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NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field

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Abstract

Dynamic nuclear polarization (DNP) has become a powerful method to enhance spectroscopic sensitivity in the context of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. We show that, compared to DNP at lower field (400 MHz/263 GHz), high field DNP (800 MHz/527 GHz) can significantly enhance spectral resolution and allows exploitation of the paramagnetic relaxation properties of DNP polarizing agents as direct structural probes under magic angle spinning conditions. Applied to a membrane-embedded K+ channel, this approach allowed us to refine the membrane-embedded channel structure and revealed conformational substates that are present during two different stages of the channel gating cycle. High-field DNP thus offers atomic insight into the role of molecular plasticity during the course of biomolecular function in a complex cellular environment.

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Abbreviations

AT:

Ambient temperature

DNP:

Dynamic nuclear polarization

LT:

Low temperature

MAS:

Magic angle spinning

PRE:

Paramagnetic relaxation enhancement

ssNMR:

Solid-state nuclear magnetic resonance

TM:

Transmembrane helix

MRI:

Magnetic resonance imaging

SF:

Selectivity filter

PDSD:

Proton-driven spin diffusion

TOTAPOL:

1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol

AMUPol:

(15-{[(7-oxyl-3,11-dioxa-7-azadispiro[5.1.5.3]hexadec-15-yl)carbamoyl][2-(2,5,8,11-tetraoxatridecan-13-ylamino)}-[3,11-dioxa-7-azadispiro[5.1.5.3]hexadec-7-yl])oxidanyl

References

  • Ader C, Schneider R, Hornig S et al (2008) A structural link between inactivation and block of a K + channel. Nat Struct Mol Biol 15:605–612. doi:10.1038/nsmb.1430

    Article  Google Scholar 

  • Ader C, Schneider R, Hornig S et al (2009a) Coupling of activation and inactivation gate in a K + -channel: potassium and ligand sensitivity. EMBO J 28:2825–2834. doi:10.1038/emboj.2009.218

    Article  Google Scholar 

  • Ader C, Schneider R, Seidel K et al (2009b) Structural rearrangements of membrane proteins probed by water-edited solid-state NMR spectroscopy. J Am Chem Soc 131:170–176. doi:10.1021/ja806306e

    Article  Google Scholar 

  • Ader C, Pongs O, Becker S, Baldus M (2010) Protein dynamics detected in a membrane-embedded potassium channel using two-dimensional solid-state NMR spectroscopy. Biochim Biophys Acta-Biomembr 1798:286–290. doi:10.1016/j.bbamem.2009.06.023

    Article  Google Scholar 

  • Akbey Ü, Franks WT, Linden A et al (2010) Dynamic nuclear polarization of deuterated proteins. Angew Chem Int Ed 49:7803–7806. doi:10.1002/anie.201002044

    Article  Google Scholar 

  • Andreas LB, Barnes AB, Corzilius B et al (2013) Dynamic nuclear polarization study of inhibitor binding to the M218-60 proton transporter from influenza A. Biochemistry 52:2774–2782. doi:10.1021/bi400150x

    Article  Google Scholar 

  • Andrew ER, Bradbury A, Eades RG (1958) Nuclear magnetic resonance spectra from a crystal rotated at high speed. Nature 182:1659

    Article  ADS  Google Scholar 

  • Ardenkjær-Larsen JH, Fridlund B, Gram A et al (2003) Increase in signal-to-noise ratio of > 10,000 times in liquid-state NMR. Proc Natl Acad Sci 100:10158–10163

    Article  ADS  Google Scholar 

  • Bajaj VS, Mak-Jurkauskas ML, Belenky M et al (2009) Functional and shunt states of bacteriorhodopsin resolved by 250 GHz dynamic nuclear polarization-enhanced solid-state NMR. Proc Natl Acad Sci USA 106:9244–9249. doi:10.1073/pnas.0900908106

