Skip to main content
SpringerLink
Log in

NMR of Membrane Proteins: Beyond Crystals

  • Chapter
The Next Generation in Membrane Protein Structure Determination

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 922))

Abstract

Membrane proteins are essential for the flow of signals, nutrients and energy between cells and between compartments of the cell. Their mechanisms can only be fully understood once the precise structures, dynamics and interactions involved are defined at atomic resolution. Through advances in solution and solid state NMR spectroscopy, this information is now available, as demonstrated by recent studies of stable peripheral and transmembrane proteins. Here we highlight recent cases of G-protein coupled receptors, outer membrane proteins, such as VDAC, phosphoinositide sensors, such as the FAPP-1 pleckstrin homology domain, and enzymes including the metalloproteinase MMP-12. The studies highlighted have resulted in the determination of the 3D structures, dynamical properties and interaction surfaces for membrane-associated proteins using advanced isotope labelling strategies, solubilisation systems and NMR experiments designed for very high field magnets. Solid state NMR offers further insights into the structure and multimeric assembly of membrane proteins in lipid bilayers, as well as into interactions with ligands and targets. Remaining challenges for wider application of NMR to membrane structural biology include the need for overexpression and purification systems for the production of isotope-labelled proteins with fragile folds, and the availability of only a few expensive perdeuterated detergents.Step changes that may transform the field include polymers, such as styrene maleic acid, which obviate the need for detergent altogether, and allow direct high yield purification from cells or membranes. Broader demand for NMR may be facilitated by MODA software, which instantly predicts membrane interactive residues that can subsequently be validated by NMR. In addition, recent developments in dynamic nuclear polarization NMR instrumentation offer a remarkable sensitivity enhancement from low molarity samples and cell surfaces. These advances illustrate the current capabilities and future potential of NMR for membrane protein structural biology and ligand discovery.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
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

  • Anderson TM, Clay MC, Cioffi AG, Diaz KA, Hisao GS et al (2014) Amphotericin forms an extramembranous and fungicidal sterol sponge. Nat Chem Biol 10(5):400–406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andreas LB, Barnes AB, Corzilius B, Chou JJ, Miller EA et al (2013) Dynamic nuclear polarization study of inhibitor binding to the M2(18–60) proton transporter from influenza A. Biochemistry 52(16):2774–2782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bajaj VS, Hornstein MK, Kreischer KE, Sirigiri JR, Woskov PP et al (2007) 250 GHz CW gyrotron oscillator for dynamic nuclear polarization in biological solid state NMR. J Magn Reson 189(2):251–279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barbet-Massin E, Pell AJ, Retel JS, Andreas LB, Jaudzems K, Franks WT, Nieuwkoop AJ, Hiller M, Higman V et al (2014) Rapid proton-detected NMR assignment for proteins with fast magic angle spinning. J Am Chem Soc 136(35):12489–12497

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berardi MJ, Shih WM, Harrison SC, Chou JJ (2011) Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature 476(7358):109–113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bonev BB (2013) High-resolution solid-state NMR of lipid membranes. Adv Planar Lipid Bilayers Liposomes 17:299–329

    Article  CAS  Google Scholar 

  • Butterwick JA, MacKinnon R (2010) Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP. J Mol Biol 403(4):591–606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carravetta M, Eden M, Zhao X, Brinkmann A, Levitt MH (2000) Symmetry principles for the design of radiofrequency pulse sequences in the nuclear magnetic resonance of rotating solids. Chem Phys Lett 321(3–4):205–215

    Article  CAS  Google Scholar 

  • Chen H, Ji F, Olman V, Charles KM, Liu Y et al (2011) Optimal mutation sites for PRE data collection and membrane protein structure prediction. Structure 19(4):484–495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daviso E, Prakash S, Alia A, Gast P, Neugebauer J, Jeschke G, Matysik J (2009) The electronic structure of the primary electron donor of reaction centers of purple bacteria at atomic resolution as observed by photo-CIDNP C-13 NMR. Proc Natl Acad Sci U S A 106(52):22281–22286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diller A, Roy E, Gast P, van Gorkom HJ, de Groot HJM et al (2007) N-15 photochemically induced dynamic nuclear polarization magic-angle spinning NMR analysis of the electron donor of photosystem II. Proc Natl Acad Sci U S A 104(31):12767–12771

