The Nanodics: A Novel Tool to Study Membrane Protein Structure and Function

Abstract

Abstract:

Membrane proteins are responsible for a wide range of essential physiological processes, and important drug targets for treating diseases. However, structural study on membrane proteins lags far behind that on soluble proteins, and this, in large part, is due to technical difficulties in preparing homogeneous, stable and structurally relevant samples in a membrane-like environment. Phospholipid bilayer Nanodisc is novel model membrane derived from highdensity lipoprotein particles, and has proven to be useful in structural studies on membrane proteins. It has been shown that Nanodisc can provide a “native-like” lipid bilayer environment for many membrane proteins, such as VDAC-1 (voltage-dependent anion channel), GPCRs (G-protein-coupled receptors) and cytochrome P450s, thus enabling structural studies on these membrane proteins with NMR/surface plasmon resonance (SPR) techniques. Furthermore, with more sophisticated techniques such as modification of membrane scaffold proteins (MSP), the use of Nanodisc may yield structural and functional insights into a wide variety of membrane proteins in a biologically relevant membrane environment.

Key words: NMR, membrane protein, Nanodisc, high-density lipoprotein

CLC Number:

O482.53
Q71

BI Yuan-Chen, WANG Yu-Juan, WANG Jun-Feng. The Nanodics: A Novel Tool to Study Membrane Protein Structure and Function[J]. Chinese Journal of Magnetic Resonance, 2011, 28(2): 177-189.

References

[1] Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
[J]. Protein Sci, 1998, 7(4): 1 029-1 038.

[2] Czerski L, Sanders C R. Functionality of a membrane protein in bicelles[J]. Anal Biochem, 2000, 284(2): 327-333.

[3] Hu Y, Li Y, Zhang X, et al. Solution structures and backbone dynamics of a flavodoxin MioC from Escherichia coli in both Apo and Holo forms: implications for cofactor binding and electron transfer[J]. J Biol Chem, 2006, 281(46): 35 454-35 466.

[4] Seddon A M, Curnow P, Booth P J. Membrane proteins, lipids and detergents: not just a soap opera[J]. Biochimica Et Biophysica Acta-Biomembranes, 2004, 1666(1-2): 105-117.

[5] Hu Yun-fei(胡蕴菲), Jin Chang-wei(金长文). NMR studies of protein solution structures and dynamics（蛋白质溶液结构及动力学的核磁共振研究）[J]. Chinese J Magn Reson(波谱学杂志)，2009, 26(2): 151-172.

[6] Zhao Bao-lu(赵保路). Applications of electron spin resonance in biology and medicine（电子自旋共振(ESR)技术在生物和医学中的应用）[J]. Chinese J Magn Reson(波谱学杂志), 2010, 27(1): 51-67.

[7] Tamm L K, Liang B Y. NMR of membrane proteins in solution[J]. Prog Nucl Mag Res Spect, 2006, 48(4): 201-210.

[8] Booth P J, Flitsch S L, Stern L J, et al. Intermediates in the folding of the membrane-protein bacteriorhodopsin[J]. Nat Struct Biol, 1995, 2(2): 139-143.

[9] Booth P J, Paulsen H. Assembly of light-harvesting chlorophyll a/b complex in vitro. Time-resolved fluorescence measurements[J]. Biochemistry, 1996, 35(16): 5 103-5 108.

[10] Paulsen H, Finkenzeller B, Kuhlein N. Pigments induce folding of light-harvesting chlorophyll alpha/beta-binding protein[J]. Eur J Biochem, 1993, 215(3): 809-816.

[11] Lau F W, Bowie J U. A method for assessing the stability of a membrane protein[J]. Biochemistry, 1997, 36(19): 5 884-5 892.

[12] Dong M Q, Baggetto L G, Falson P, et al. Complete removal and exchange of sodium dodecyl sulfate bound to soluble and membrane proteins and restoration of their activities, using ceramic hydroxyapatite chromatography[J]. Anal Biochem, 1997, 247(2): 333-341.

[13] Lund S, Orlowski S, Deforesta B, et al. Detergent structure and associated lipid as determinants in the stabilization of solubilized Ca²⁺-Atpase from sarcoplasmic-reticulum[J]. J Biol Chem, 1989, 264(9): 4 907-4 915.

[14] Fleming K G, Ackerman A L, Engelman D M. The effect of point mutations on the free energy of transmembrane alpha-helix dimerization[J]. J Mol Biol, 1997, 272(2): 266-275.

