Skip to main content
SpringerLink
Log in

Strategies for Efficient Sample Preparation for Dynamic Nuclear Polarization Solid-State NMR of Biological Macromolecules

  • Protocol
  • First Online:
Protein NMR

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1688))

Abstract

Solid-state NMR (SSNMR) is a powerful tool for the elucidation of structure and dynamics in biological macromolecules. Over the years, SSNMR spectroscopists have developed an array of techniques enabling the measurement of internuclear correlations, distances, and torsional angles; these have been applied to the study of a number of biological systems that are difficult to study by X-ray crystallography and solution NMR, including key biological targets such as membrane proteins and amyloid fibrils. Applications of SSNMR to other topic areas, including materials science, pharmaceuticals, and small molecules, have also flourished in recent years. These studies, however, have always been hampered by the low inherent sensitivity of SSNMR, requiring large amounts of both sample and time for data collection. By taking advantage of unpaired electrons doped into a sample as a ready source of additional nuclear polarization, dynamic nuclear polarization (DNP) has brought about large improvements in SSNMR sensitivity. These, in turn, have enabled structural studies of previously inaccessible targets, such as large protein complexes, nucleic acids, viral capsids, and membrane proteins in vivo. Herein, we focus on sample preparation strategies and considerations for scientists interested in applying DNP to challenging systems.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Hirsch ML, Kalechofsky N, Belzer A et al (2015) Brute-force hyperpolarization for NMR and MRI. J Am Chem Soc 137(26):8428–8434. doi:10.1021/jacs.5b01252

    Article  CAS  PubMed  Google Scholar 

  2. Sauvée 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 

  3. Smith AN, Caporini MA, Fanucci GE, Long JR (2015) A method for dynamic nuclear polarization enhancement of membrane proteins. Angew Chem Int Ed 54:1542–1546. doi:10.1002/anie.201410249

    Article  CAS  Google Scholar 

  4. Ni QZ, Daviso E, Can TV et al (2013) High frequency dynamic nuclear polarization. Acc Chem Res 46:1933–1941. doi:10.1021/ar300348n

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 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  CAS  PubMed  Google Scholar 

  6. Cheng C-Y, Han S (2013) Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems. Annu Rev Phys Chem 64:507–532. doi:10.1146/annurev-physchem-040412-110028

    Article  CAS  PubMed  Google Scholar 

  7. Kaplan M, Pinto C, Houben K, Baldus M (2016) Nuclear magnetic resonance (NMR) applied to membrane–protein complexes. Q Rev Biophys 49:e15. doi:10.1017/S003358351600010X

    Article  PubMed  Google Scholar 

  8. Warnet XL, Arnold AA, Marcotte I, Warschawski DE (2015) In-cell solid-state NMR: an emerging technique for the study of biological membranes. Biophys J 109:2461–2466. doi:10.1016/j.bpj.2015.10.041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  Google Scholar 

  10. Lee D, Bouleau E, Saint-Bonnet P et al (2016) Ultra-low temperature MAS-DNP. J Magn Reson 264:116–124. doi:10.1016/j.jmr.2015.12.010

    Article  CAS  PubMed  Google Scholar 

  11. Hu KN (2011) Polarizing agents and mechanisms for high-field dynamic nuclear polarization of frozen dielectric solids. Solid State Nucl Magn Reson 40:31–41. doi:10.1016/j.ssnmr.2011.08.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Smith AN, Long JR (2016) Dynamic nuclear polarization as an enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy. Anal Chem 88:122–132. doi:10.1021/acs.analchem.5b04376

    Article  CAS  PubMed  Google Scholar 

  13. Akbey Ü, Oschkinat H (2016) Structural biology applications of solid state MAS DNP NMR. J Magn Reson 269:213–224. doi:10.1016/j.jmr.2016.04.003

    Article  CAS  PubMed  Google Scholar 

  14. Bruun S, Stoeppler D, Keidel A et al (2015) Light-dark adaptation of channelrhodopsin involves photoconversion between the all-trans and 13-cis retinal isomers. Biochemistry 54:5389–5400. doi:10.1021/acs.biochem.5b00597

