From nanodiscs to isotropic bicelles: a procedure for solution NMR studies of detergent sensitive integral membrane proteins

, Summary Nanodiscs and isotropic bicelles are promising membrane mimetics in the field of solution NMR spectroscopy of integral membrane proteins (IMPs). Despite varied challenges to solution NMR studies of IMPs, we attribute the paucity of solution NMR structures in these environments to the inability of diverse IMPs to withstand detergent treatment during standard nanodisc and bicelle preparations. Here, we present a strategy that creates small isotropic bicelles from IMPs cotranslationally embedded in large nanodiscs using cell-free expression. Our results demonstrate appreciable gains in NMR spectral quality while preserving lipid-IMP contacts. We validate the approach on the detergent sensitive LspA, which finally allowed us to perform high quality triple resonance NMR experiments for structural studies. Our strategy of producing bicelles from nanodiscs comprehensively avoids detergent during expression and preparation and is suitable for solution NMR spectroscopy of lipid-IMPs complexes. Graphical abstract Laguerre et al. show that nanodisc bilayers can be peeled away from embedded membrane proteins by detergent titration to make bicelles. Avoiding initial detergent solubilization, this method preserves lipid contacts and functional folds of detergent-sensitive membrane proteins. The resulting improvements in spectral intensity facilitate high resolution NMR spectroscopy for structure determination.

[1]  M. Caffrey,et al.  Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin , 2016, Science.

[2]  V. Dötsch,et al.  Lipid Requirements for the Enzymatic Activity of MraY Translocases and in Vitro Reconstitution of the Lipid II Synthesis Pathway* , 2015, The Journal of Biological Chemistry.

[3]  F. Bezanilla,et al.  Resting state of the human proton channel dimer in a lipid bilayer , 2015, Proceedings of the National Academy of Sciences.

[4]  Rémy Sounier,et al.  Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins. , 2015, Current opinion in structural biology.

[5]  Gunnar von Heijne,et al.  Mechanisms of integral membrane protein insertion and folding. , 2015, Journal of molecular biology.

[6]  R. Renthal,et al.  Kinetics of lipid mixing between bicelles and nanolipoprotein particles. , 2015, Biophysical chemistry.

[7]  Martin Caffrey,et al.  A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes , 2015, Acta crystallographica. Section F, Structural biology communications.

[8]  J. Killian,et al.  Detergent-free isolation, characterization, and functional reconstitution of a tetrameric K+ channel: The power of native nanodiscs , 2014, Proceedings of the National Academy of Sciences.

[9]  Gunnar von Heijne,et al.  SPONTANEOUS TRANSMEMBRANE HELIX INSERTION THERMODYNAMICALLY MIMICS TRANSLOCON-GUIDED INSERTION , 2014, Nature Communications.

[10]  M. Ubbink,et al.  Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints. , 2014, Current opinion in structural biology.

[11]  V. Dötsch,et al.  Functional properties of cell-free expressed human endothelin A and endothelin B receptors in artificial membrane environments. , 2013, Biochimica et biophysica acta.

[12]  G. Wagner,et al.  Cell-free expressed bacteriorhodopsin in different soluble membrane mimetics: biophysical properties and NMR accessibility. , 2013, Structure.

[13]  G. Wagner,et al.  Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins. , 2013, Journal of the American Chemical Society.

[14]  R. Soong,et al.  When detergent meets bilayer: birth and coming of age of lipid bicelles. , 2013, Progress in nuclear magnetic resonance spectroscopy.

[15]  Klaus Schulten,et al.  Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain , 2013, Nature Structural &Molecular Biology.

[16]  V. Dötsch,et al.  Characterization of co-translationally formed nanodisc complexes with small multidrug transporters, proteorhodopsin and with the E. coli MraY translocase. , 2012, Biochimica et biophysica acta.

[17]  N. Alder,et al.  The Cell-Free Integration of a Polytopic Mitochondrial Membrane Protein into Liposomes Occurs Cotranslationally and in a Lipid-Dependent Manner , 2012, PloS one.

[18]  Ayyalusamy Ramamoorthy,et al.  The Magic of Bicelles Lights Up Membrane Protein Structure , 2012, Chemical reviews.

[19]  S. Grage,et al.  Magnetically oriented dodecylphosphocholine bicelles for solid-state NMR structure analysis. , 2012, Biochimica et biophysica acta.

[20]  Ahu Arslan Yildiz,et al.  Cell-free synthesis of cytochrome bo(3) ubiquinol oxidase in artificial membranes. , 2012, Analytical biochemistry.

[21]  K. Henzler-Wildman,et al.  Reconstitution of integral membrane proteins into isotropic bicelles with improved sample stability and expanded lipid composition profile. , 2012, Biochimica et biophysica acta.