[15] Deisenhofer J, Epp O, Miki K, et al. Structure of the protein subunits in the photosynthetic reaction center of rhodopseudomonasviridis at 3a resolution[J]. Nature, 1985, 318(6047): 618-624.

[16] Sardet C, Tardieu A, Luzzati V. Shape and size of bovine rhodopsin-small-angle X-ray-scattering study of a rhodopsin-detergent complex[J]. J Mol Biol, 1976, 105(3): 383-407.

[17] Hu Y, Zhao E, Li H, et al. Solution NMR structure of the TatA component of the twin-arginine protein transport system from GramPositive bacterium bacillus subtilis[J]. J Am Chem Soc, 2010, 132(45): 15 942-15 944.

[18] Page R C, Moore J D, Nguyen H B, et al. Comprehensive evaluation of solution nuclear magnetic resonance spectroscopy sample preparation for helical integral membrane proteins[J]. J Struct Funct Genomics, 2006, 7(1): 51-64.

[19] Krueger-Koplin R D, Sorgen P L, Krueger-Koplin S T, et al. An evaluation of detergents for NMR structural studies of membrane proteins[J]. J Biomol NMR, 2004, 28(1): 43-57.

[20] Fernandez C, Wuthrich K. NMR solution structure determination of membrane proteins reconstituted in detergent micelles[J]. FEBS Lett, 2003, 555(1): 144-150.

[21] Sanders C R, Sonnichsen F. Solution NMR of membrane proteins: practice and challenges[J]. Magn Reson Chem, 2006, 44: S24-S40.

[22] Krueger-Koplin R D, Sorgen P L, Krueger-Koplin S T, et al. An evaluation of detergents for NMR structural studies of membrane proteins[J]. J Biomol NMR, 2004, 28(1): 43-57.

[23] Shenkarev Z O, Lyukmanova E N, Solozhenkin O I, et al. Lipid-protein nanodiscs: possible application in high-resolution NMR investigations of membrane proteins and membrane-active peptides[J]. Biochemistry (Mosc), 2009, 74(7): 756-765.

[24] Chou J J, Kaufman J D, Stahl S J, et al. Micelle-induced curvature in a water-insoluble HIV-1 Env peptide revealed by NMR dipolar coupling measurement in stretched polyacrylamide gel[J]. J Am Chem Soc, 2002, 124(11): 2 450-2 451.

[25] Poget S F, Girvin M E. Solution NMR of membrane proteins in bilayer mimics: Small is beautiful, but sometimes bigger is better[J]. Biochimica Et Biophysica Acta-Biomembranes, 2007, 1 768(12): 3 098-3 106.

[26] Poget S F, Cahill S M, Girvin M E. Isotropic bicelles stabilize the functional form of a small multidrug-resistance pump for NMR structural studies[J]. J Am Chem Soc, 2007, 129(9): 2 432-2 433.

[27] Sanders C R, Prosser R S. Bicelles: a model membrane system for all seasons?[J]. Structure, 1998, 6(10): 1 227-1 234.

[28] Czerski L, Sanders C R. Functionality of a membrane protein in bicelles[J]. Anal Biochem, 2000, 284(2): 327-333.

[29] Sanders C R, Landis G C. Reconstitution of membrane-proteins into lipid-rich bilayered mixed micelles for nmr-studies[J]. Biochemistry, 1995, 34(12): 4 030-4 040.

[30] Howard K P, Opella S J. High-resolution solid-state NMR spectra of integral membrane proteins reconstituted into magnetically oriented phospholipid bilayers[J]. J Magn Reson Series B, 1996, 112(1): 91-94.

[31] Picard F, Paquet M J, Levesque J, et al. P-31 NMR first spectral moment study of the partial magnetic orientation of phospholipid membranes[J]. Biophys J, 1999, 77(2): 888-902.

[32] Prosser R S, Volkov V B, Shiyanovskaya I V. Novel chelate-induced magnetic alignment of biological membranes[J]. Biophys J, 1998, 75(5): 2 163-2 169.

[33] McQuade D T, Quinn M A, Yu S M, et al. Rigid amphiphiles for membrane protein manipulation[J]. Angew Chem-Int Edit, 2000, 39(4): 758-761.

[34] Tribet C, Audebert R, Popot J L. Amphipols: Polymers that keep membrane proteins soluble in aqueous solutions[J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93(26): 15 047-15 050.