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dominguez C, Boelens R, Bonvin A (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737

    Article  CAS  PubMed  Google Scholar 

  • Eichmann C, Tzitzilonis C, Bordignon E, Maslennikov I, Choe S, Riek R (2014) Solution NMR structure and functional analysis of the integral membrane protein YgaP from Escherichia coli. J Biol Chem 289(34):23482–23503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fan Y, Shi L, Ladizhansky V, Brown L (2011) Uniform isotope labeling of a eukaryotic seven-transmembrane helical protein in yeast enables high-resolution solid-state NMR studies in the lipid environment. J Biomol NMR 49(2):151–161

    Article  CAS  PubMed  Google Scholar 

  • Fogh R, Ionides J, Ulrich E, Boucher W, Vranken W, Linge JP et al (2002) The CCPN project: an interim report on a data model for the NMR community. Nat Struct Mol Biol 9(6):416–418

    Article  CAS  Google Scholar 

  • Gautier A, Nietlispach D (2012) Solution NMR studies of integral polytopic α-helical membrane proteins: the structure determination of the seven-helix transmembrane receptor sensory rhodopsin II, pSRII. In: Membrane protein structure and dynamics. Humana Press, New York, pp 25–45

    Chapter  Google Scholar 

  • Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, Nietlispach D (2010) Structure determination of the seven-helical transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy. Nat Struct Mol Biol 17(6):768–774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gulati S, Jamshad M, Knowles TJ, Morrison KA, Downing R et al (2014) Detergent-free purification of ABC (ATP-binding-cassette) transporters. Biochem J 461(2):269–278

    Article  CAS  PubMed  Google Scholar 

  • Haeberlen U, Waugh JS (1968) Coherent averaging effects in magnetic resonance. Phys Rev 175(2):453–467

    Article  CAS  Google Scholar 

  • 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(5):1919–1925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, Wagner G (2008) Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 321(5893):1206–1210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Horst R, Stanczak P, Serrano P, Wüthrich K (2012) Translational diffusion measurements by micro-coil NMR in aqueous solutions of the Fos-10 detergent-solubilized membrane protein OmpX. J Phys Chem B 116(23):6775–6780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jamshad M, Charlton J, Lin Y-P, Routledge SJ, Bawa Z et al (2015) G-protein coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent. Biosci Rep 35(2):e00188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Janssen GJ, Daviso E, van Son M, de Groot HJM, Alia A, Matysik J (2010) Observation of the solid-state photo-CIDNP effect in entire cells of cyanobacteria Synechocystis. Photosynth Res 104(2–3):275–282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Janssen GJ, Roy E, Matysik J, Alia A (2012) N-15 photo-CIDNP MAS NMR to reveal functional heterogeneity in electron donor of different plant organisms. Appl Magn Reson 42(1):57–67

    Article  CAS  PubMed  Google Scholar 

  • Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440(7080):52–57

    Article  CAS  PubMed  Google Scholar 

  • Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N et al (2012) Facile backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods 9(8):834–839

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knowles TJ, Finka R, Smith C, Lin Y-P, Dafforn T, Overduin M (2009) Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer. J Am Chem Soc 131(22):7484–7485

    Article  CAS  PubMed  Google Scholar 

  • Kofuku Y, Ueda T, Okude J, Shiraishi Y, Kondo K, Maeda M, Tsujishita H, Shimada I (2012) Efficacy of the β(2)-adrenergic receptor is determined by conformational equilibrium in the transmembrane region. Nat Commun 3:1045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koppisetti RK, Fulcher YG, Jurkevich A, Prior SH, Xu J et al (2014) Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12. Nat Commun 5:5552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E et al (2014) Discovery of novel membrane binding structures and functions. Biochem Cell Biol 92(6):555–563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lemmon MA (2008) Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol 9:99–111

    Article  CAS  PubMed  Google Scholar 

  • Lenoir M, Grzybek M, Majkowski M, Rajesh S, Kaur J et al (2015a) Structural basis of dynamic membrane recognition by trans-Golgi network specific FAPP proteins. J Mol Biol 427(4):966–981

    Article  CAS  PubMed  Google Scholar 

  • Lenoir M, Kufareva I, Abagyan R, Overduin M (2015b) Membrane and protein interactions of the pleckstrin homology domain superfamily. Membranes (Basel) 5(4):646–663

    Article  CAS  Google Scholar 

  • Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V et al (2012) Structural basis for allosteric regulation of GPCRs by sodium ions. Science 337(6091):232–236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu GJ, Tian Y, Vora N, Marassi FM, Opella SJ (2013) The structure of the mercury transporter MerF in phospholipid bilayers: a large conformational rearrangement results from N-terminal truncation. J Am Chem Soc 135(25):9299–9302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Madono M, Sawasaki T, Morishita R, Endo Y (2011) Wheat germ cell-free protein production system for post-genomic research. Nat Biotechnol 28(3):211–217

    CAS  Google Scholar 

  • Mao J, Do NN, Scholz F, Reggie L, Mehler M et al (2014) Structural basis of the green-blue color switching in proteorhodopsin as determined by NMR spectroscopy. J Am Chem Soc 136(50):17578–17590

    Article  CAS  PubMed  Google Scholar 

  • Mowrey D, Cui T, Jia Y, Ma D, Makhov AM et al (2013) Open-channel structures of the human glycine receptor α1 full-length transmembrane domain. Structure 21(10):1897–1904

    Article  CAS  PubMed  Google Scholar 

  • Ong YS, Lakatos A, Becker-Baldus J, Pos KM, Glaubitz C (2013) Detecting substrates bound to the secondary multidrug efflux pump EmrE by DNP-enhanced solid-state NMR. J Am Chem Soc 135(42):15754–15762

    Article  CAS  PubMed  Google Scholar 

  • Opella SJ (2013) Structure determination of membrane proteins in their native phospholipid bilayer environment by rotationally aligned solid-state NMR spectroscopy. Acc Chem Res 46(9):2145–2153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Overduin M, Cheever ML (2001) Signaling with phosphoinositides: better than binary. Mol Interv 3:10

    Google Scholar 

  • Park SH, Das BB, Casagrande F, Tian Y, Nothnagel HJ, Chu M et al (2012) Structure of the chemokine receptor CXCR1 in phospholipid bilayers. Nature 491(7426):779–783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reckel S, Gottstein D, Stehle J, Löhr F, Verhoefen MK et al (2011) Solution NMR structure of proteorhodopsin. Angew Chem Int Ed 50(50):11942–11946

    Article  CAS  Google Scholar 

  • Reggie L, Lopez JJ, Collinson I, Glaubitz C, Lorch M (2011) Dynamic nuclear polarization-enhanced solid-state NMR of a C-13-labeled signal peptide bound to lipid-reconstituted sec translocon. J Am Chem Soc 133(47):19084–19086

    Article  CAS  PubMed  Google Scholar 

  • Renault M, Bos MP, Tommassen J, Baldus M (2011) Solid-state NMR on a large multidomain integral membrane protein: the outer membrane protein assembly factor BamA. J Am Chem Soc 133(12):4175–4177

    Article  CAS  PubMed  Google Scholar 

  • Renault M, Pawsey S, Bos MP, Koers EJ et al (2012) Solid-state NMR spectroscopy on cellular preparations enhanced by dynamic nuclear polarization. Angew Chem Int Ed 51(12):2998–3001

    Article  CAS  Google Scholar 

  • Rout AK, Strub M-P, Piszczek G, Tjandra N (2014) Structure of transmembrane domain of lysosome-associated membrane protein type 2a (LAMP-2A) reveals key features for substrate specificity in chaperone-mediated autophagy. J Biol Chem 289(51):35111–35123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roy E, Gast P, van Gorkom H, de Groot HJ (2007) Photochemically induced dynamic nuclear polarization in the reaction center of the green sulphur bacterium chlorobium tepidum observed by (13)C MAS NMR. Biochim Biophys Acta -Bioenergetics 1767(6):610–615

    Article  CAS  Google Scholar 

  • Sanghera N, Correia BE, Correia JR, Ludwig C et al (2011) Deciphering the molecular details for the binding of the prion protein to main ganglioside GM1 of neuronal membranes. Chem Biol 18(11):1422–1431

    Article  CAS  PubMed  Google Scholar 

  • Shahid SA, Bardiaux B, Franks WT, Krabben L, Habeck M et al (2012) Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals. Nat Methods 9:1212–1217