    Article  CAS  PubMed  Google Scholar 

  15. Salnikov ES, Aisenbrey C, Aussenac F et al (2016) Membrane topologies of the PGLa antimicrobial peptide and a transmembrane anchor sequence by dynamic nuclear polarization/solid-state NMR spectroscopy. Sci Rep 6:20895. doi:10.1038/srep20895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Yamamoto K, Caporini MA, Im S-C et al (2015) Cellular solid-state NMR investigation of a membrane protein using dynamic nuclear polarization. Biochim Biophys Acta Biomembr 1848:342–349. doi:10.1016/j.bbamem.2014.07.008

    Article  CAS  Google Scholar 

  17. Williams JK, Tietze D, Lee M et al (2016) Solid-state NMR investigation of the conformation, proton conduction, and hydration of the influenza B virus M2 transmembrane proton channel. J Am Chem Soc 138:8143–8155. doi:10.1021/jacs.6b03142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Frederick KK, Michaelis VK, Corzilius B et al (2015) Sensitivity-enhanced NMR reveals alterations in protein structure by cellular milieus. Cell 163:620–628. doi:10.1016/j.cell.2015.09.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  20. Torrezan AC, Shapiro MA, Sirigiri JR et al (2011) Operation of a continuously frequency-tunable second-harmonic CW 330-GHz Gyrotron for dynamic nuclear polarization. IEEE Trans Electron Devices 58:2777–2783. doi:10.1109/TED.2011.2148721

    Article  Google Scholar 

  21. Wollan DS (1976) Dynamic nuclear polarization with an inhomogeneously broadened ESR line. II. Experiment. Phys Rev B 13:3686–3696

    Article  CAS  Google Scholar 

  22. Song C, Hu K-NN, Joo C-GG et al (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  CAS  PubMed  Google Scholar 

  23. Wenk P, Kaushik M, Richter D et al (2015) Dynamic nuclear polarization of nucleic acid with endogenously bound manganese. J Biomol NMR 63:97–109. doi:10.1007/s10858-015-9972-1

    Article  CAS  PubMed  Google Scholar 

  24. Mathies G, Caporini MA, Michaelis VK et al (2015) Efficient dynamic nuclear polarization at 800 MHz/527 GHz with Trityl-Nitroxide Biradicals. Angew Chem Int Ed 54:11770–11774. doi:10.1002/anie.201504292

    Article  CAS  Google Scholar 

  25. Zagdoun A, Rossini AJ, Conley MP et al (2013) 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  CAS  Google Scholar 

  26. Barnes AB, De Paëpe G, van der Wel PCA et al (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  CAS  PubMed  PubMed Central  Google Scholar 

  27. Elisei E, Filibian M, Carretta P et al (2015) Dynamic nuclear polarization of a glassy matrix prepared by solid state mechanochemical amorphization of crystalline substances. Chem Commun 51:2080–2083. doi:10.1039/C4CC08348B

    Article  CAS  Google Scholar 

  28. Schrader AM, Cheng CY, Israelachvili JN, Han S (2016) Communication: contrasting effects of glycerol and DMSO on lipid membrane surface hydration dynamics and forces. J Chem Phys 145(4):041101. doi:10.1063/1.4959904

    Article  PubMed  PubMed Central  Google Scholar 

  29. 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 12:5799–5803. doi:10.1039/C002268C

    Article  CAS  PubMed  Google Scholar 

  30. Meyer B (1971) Low temperature spectroscopy. American Elsevier Publ. Comp, New York

    Google Scholar 

  31. Gupta R, Lu M, Hou G et al (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  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sergeyev IV, Itin B, Rogawski R, Day LA, McDermott AE (2017) Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization. Proc Natl Acad Sci USA 114 (20):5171–5176. doi:10.1073/pnas.1701484114

  33. Chaudhari S, Berruyer P, Gajan D et al (2016) Dynamic nuclear polarization at 40 kHz magic angle spinning. Phys Chem Chem Phys 18:10616–10622. doi:10.1039/C6CP00839A

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kaplan M, Cukkemane A, van Zundert GCP et al (2015) Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nat Methods 12:5–9. doi:10.1038/nmeth.3406