[22]  K. Mineev,et al.  Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes. , 2012, Biochimica et biophysica acta.

[23]  V. Dötsch,et al.  Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment , 2012, Journal of biomolecular NMR.

[24]  H. Schwalbe,et al.  Solution NMR structure of proteorhodopsin. , 2011, Angewandte Chemie.

[25]  D. Kern,et al.  Antiparallel EmrE exports drugs by exchanging between asymmetric structures , 2011, Nature.

[26]  Hector Viadiu,et al.  Nanodiscs versus macrodiscs for NMR of membrane proteins. , 2011, Biochemistry.

[27]  D. Nietlispach,et al.  Solution NMR studies of polytopic α-helical membrane proteins. , 2011, Current opinion in structural biology.

[28]  A. Arnold,et al.  Choosing membrane mimetics for NMR structural studies of transmembrane proteins. , 2011, Biochimica et biophysica acta.

[29]  Qingxin Li,et al.  Solution NMR study of integral membrane proteins. , 2011, Current opinion in chemical biology.

[30]  G. Wagner,et al.  Nonmicellar systems for solution NMR spectroscopy of membrane proteins. , 2010, Current opinion in structural biology.

[31]  Tim J Stevens,et al.  DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure. , 2010, Journal of magnetic resonance.

[32]  C. Sanders,et al.  Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. , 2009, Progress in nuclear magnetic resonance spectroscopy.

[33]  A. Pardi,et al.  Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution. , 2009, Journal of the American Chemical Society.

[34]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[35]  T. Sulchek,et al.  Insertion of membrane proteins into discoidal membranes using a cell-free protein expression approach. , 2008, Journal of proteome research.

[36]  V. Dötsch,et al.  Preparative scale expression of membrane proteins in Escherichia coli-based continuous exchange cell-free systems , 2007, Nature Protocols.

[37]  E. Bamberg,et al.  Functional cell-free synthesis of a seven helix membrane protein: in situ insertion of bacteriorhodopsin into liposomes. , 2007, Journal of molecular biology.

[38]  J. Iwahara,et al.  Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules. , 2007, Journal of magnetic resonance.

[39]  C. Sanders,et al.  Solution NMR of membrane proteins: practice and challenges , 2006, Magnetic resonance in chemistry : MRC.

[40]  Paul Schanda,et al.  Speeding up three-dimensional protein NMR experiments to a few minutes. , 2006, Journal of the American Chemical Society.

[41]  Paul Schanda,et al.  SOFAST-HMQC Experiments for Recording Two-dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds , 2005, Journal of biomolecular NMR.

[42]  S. Sligar,et al.  Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size. , 2004, Journal of the American Chemical Society.

[43]  Christopher G Tate,et al.  Three‐dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer , 2003, The EMBO journal.

[44]  S. Sligar,et al.  Self‐assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers , 2003, Protein science : a publication of the Protein Society.

[45]  L. Kay,et al.  Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. , 2003, Journal of the American Chemical Society.

[46]  A. Palmer,et al.  Mapping chemical exchange in proteins with MW > 50 kD. , 2003, Journal of the American Chemical Society.

[47]  Kurt Wüthrich,et al.  TROSY-TYPE TRIPLE-RESONANCE EXPERIMENTS FOR SEQUENTIAL NMR ASSIGNMENTS OF LARGE PROTEINS , 1999 .

[48]  K Wüthrich,et al.  TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[49]  R. Riek,et al.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[50]  J. Bowie,et al.  A method for assessing the stability of a membrane protein. , 1997, Biochemistry.

[51]  H. Khorana,et al.  Denaturation and renaturation of bacteriorhodopsin in detergents and lipid-detergent mixtures. , 1982, The Journal of biological chemistry.

[52]  V. Dötsch,et al.  High-level cell-free production of membrane proteins with nanodiscs. , 2014, Methods in molecular biology.

[53]  B. Brutscher,et al.  Recovering lost magnetization: polarization enhancement in biomolecular NMR , 2011, Journal of biomolecular NMR.

[54]  V. Dötsch,et al.  Cell-free expression and stable isotope labelling strategies for membrane proteins , 2010, Journal of biomolecular NMR.

[55]  Michael A. Goren,et al.  Cell-free translation of integral membrane proteins into unilamelar liposomes. , 2009, Methods in enzymology.

[56]  S. Opella,et al.  Bicelle samples for solid-state NMR of membrane proteins , 2007, Nature Protocols.

[57]  Kurt Wüthrich,et al.  Effective rotational correlation times of proteins from NMR relaxation interference. , 2006, Journal of magnetic resonance.