    Article  ADS  Google Scholar 

  • Baldus M, Petkova AT, Herzfeld J, Griffin RG (1998) Cross polarization in the tilted frame: assignment and spectral simplification in heteronuclear spin systems. Mol Phys 95:1197–1207

    Article  ADS  Google Scholar 

  • Barnes AB, Markhasin E, Daviso E et al (2012) Dynamic nuclear polarization at 700 MHz/460GHz. J Mag Reson 224:1–7. doi:10.1016/j.jmr.2012.08.002

    Article  ADS  Google Scholar 

  • Bernini A, Spiga O, Venditti V et al (2006) NMR studies of lysozyme surface accessibility by using different paramagnetic relaxation probes. J Am Chem Soc 128:9290–9291. doi:10.1021/ja062109y

    Article  Google Scholar 

  • Bertini I, Luchinat C, Parigi G, Pierattelli R (2005) NMR spectroscopy of paramagnetic metalloproteins. ChemBioChem 6:1536–1549. doi:10.1002/cbic.200500124

    Article  Google Scholar 

  • Bhate MP, Wylie BJ, Tian L, McDermott AE (2010) Conformational dynamics in the selectivity filter of KcsA in response to potassium ion concentration. J Mol Biol 401:155–166. doi:10.1016/j.jmb.2010.06.031

    Article  Google Scholar 

  • Bloembergen N, Morgan LO (1961) Proton relaxation times in paramagnetic solutions. Effects of electron spin relaxation. J Chem Phys 34:842. doi:10.1063/1.1731684

    Article  ADS  Google Scholar 

  • Buffy JJ, Hong T, Yamaguchi S et al (2003) Solid-state NMR investigation of the depth of insertion of protegrin-1 in lipid bilayers using paramagnetic Mn2. Biophys J 85:2363–2373. doi:10.1016/S0006-3495(03)74660-8

    Article  Google Scholar 

  • Cassidy MC, Chan HR, Ross BD et al (2013) In vivo magnetic resonance imaging of hyperpolarized silicon particles. Nat Nanotechnol 8:363–368. doi:10.1038/nnano.2013.65

    Article  ADS  Google Scholar 

  • Chakrapani S, Cordero-Morales JF, Perozo E (2007) A quantitative description of KcsA gating II: single-channel currents. J Gen Physiol 130:479–496. doi:10.1085/jgp.200709844

    Article  Google Scholar 

  • Chakrapani S, Cordero-Morales JF, Jogini V et al (2011) On the structural basis of modal gating behavior in K(+) channels. Nat Struct Mol Biol 18:67–74. doi:10.1038/nsmb.1968

    Article  Google Scholar 

  • Cuello LG, Jogini V, Cortes DM et al (2010a) Structural basis for the coupling between activation and inactivation gates in K + channels. Nature 466:272–277. doi:10.1038/nature09136

    Article  ADS  Google Scholar 

  • Cuello LG, Jogini V, Cortes DM, Perozo E (2010b) Structural mechanism of C-type inactivation in K + channels. Nature 466:203–207. doi:10.1038/nature09153

    Article  ADS  Google Scholar 

  • Esposito G, Lesk AM, Molinari H et al (1992) Probing protein structure by solvent perturbation of nuclear magnetic resonance spectra. Nuclear magnetic resonance spectral editing and topological mapping in proteins by paramagnetic relaxation filtering. J Mol Biol 224:659–670

    Article  Google Scholar 

  • Fricke P, Demers J-P, Becker S, Lange A (2013) Studies on the MxiH protein in T3SS needles using DNP-enhanced ssNMR spectroscopy. ChemPhysChem 15:57–60. doi:10.1002/cphc.201300994

    Article  Google Scholar 

  • Gallagher FA, Kettunen MI, Day SE et al (2008) Magnetic resonance imaging of pH in vivo using hyperpolarized 13C-labelled bicarbonate. Nature 453:940–943. doi:10.1038/nature07017

    Article  ADS  Google Scholar 

  • Gelis I, Vitzthum V, Dhimole N et al (2013) Solid-state NMR enhanced by dynamic nuclear polarization as a novel tool for ribosome structural biology. J Biomol NMR 56:85–93. doi:10.1007/s10858-013-9721-2

    Article  Google Scholar 

  • Hall DA, Maus DC, Gerfen GJ et al (1997) Polarization-enhanced NMR spectroscopy of biomolecules in frozen solution. Science 276:930–932

    Article  Google Scholar 

  • Havlin RH, Tycko R (2005) Probing site-specific conformational distributions in protein folding with solid-state NMR. Proc Natl Acad Sci USA 102:3284–3289

    Article  ADS  Google Scholar 

  • Heise H, Luca S, de Groot BL et al (2005) Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J 89:2113–2120. doi:10.1529/biophysj.105.059964

    Article  Google Scholar 

  • Hocking HG, Zangger K, Madl T (2013) Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes. ChemPhysChem 14:3082–3094. doi:10.1002/cphc.201300219

    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

    Article  ADS  Google Scholar 

  • Hu K-N, Debelouchina GT, Smith AA, Griffin RG (2011) Quantum mechanical theory of dynamic nuclear polarization in solid dielectrics. J Chem Phys 134:125105. doi:10.1063/1.3564920

    Article  ADS  Google Scholar 

  • Jacso T, Franks WT, Rose H et al (2012) Characterization of membrane proteins in isolated native cellular membranes by dynamic nuclear polarization solid-state NMR spectroscopy without purification and reconstitution. Angew Chem 124:447–450. doi:10.1002/ange.201104987

    Article  Google Scholar 

  • Kagawa A, Murokawa Y, Takeda K, Kitagawa M (2009) Optimization of 1H spin density for dynamic nuclear polarization using photo-excited triplet electron spins. J Mag Reson 197:9–13. doi:10.1016/j.jmr.2008.11.009

    Article  ADS  Google Scholar 

  • Koers EJ, López-Deber MP, Weingarth M et al (2013) Dynamic nuclear polarization NMR spectroscopy: revealing multiple conformations in lipid-anchored peptide vaccines. Angew Chem Int Ed 52:10905–10908. doi:10.1002/anie.201303374

    Article  Google Scholar 

  • Lauterbur PC (1973) Image formation by induced local interactions-examples employing nuclear magnetic resonance. Nature 242:190–191. doi:10.1038/242190a0

    Article  ADS  Google Scholar 

  • Linden AH, Franks WT, Akbey Ü et al (2011a) 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 

  • Linden AH, Lange S, Franks WT et al (2011b) Neurotoxin II bound to acetylcholine receptors in native membranes studied by dynamic nuclear polarization NMR. J Am Chem Soc 133:19266–19269. doi:10.1021/ja206999c

    Article  Google Scholar 

  • Maly T, Cui D, Griffin RG, Miller A-F (2012) H-1 dynamic nuclear polarization based on an endogenous radical. J Phys Chem B 116:7055–7065. doi:10.1021/jp300539j

    Article  Google Scholar 

  • Matsuki Y, Takahashi H, Ueda K et al (2010) Dynamic nuclear polarization experiments at 14.1 T for solid-state NMR. Phys Chem Chem Phys 12:5799. doi:10.1039/c002268c

    Article  Google Scholar 

  • Nadaud PS, Helmus JJ, Höfer N, Jaroniec CP (2007) Long-range structural restraints in spin-labeled proteins probed by solid-state nuclear magnetic resonance spectroscopy. J Am Chem Soc 129:7502–7503. doi:10.1021/ja072349t

    Article  Google Scholar 

  • Ni QZ, Daviso E, Can TV et al (2013) High frequency dynamic nuclear polarization. Acc Chem Res 46:130425010025008. doi:10.1021/ar300348n

    Article  Google Scholar 

  • Otting G (2010) Protein NMR using paramagnetic ions. Annu Rev Biophys 39:387–405. doi:10.1146/annurev.biophys.093008.131321

    Article  Google Scholar 

  • Overhauser AW (1953) Polarization of nuclei in metals. Phys Rev 92:411–415

    Article  MATH  ADS  Google Scholar 

  • Pintacuda G, Otting G (2002) Identification of protein surfaces by NMR measurements with a paramagnetic Gd(III) chelate. J Am Chem Soc 124:372–373. doi:10.1021/ja016985h

    Article  Google Scholar 

  • Reggie L, Lopez JJ, Collinson I et al (2011) Dynamic nuclear polarization-enhanced solid-state NMR of a 13C-labeled signal peptide bound to lipid-reconstituted sec translocon. J Am Chem Soc 133:19084–19086. doi:10.1021/ja209378h

    Article  Google Scholar 

  • Renault M, Pawsey S, Bos MP et al (2012a) Solid-state NMR spectroscopy on cellular preparations enhanced by dynamic nuclear polarization. Angew Chem Int Ed 51:2998–3001. doi:10.1002/anie.201105984

    Article  Google Scholar 

  • Renault M, Tommassen-van Boxtel R, Bos MP et al (2012b) Cellular solid-state nuclear magnetic resonance spectroscopy. Proc Natl Acad Sci 109:4863–4868. doi:10.1073/pnas.1116478109

    Article  ADS  Google Scholar 

  • Rosay M, Tometich L, Pawsey S et al (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 

  • Rossini AJ, Zagdoun A, Lelli M et al (2013) Dynamic nuclear polarization surface enhanced NMR spectroscopy. Acc Chem Res 46:1942–1951. doi:10.1021/ar300322x

    Article  Google Scholar 

  • Salnikov E, Rosay M, Pawsey S et al (2010) Solid-state NMR spectroscopy of oriented membrane polypeptides at 100 K with signal enhancement by dynamic nuclear polarization. J Am Chem Soc 132:5940–5941. doi:10.1021/ja1007646

    Article  Google Scholar 

  • Sauvee C, Rosay M, Casano G et al (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 

  • Schneider R, Ader C, Lange A et al (2008) Solid-state NMR spectroscopy applied to a chimeric potassium channel in lipid bilayers†. J Am Chem Soc 130:7427–7435. doi:10.1021/ja800190c

    Article  Google Scholar 

  • Sengupta I, Nadaud PS, Helmus JJ et al (2012) Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy. Nat Chem 4:410–417. doi:10.1038/nchem.1299

    Article  Google Scholar 

  • Shen Y, Bax A (2010) SPARTA + : a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48:13–22. doi:10.1007/s10858-010-9433-9

    Article  Google Scholar 

  • Siemer AB, Huang K-Y, McDermott AE (2012) Protein linewidth and solvent dynamics in frozen solution NMR. PLoS ONE 7:e47242. doi:10.1371/journal.pone.0047242.g001

    Article  ADS  Google Scholar 

  • Smith AA, Corzilius B, Bryant JA et al (2012) A 140 GHz pulsed EPR/212 MHz NMR spectrometer for DNP studies. J Mag Reson 223:170–179. doi:10.1016/j.jmr.2012.07.008

    Article  ADS  Google Scholar 

  • Soares TA, Hünenberger PH, Kastenholz MA et al (2005) An improved nucleic acid parameter set for the GROMOS force field. J Comput Chem 26:725–737. doi:10.1002/jcc.20193

    Article  Google Scholar 

  • Solomon I (1955) Relaxation processes in a system of two spins. Phys Rev 99:559–565. doi:10.1103/PhysRev.99.559

    Article  ADS  Google Scholar 

  • Takahashi H, Ayala I, Bardet M et al (2013) Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization. J Am Chem Soc 135:5105–5110. doi:10.1021/ja312501d

    Article  Google Scholar 

  • Uysal S, Vasquez V, Tereshko V et al (2009) Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci USA 106:6644–6649. doi:10.1073/pnas.0810663106

    Article  ADS  Google Scholar 

  • van der Cruijsen EAW, Nand D, Weingarth M et al (2013) Importance of lipid–pore loop interface for potassium channel structure and function. Proc Natl Acad Sci 110:13008–13013. doi:10.1073/pnas.1305563110/-/DCSupplemental

    Article  ADS  Google Scholar 

  • van der Wel PCA, Hu K-N, Lewandowski J, Griffin RG (2006) Dynamic nuclear polarization of amyloidogenic peptide nanocrystals: GNNQQNY, a core segment of the yeast prion protein Sup35p. J Am Chem Soc 128:10840–10846. doi:10.1021/ja0626685

    Article  Google Scholar 

  • Wang T, Park YB, Caporini MA et al (2013) Sensitivity-enhanced solid-state NMR detection of expansin’s target in plant cell walls. Proc Natl Acad Sci USA 110:16444–16449. doi:10.1073/pnas.1316290110

    Article  ADS  Google Scholar 

  • Weingarth M, Prokofyev A, van der Cruijsen EAW et al (2013) Structural determinants of specific lipid binding to potassium channels. J Am Chem Soc 135:3983–3988. doi:10.1021/ja3119114

    Article  Google Scholar 

  • Weingarth M, van der Cruijsen EAW, Ostmeyer J et al (2014) Quantitative analysis of the water occupancy around the selectivity filter of a K + channel in different gating modes. J Am Chem Soc 136:2000–2007. doi:10.1021/ja411450y

    Article  Google Scholar 

  • Wickramasinghe NP, Parthasarathy S, Jones CR et al (2009) Nanomole-scale protein solid-state NMR by breaking intrinsic 1H T1 boundaries. Nat Method 6:215–218. doi:10.1038/nmeth.1300

    Article  Google Scholar 

  • Zachariae U, Schneider R, Velisetty P et al (2008) The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure 16:747–754

    Article  Google Scholar 

  • Zagdoun A, Casano G, Ouari O et al (2013a) 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 

  • Zagdoun A, Rossini AJ, Conley MP et al (2013b) Improved dynamic nuclear polarization surface-enhanced NMR spectroscopy through controlled incorporation of deuterated functional groups. Angew Chem Int Ed 52:1222–1225. doi:10.1002/anie.201208699

    Article  Google Scholar 

  • Zhou YF, Morais-Cabral JH, Kaufman A, Mackinnon R (2001) Chemistry of ion coordination and hydration revealed by a K + channel-Fab complex at 2.0 angstrom resolution. Nature 414:43–48

    Article  ADS  Google Scholar 

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Acknowledgments

We thank Mark Daniels for excellent technical support. This work was supported by NWO (grants 722.012.002 to MW and 700.11.344 and 700.58.102 to MB), DFG (Po137, 40-1 and 41-1) and NIH (NIH/NIGNS grant GM087519).

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Authors and Affiliations

  1. NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands

    Eline J. Koers, Elwin A. W. van der Cruijsen, Markus Weingarth, Alexander Prokofyev, Johan van der Zwan & Marc Baldus

  2. Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA

    Melanie Rosay & Werner E. Maas

  3. Department of Physiology, Faculty of Medicine, Saarland University, Building 56, 66421, Homburg, Germany

    Alexander Prokofyev & Olaf Pongs

  4. CNRS, ICR UMR 7273, Aix-Marseille Université, 13397, Marseille, France

    Claire Sauvée, Olivier Ouari & Paul Tordo

Authors
  1. Eline J. Koers
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  2. Elwin A. W. van der Cruijsen
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  3. Melanie Rosay
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  4. Markus Weingarth
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  5. Alexander Prokofyev
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  6. Claire Sauvée
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  9. Olaf Pongs
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  10. Paul Tordo
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  11. Werner E. Maas
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  12. Marc Baldus
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Correspondence to Marc Baldus.

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Eline J. Koers and Elwin A. W. van der Cruijsen have contributed equally.

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Koers, E.J., van der Cruijsen, E.A.W., Rosay, M. et al. NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. J Biomol NMR 60, 157–168 (2014). https://doi.org/10.1007/s10858-014-9865-8

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