    Article  Google Scholar 

  35. Kubicki DJ, Casano G, Schwarzwälder M et al (2016) Rational design of dinitroxide biradicals for efficient cross-effect dynamic nuclear polarization. Chem Sci 7:550–558. doi:10.1039/C5SC02921J

    Article  CAS  Google Scholar 

  36. Le D, Ziarelli F, Phan TNT et al (2015) Up to 100% improvement in dynamic nuclear polarization solid-state NMR sensitivity enhancement of polymers by removing oxygen. Macromol Rapid Commun 36:1416–1421. doi:10.1002/marc.201500133

    Article  CAS  PubMed  Google Scholar 

  37. Kubicki DJ, Rossini AJ, Purea A et al (2014) Amplifying dynamic nuclear polarization of frozen solutions by incorporating dielectric particles. J Am Chem Soc 136:15711–15718. doi:10.1021/ja5088453

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Liao SY, Lee M, Wang T et al (2016) Efficient DNP NMR of membrane proteins : sample preparation protocols , sensitivity , and radical location. J Biomol NMR 64(3):223–237. doi:10.1007/s10858-016-0023-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Cady S, Wang T, Hong M (2011) Membrane-dependent effects of a cytoplasmic helix on the structure and drug binding of the influenza virus M2 protein. J Am Chem Soc 133:11572–11579. doi:10.1021/ja202051n

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Lesage A, Lelli M, Gajan D et al (2010) Surface enhanced NMR spectroscopy by dynamic nuclear polarization. J Am Chem Soc 132:15459–15461. doi:10.1021/ja104771z

    Article  CAS  PubMed  Google Scholar 

  41. Lelli M, Chaudhari SR, Gajan D et al (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  CAS  PubMed  PubMed Central  Google Scholar 

  42. Koers EJ, Lõpez-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  CAS  Google Scholar 

  43. Morcombe CR, Zilm KW (2003) Chemical shift referencing in MAS solid state NMR. J Magn Reson 162:479–486. doi:10.1016/S1090-7807(03)00082-X

    Article  CAS  PubMed  Google Scholar 

  44. Smith AA, Corzilius B, Barnes AB et al (2012) Solid effect dynamic nuclear polarization and polarization pathways. J Chem Phys 136(1):015101. doi:10.1063/1.3670019

    Article  PubMed  PubMed Central  Google Scholar 

  45. Corzilius B, Andreas LB, Smith AA et al (2014) Paramagnet induced signal quenching in MAS-DNP experiments in frozen homogeneous solutions. J Magn Reson 240:113–123. doi:10.1016/j.jmr.2013.11.013

    Article  CAS  PubMed  Google Scholar 

  46. Mentink-Vigier F, Paul S, Lee D et al (2015) Nuclear depolarization and absolute sensitivity in magic-angle spinning cross-effect dynamic nuclear polarization. Phys Chem Chem Phys 17(34):21824–21836. doi:10.1039/C5CP03457D

    Article  CAS  PubMed  Google Scholar 

  47. Takahashi H, Fernández-De-Alba C, Lee D et al (2014) Optimization of an absolute sensitivity in a glassy matrix during DNP-enhanced multidimensional solid-state NMR experiments. J Magn Reson 239:91–99. doi:10.1016/j.jmr.2013.12.005

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

The authors would like to thank Dr. James Kempf, Dr. Shane Pawsey, Bryce Smith, and Christopher Hickey of Bruker Biospin for many helpful discussions, figures, and photographs.

Author information

Authors and Affiliations

  1. New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA

    Boris Itin

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

    Ivan V. Sergeyev

Authors
  1. Boris Itin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivan V. Sergeyev
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Boris Itin .

Editor information

Editors and Affiliations

  1. Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA

    Ranajeet Ghose

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Itin, B., Sergeyev, I.V. (2018). Strategies for Efficient Sample Preparation for Dynamic Nuclear Polarization Solid-State NMR of Biological Macromolecules. In: Ghose, R. (eds) Protein NMR. Methods in Molecular Biology, vol 1688. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7386-6_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7386-6_7

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7385-9

  • Online ISBN: 978-1-4939-7386-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation