Skip to main content
SpringerLink
Log in

Off-resonance 13C–2H REDOR NMR for site-resolved studies of molecular motion

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

Abstract

We introduce a 13C–2H Rotational Echo DOuble Resonance (REDOR) technique that uses the difference between on-resonance and off-resonance 2H irradiation to detect dynamic segments in deuterated molecules. By selectively inverting specific regions of the 2H magic-angle spinning (MAS) sideband manifold to recouple some of the deuterons to nearby carbons, we distinguish dynamic and rigid residues in 1D and 2D 13C spectra. We demonstrate this approach on deuterated GB1, H/D exchanged GB1, and perdeuterated bacterial cellulose. Numerical simulations reproduce the measured mixing-time and 2H carrier-frequency dependence of the REDOR dephasing of bacterial cellulose. Combining numerical simulations with experiments thus allow the extraction of motionally averaged quadrupolar couplings from REDOR dephasing values.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Data Availability

Data Availability1D and 2D spectral datasets and Bruker pulse programs are available upon request from Mei Hong at meihong@mit.edu.

References

  • Alam TM, Orban J, Drobny GP (1991) Deuterium NMR investigation of backbone dynamics in the synthetic oligonucleotide [d(CGCGAATTCGCG)]2. Biochemistry 30:9229–9237

    Article  Google Scholar 

  • Alderman DW, Solum MS, Grant DM (1986) Methods for analyzing spectroscopic line shapes. NMR solid powder patterns. J Chem Phys 84:3717–3725

    Article  ADS  Google Scholar 

  • Bak M, Nielsen NC (1997) REPULSION, a novel approach to efficient powder averaging in solid-state NMR. J Magn Reson 125:132–139

    Article  ADS  Google Scholar 

  • Bali G, Foston MB, O’Neill HM, Evans BR, He J, Ragauskas AJ (2013) The effect of deuteration on the structure of bacterial cellulose. Carbohyd Res 374:82–88

    Article  Google Scholar 

  • Bennett AE, Rienstra CM, Auger M, Lakshmi KV, Griffin RG (1995) Heteronuclear decoupling in rotating solids. J Chem Phys 103:6951–6958

    Article  ADS  Google Scholar 

  • Bernard GM, Goyal A, Miskolzie M, McKay R, Wu Q, Wasylishen RE, Michaelis VK (2017) Methylammonium lead chloride: a sensitive sample for an accurate NMR thermometer. J Magn Reson 283:14–21

    Article  ADS  Google Scholar 

  • Borle F, Seelig J (1983) Hydration of Escherichia coli lipids: Deuterium T1 relaxation time studies of phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine Biochim Biophys Acta. Biomembr 735:131–136

    Article  Google Scholar 

  • Browning JL, Seelig J (1980) Bilayers of phosphatidylserine: a deuterium and phosphorus nuclear magnetic resonance study. Biochemistry 19:1262–1270

    Article  Google Scholar 

  • Cady SD, Schmidt-Rohr K, Wang J, Soto CS, DeGrado WF, Hong M (2010) Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature 463:689–692

    Article  ADS  Google Scholar 

  • Cegelski L (2013) REDOR NMR for drug discovery. Bioorg Med Chem Lett 23:5767–5775

    Article  Google Scholar 

  • Davis JH (1983) The description of membrane lipid conformation, order and dynamics by 2H-NMR. Biochim Biophys Acta 737:117–171

    Article  Google Scholar 

  • Dick-Pérez M, Zhang Y, Hayes J, Salazar A, Zabotina OA, Hong M (2011) Structure and interactions of plant cell-wall polysaccharides by two- and three-dimensional magic-angle-spinning solid-state. Biochemistry  50:989–1000

    Article  Google Scholar 

  • Dregni AJ et al (2019) In vitro 0N4R tau fibrils contain a monomorphic β-sheet core enclosed by dynamically heterogeneous fuzzy coat segments. Proc Natl Acad Sci USA 116:16357–16366

    Article  Google Scholar 

  • Franks WT et al (2005) Magic-angle spinning solid-state NMR spectroscopy of the β1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. J Am Chem Soc 127:12291–12305

    Article  Google Scholar 

  • Gall CM, Cross TA, DiVerdi JA, Opella SJ (1982) Protein dynamics by solid-state NMR: aromatic rings of the coat protein in fd bacteriophage. Proc Natl Acad Sci USA 79:101–105

    Article  ADS  Google Scholar 

  • Gelenter MD, Wang T, Liao SY, O’Neill H, Hong M (2017) (2)H-(13)C correlation solid-state NMR for investigating dynamics and water accessibilities of proteins and carbohydrates. J Biomol NMR 68:257–270

    Article  Google Scholar 

  • Gullion T, Schaefer J (1989) Rotational-echo double-resonance NMR. J Magn Reson 81:196–200

    ADS  Google Scholar 

  • He J et al (2014) Controlled incorporation of deuterium into bacterial cellulose. Cellulose 21:927–936

    Article  Google Scholar 

  • Hilger D, Masureel M, Kobilka BK (2018) Structure and dynamics of GPCR signaling complexes. Nat Struct Mol Biol 25:4–12

    Article  Google Scholar 

  • Hologne M, Faelber K, Diehl A, Reif B (2005) Characterization of dynamics of perdeuterated proteins by MAS solid-state NMR . J Am Chem Soc 127:11208–11209

    Article  Google Scholar 

  • Hou G, Yan S, Trébosc J, Amoureux JP, Polenova T (2013) Broadband homonuclear correlation spectroscopy driven by combined R2(n)(v) sequences under fast magic angle spinning for NMR structural analysis of organic and biological solids. J Magn Reson 232:18–30

    Article  ADS  Google Scholar 

  • Jain S, Bjerring M, Nielsen NC (2012) Efficient and robust heteronuclear cross-polarization for high-speed-spinning biological solid-state NMR. J Phys Chem Lett 3:703–708

    Article  Google Scholar 

  • Jain SK et al (2014) Low-power polarization transfer between deuterons and spin-1/2 nuclei using adiabatic (RESPIRATION)CP in solid-state NMR. Phys Chem Chem Phys 16:2827–2830

    Article  Google Scholar 

  • Jaroniec CP, Tounge BA, Rienstra CM, Herzfeld J, Griffin RG (1999) Measurement of 13C– 5N distances in uniformly 13C labeled biomolecules: J-decoupled REDOR. J Am Chem Soc 121:10237–10238

    Article  Google Scholar 

  • Kang X, Kirui A, Dickwella Widanage MC, Mentink-Vigier F, Cosgrove DJ, Wang T (2019) Lignin-polysaccharide interactions in plant secondary cell walls revealed by solid-state NMR. Nat Commun 10:347

    Article  ADS  Google Scholar 

  • Kinsey RA, Kintanar A, Tsai MD, Smith RL, Janes N, Oldfield E (1981) First observation of amino acid side chain dynamics in membrane proteins using high field deuterium nuclear magnetic resonance spectroscopy. J Biol Chem 256:4146–4149

    Article  Google Scholar 

  • Latorraca NR, Venkatakrishnan AJ, Dror RO (2017) GPCR dynamics: structures in motion. Chem Rev 117:139–155

    Article  Google Scholar 

  • Lewandowski JR, Halse ME, Blackledge M, Emsley L (2015) Protein dynamics direct observation of hierarchical protein dynamics. Science 348:578–581

    Article  ADS  Google Scholar 

  • Mandala VS, Williams JK, Hong M (2018) Structure and dynamics of membrane proteins from solid-state NMR.  Annu Rev Biophys 47:201–222

    Article  Google Scholar 

  • Mandala VS, McKay MJ, Shcherbakov AA, Dregni AJ, Kolocouris A, Hong M (2020) Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers. Nat Struct Mol Biol 27:1202–1208

    Article  Google Scholar 

  • McCrate OA, Zhou X, Reichhardt C, Cegelski L (2013) Sum of the parts: composition and architecture of the bacterial extracellular matrix. J Mol Biol 425:4286–4294

    Article  Google Scholar 

  • McNeill SA, Gor’kov PL, Shetty K, Brey WW, Long JR (2009) A low-E magic angle spinning probe for biological solid state NMR at 750 MHz. J Magn Reson 197:135–144

    Article  ADS  Google Scholar 

  • Meints GA, Karlsson T, Drobny GP (2001) Modeling furanose ring dynamics in DNA. J Am Chem Soc 123:10030–10038

    Article  Google Scholar 

  • Morcombe CR, Zilm KW (2003) Chemical shift referencing in MAS solid state NMR. J Magn Reson 162:479–486