    Article  CAS  PubMed  Google Scholar 

  • Simons K, Ikonen E (1997) Functional rafts in cell membranes. Nature 387(6633):569–572

    Article  CAS  Google Scholar 

  • Sobhanifar S, Reckel S, Junge F, Schwarz D, Kai L et al (2010) Cell-free expression and stable isotope labelling strategies for membrane proteins. J Biomol NMR 46(1):33–43

    Article  CAS  PubMed  Google Scholar 

  • Sounier R, Mas C, Steyaert J, Laeremans T, Manglik A et al (2015) Propagation of conformational changes during [mgr]-opioid receptor activation. Nature 524(7565):375–378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE et al (2011) High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. J Biomol NMR 51(3):227–233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thamarath SS, Alia A, Daviso E, Mance D, Golbeck JH et al (2012) Whole cell nuclear magnetic resonance characterization of two photochemically active states of the photosynthetic reaction center in heliobacteria. Biochemistry 51(29):5763–5773

    Article  CAS  PubMed  Google Scholar 

  • Van Horn W, Ogilvie M, Flynn P (2008) Use of reverse micelles in membrane protein structural biology. J Biomol NMR 40(3):203–211

    Article  CAS  PubMed  Google Scholar 

  • Van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A et al (2009) Solution NMR structure of membrane-integral diacylglycerol kinase. Science 324(5935):1726–1729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vinarov DA, Newman CLL, Markley JL (2006) Wheat germ cell-free platform for eukaryotic protein production. FEBS J 273(18):4160–4169

    Article  CAS  PubMed  Google Scholar 

  • Vostrikov VV, Mote KR, Verardi R, Veglia G (2013) Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport. Structure 21(12):2119–2130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warschawski DE, Arnold AA, Beaugrand M, Gravel A, Chartrand E, Marcotte I (2011) Choosing membrane mimetics for NMR structural studies of transmembrane proteins. Biochim Biophys Acta-Biomembranes 1808(8):1957–1974

    Article  CAS  Google Scholar 

  • Williamson PTF, Verhoeven A, Miller KW, Meier BH, Watts A (2007) The conformation of acetylcholine at its target site in the membrane-embedded nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A 104(46):18031–18036

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu CH, Ramamoorthy A, Opella SJ (1994) High-resolution heteronuclear dipolar solid state NMR spectroscopy. J Magn Reson A 109(2):270–272

    Article  Google Scholar 

  • Yamamoto K, Caporini MA, Im S-C, Waskell L, Ramamoorthy A (2015) Cellular solid-state NMR investigation of a membrane protein using dynamic nuclear polarization. Biochim Biophys Acta-Biomembranes 1848(1):342–349

    Article  CAS  Google Scholar 

  • Zech SG, Olejniczak E, Hajduk P, Mack J, McDermot AE (2004) Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy. J Am Chem Soc 126(43):13948–13953

    Article  CAS  PubMed  Google Scholar 

  • Zhou Y, Cierpicki T, Jimenez RHF, Lukasik SM, Ellena JF et al (2008) NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation. Mol Cell 31(6):896–908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The authors would like to thank the Biotechnology an Biological Sciences Research Council, Campus Alberta Innovates Program, the Engineering and Physical Sciences Research Council and the Wellcome Trust for funding.

Author information

Authors and Affiliations

  1. Henry Wellcome Building for Biomolecular NMR Spectroscopy, School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

    Sundaresan Rajesh

  2. Faculty of Medicine & Dentistry, Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada

    Michael Overduin

  3. School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH, UK

    Boyan B. Bonev

Authors
  1. Sundaresan Rajesh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael Overduin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Boyan B. Bonev
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Michael Overduin or Boyan B. Bonev .

Editor information

Editors and Affiliations

  1. Membrane Protein Laboratory, Diamond Light Source/Imperial College London, Harwell Campus, Didcot, Oxfordshire, UK

    Isabel Moraes

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Rajesh, S., Overduin, M., Bonev, B.B. (2016). NMR of Membrane Proteins: Beyond Crystals. In: Moraes, I. (eds) The Next Generation in Membrane Protein Structure Determination. Advances in Experimental Medicine and Biology, vol 922. Springer, Cham. https://doi.org/10.1007/978-3-319-35072-1_3

Download citation

Publish with us

Policies and ethics

Search

Navigation