajan D, Casano G, Rossini AJ, Ouari O, Tordo P, Lesage A, Emsley L (2015) Solid-state dynamic nuclear polarization at 9.4 and 18.8 T from 100 K to room temperature. J Am Chem Soc 137:14558–14561. doi:10.1021/jacs.5b08423

    Article  Google Scholar 

  • Lewandowski JR, Halse ME, Blackledge M, Emsley L (2015) Protein dynamics. Direct observation of hierarchical protein dynamics. Science 348:578–581. doi:10.1126/science.aaa6111

    Article  ADS  Google Scholar 

  • Liao SY, Lee M, Wang T, Sergeyev IV, Hong M (2016) Efficient DNP NMR of membrane proteins: sample preparation protocols, sensitivity, and radical location. J Biomol NMR. doi:10.1007/s10858-016-0023-3

    Google Scholar 

  • Linden AH, Franks WT, Akbey U, Lange S, van Rossum BJ, Oschkinat H (2011) Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR. J Biomol NMR 51:283–292. doi:10.1007/s10858-011-9535-z

    Article  Google Scholar 

  • Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A (2012) Atomic model of the type III secretion system needle. Nature 486:276–279. doi:10.1038/nature11079

    ADS  Google Scholar 

  • Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier JP, Skrynnikov NR, Schanda P (2015) Observing the overall rocking motion of a protein in a crystal. Nat Commun 6:8361. doi:10.1038/ncomms9361

    Article  ADS  Google Scholar 

  • Mance D, Gast P, Huber M, Baldus M, Ivanov KL (2015) The magnetic field dependence of cross-effect dynamic nuclear polarization under magic angle spinning. J Chem Phys 142:234201. doi:10.1063/1.4922219

    Article  ADS  Google Scholar 

  • Ni QZ, Daviso E, Can TV, Markhasin E, Jawla SK, Swager TM, Temkin RJ, Herzfeld J, Griffin RG (2013) High frequency dynamic nuclear polarization. Acc Chem Res 46:1933–1941. doi:10.1021/ar300348n

    Article  Google Scholar 

  • Pauli J, Baldus M, van Rossum B, de Groot H, Oschkinat H (2001) Backbone and side-chain 13C and 15 N signal assignments of the alpha-spectrin SH3 domain by magic angle spinning solid-state NMR at 17.6 Tesla. ChemBioChem 2:272–281

    Article  Google Scholar 

  • Perras FA, Reinig RR, Slowing II, Sadow AD, Pruski M (2016) Effects of biradical deuteration on the performance of DNP: towards better performing polarizing agents. Phys Chem Chem Phys 18:65–69. doi:10.1039/c5cp06505d

    Article  Google Scholar 

  • Potapov A, Yau WM, Ghirlando R, Thurber KR, Tycko R (2015) Successive stages of Amyloid-beta self-assembly characterized by solid-state nuclear magnetic resonance with dynamic nuclear polarization. J Am Chem Soc 137:8294–8307. doi:10.1021/jacs.5b04843

    Article  Google Scholar 

  • Rosay M, Tometich L, Pawsey S, Bader R, Schauwecker R, Blank M, Borchard PM, Cauffman SR, Felch KL, Weber RT, Temkin RJ, Griffin RG, Maas WE (2010) Solid-state dynamic nuclear polarization at 263 GHz: spectrometer design and experimental results. Phys Chem Chem Phys 12:5850–5860. doi:10.1039/c003685b

    Article  Google Scholar 

  • Sauvee C, Rosay M, Casano G, Aussenac F, Weber RT, Ouari O, Tordo P (2013) Highly efficient, water-soluble polarizing agents for dynamic nuclear polarization at high frequency. Angew Chem Int Ed 52:10858–10861. doi:10.1002/anie.201304657

    Article  Google Scholar 

  • Schanda P, Meier BH, Ernst M (2010) Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. J Am Chem Soc 132:15957–15967. doi:10.1021/ja100726a

    Article  Google Scholar 

  • Shi C, Fricke P, Lin L, Chevelkov V, Wegstroth M, Giller K, Becker S, Thanbichler M, Lange A (2015) Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR. Sci Adv 1:e1501087. doi:10.1126/sciadv.1501087

    Article  ADS  Google Scholar 

  • Siemer AB, Huang KY, McDermott AE (2012) Protein linewidth and solvent dynamics in frozen solution NMR. PLoS One 7:e47242. doi:10.1371/journal.pone.0047242

    Article  ADS  Google Scholar 

  • Song C, Hu KN, Joo CG, Swager TM, Griffin RG (2006) TOTAPOL: a biradical polarizing agent for dynamic nuclear polarization experiments in aqueous media. J Am Chem Soc 128:11385–11390. doi:10.1021/ja061284b

    Article  Google Scholar 

  • Su Y, Andreas L, Griffin RG (2015) Magic angle spinning NMR of proteins: high-frequency dynamic nuclear polarization and (1)H detection. Annu Rev Biochem 84:465–497. doi:10.1146/annurev-biochem-060614-034206

    Article  Google Scholar 

  • Takahashi H, Lee D, Dubois L, Bardet M, Hediger S, De Paepe G (2012) Rapid natural-abundance 2D 13C-13C correlation spectroscopy using dynamic nuclear polarization enhanced solid-state NMR and matrix-free sample preparation. Angew Chem Int Ed 51:11766–11769. doi:10.1002/anie.201206102

    Article  Google Scholar 

  • Takahashi H, Hediger S, De Paepe G (2013) Matrix-free dynamic nuclear polarization enables solid-state NMR 13C-13C correlation spectroscopy of proteins at natural isotopic abundance. Chem Commun 49:9479–9481. doi:10.1039/c3cc45195j

    Article  Google Scholar 

  • van der Cruijsen EA, Koers EJ, Sauvee C, Hulse RE, Weingarth M, Ouari O, Perozo E, Tordo P, Baldus M (2015) Biomolecular DNP-supported NMR spectroscopy using site-directed spin labeling. Chemistry 21:12971–12977. doi:10.1002/chem.201501376

    Article  Google Scholar 

  • Zagdoun A, Casano G, Ouari O, Schwarzwalder M, Rossini AJ, Aussenac F, Yulikov M, Jeschke G, Coperet C, Lesage A, Tordo P, Emsley L (2013) Large molecular weight nitroxide biradicals providing efficient dynamic nuclear polarization at temperatures up to 200 K. J Am Chem Soc 135:12790–12797. doi:10.1021/ja405813t

    Article  Google Scholar 

Download references

Acknowledgments

We thank Brigitta Angerstein for technical help, and Maximilian Zinke and Eve Ousby for valuable discussions. This work was supported by the Leibniz-Institut für Molekulare Pharmakologie, the Max Planck Society, the European Research Council (ERC Starting Grant to A.L.), the German Research Foundation (Deutsche Forschungsgemeinschaft; Emmy Noether Fellowship to A.L.) and the Fonds der Chemischen Industrie (Kekulé Scholarship to P.F.). Work at the 800 MHz DNP instrument at Utrecht was supported by NWO (Grants 700.11.344 and 700.58.102 to M.B.).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Adam Lange.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 557 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fricke, P., Mance, D., Chevelkov, V. et al. High resolution observed in 800 MHz DNP spectra of extremely rigid type III secretion needles. J Biomol NMR 65, 121–126 (2016). https://doi.org/10.1007/s10858-016-0044-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-016-0044-y

Keywords

Navigation