    Article  ADS  Google Scholar 

  • Munowitz M, Griffin R, Bodenhausen G, Huang T (1981) Two-dimensional rotational spin-echo nuclear magnetic resonance in solids: correlation of chemical shift and dipolar interactions. J Am Chem Soc 103:2529–2533

    Article  Google Scholar 

  • Nielsen AB, Jain S, Ernst M, Meier BH, Nielsen NC (2013) Adiabatic rotor-echo-short-pulse-irradiation mediated cross-polarization. J Magn Reson 237:147–151

    Article  ADS  Google Scholar 

  • Nishiyama Y, Sugiyama J, Chanzy H, Langan P (2003) Crystal Structure and hydrogen bonding system in cellulose Iα from synchrotron x-ray and neutron fiber diffraction. J Am Chem Soc 125:14300–14306

    Article  Google Scholar 

  • Pines A, Gibby MG, Waugh JS (1972) Proton‐enhanced nuclear induction spectroscopy. A method for high resolution NMR of dilute spins in solids. J Chem Phys 56:1776–1777

    Article  ADS  Google Scholar 

  • Reif B, Ashbrook SE, Emsley L, Hong M (2021) Solid-state NMR spectroscopy. Nat Rev Methods Primers 1:2

    Article  Google Scholar 

  • Sack I, Goldbourt A, Vega S, Buntkowsky G (1999) Deuterium REDOR: principles and applications for distance measurements. J Magn Reson 138:54–65

    Article  ADS  Google Scholar 

  • Sack I, Balazs YS, Rahimipour S, Vega S (2000) Solid-state NMR determination of peptide torsion angles: application of 2H-dephased REDOR. J Am Chem Soc 122:12263–12269

    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

    Article  Google Scholar 

  • Schmidt-Rohr K, Spiess HW (1994) Multidimensional Solid-State NMR and Polymers, 1st edn. edn. Academic Press, San Diego

    Google Scholar 

  • Seelig J (1977) Deuterium magnetic resonance: theory and application to lipid membranes. Q Rev Biophys 10:353–418

    Article  Google Scholar 

  • Shi X, Rienstra CM (2016) Site-specific internal motions in GB1 protein microcrystals revealed by 3D2H–13C–13C solid-state NMR spectroscopy. J Am Chem Soc 138:4105–4119

    Article  Google Scholar 

  • Struts AV, Salgado GF, Brown MF (2011) Solid-state 2H NMR relaxation illuminates functional dynamics of retinal cofactor in membrane activation of rhodopsin. Proc Natl Acad Sci USA 108:8263–8268

    Article  ADS  Google Scholar 

  • Veshtort M, Griffin RG (2006) SPINEVOLUTION: a powerful tool for the simulation of solid and liquid state NMR experiments. J Magn Reson 178:248–282

    Article  ADS  Google Scholar 

  • Wang T, Phyo P, Hong M (2016) Multidimensional solid-state NMR spectroscopy of plant cell walls. Solid State Nucl Mag 78:56–63

    Article  Google Scholar 

  • Witterbort RJ, Olejniczak ET, Griffin RG (1987) Analysis of 2H NMR lineshapes in anisotropic media. J Chem Phys 86:5411–5420

    Article  ADS  Google Scholar 

  • Wright PE, Dyson HJ (2015) Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 16:18–29

    Article  Google Scholar 

  • Wylie BJ, Sperling LJ, Nieuwkoop AJ, Franks WT, Oldfield E, Rienstra CM (2011) Ultrahigh resolution protein structures using NMR chemical shift tensors. Proc Natl Acad Sci USA 108:16974–16979

    Article  ADS  Google Scholar 

Download references

Acknowledgements

This work is supported by NIH Grant AG059661 to M.H. The bacterial cellulose work is supported by the Center for Lignocellulose Structure and Formation, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award #DE-SC0001090. M.D.G. is supported by an NIH Ruth L. Kirschstein Individual National Research Service Award (1F31AI133989).

Author information

Authors and Affiliations

  1. Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA

    Martin D. Gelenter, Kelly J. Chen & Mei Hong

Authors
  1. Martin D. Gelenter
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kelly J. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mei Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mei Hong.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gelenter, M.D., Chen, K.J. & Hong, M. Off-resonance 13C–2H REDOR NMR for site-resolved studies of molecular motion. J Biomol NMR 75, 335–345 (2021). https://doi.org/10.1007/s10858-021-00377-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-021-00377-7

Keywords

Search

Navigation