[35] Deamer D, Bangham A D. Large volume liposomes by an ether vaporization method[J]. Biochimica Et Biophysica Acta, 1976, 443(3): 629-634.

[36] Szoka F, Papahadjopoulos D. Procedure for preparation of liposomes with large internal aqueous space and high capture by reverse-phase evaporation[J]. Proceedings of the National Academy of Sciences of the United States of America, 1978, 75(9): 4 194-4 198.

[37] Darszon A, Vandenberg C A, Schonfeld M, et al. Reassembly of protein-lipid complexes into large bilayer vesicles-perspectives for membrane reconstitution[J]. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences, 1980, 77(1): 239-243.

[38] Darszon A, Vandenberg C A, Ellisman M H, et al. Incorporation of membrane-proteins into large single bilayer vesicles-application to rhodopsin[J]. J Cell Biology, 1979, 81(2): 446-452.

[39] Rigaud J L, Bluzat A, Buschlen S. Incorporation of bacteriorhodopsin into large unilamellar liposomes by reverse phase evaporation
[J]. Biochem Biophys Res Comm, 1983, 111(2): 373-382.

[40] Kasahara M, Hinkle P C. Reconstitution and purification of D-Glucose transporter from human erythrocytes[J]. J Biol Chem, 1977, 252(20): 7 384-7 390.

[41] Seddon A M, Curnow P, Booth P J. Membrane proteins, lipids and detergents: not just a soap opera[J]. Biochimica Et Biophysica Acta, 2004, 1 666(1-2): 105-117.

[42] Shih A Y, Sligar S G, Schulten K. Maturation of high-density lipoproteins[J]. J R Soc Interface, 2009, 6(39): 863-871.

[43] Phillips J C, Wriggers W, Li Z, et al. Predicting the structure of apolipoprotein A-I in reconstituted high-density lipoprotein disks[J]. Biophys J, 1997, 73(5): 2 337-2 346.

[44] Borhani D W, Rogers D P, Engler J A, et al. Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation[J]. Proc Natl Acad Sci USA, 1997, 94(23): 12 291-12 296.

[45] Shih A Y, Freddolino P L, Arkhipov A, et al. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations[J]. J Struct Biol, 2007, 157(3): 579-592.

[46] Shih A Y, Denisov I G, Phillips J C, et al. Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins[J]. Biophys J, 2005, 88(1): 548-556.

[47] Denisov I G, Grinkova Y V, Lazarides A A, et al. Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size[J]. J Am Chem Soc, 2004, 126(11): 3 477-3 487.

[48] Nath A, Atkins W M, Sligar S G. Applications of phospholipid bilayer Nanodiscs in the study of membranes and membrane proteins
[J]. Biochemistry, 2007, 46(8): 2 059-2 069.

[49] Brouillette C G, Anantharamaiah G M, Engler J A, et al. Structural models of human apolipoprotein A-: a critical analysis and review
[J]. Biochimica Et Biophysica Acta, 2001, 1531(1-2): 4-46.

[50] Segrest J P. Amphipathic helixes and plasma lipoproteins: thermodynamic and geometric considerations[J]. Chem Phys Lipids, 1977, 18(1): 7-22.

[51] Brouillette C G, Jones J L, Ng T C, et al. Structural studies of apolipoprotein A-I/phosphatidylcholine recombinants by high-field proton NMR, nondenaturing gradient gel electrophoresis, and electron microscopy[J]. Biochemistry, 1984, 23(2): 359-367.

[52] Koppaka V, Silvestro L, Engler J A, et al. The structure of human lipoprotein A-I. Evidence for the "belt" model[J]. J Biol Chem, 1999, 274(21): 14 541-14 544.

[53] Davidson W S, Hilliard G M. The spatial organization of apolipoprotein A-I on the edge of discoidal high density lipoprotein particles: a mass specrometry study[J]. J Biol Chem, 2003, 278(29): 27 199-27 207.

[54] Silva R A, Hilliard G M, Li L, et al. A mass spectrometric determination of the conformation of dimeric apolipoprotein A-I in discoidal high density lipoproteins[J]. Biochemistry, 2005, 44(24): 8 600-8 607.

[55] Thomas M J, Bhat S, Sorci-Thomas M G. The use of chemical cross-linking and mass spectrometry to elucidate the tertiary conformation of lipid-bound apolipoprotein A-I[J]. Curr Opin Lipidol, 2006, 17(3): 214-220.

[56] Bhat S, Sorci-Thomas M G, Alexander E T, et al. Intermolecular contact between globular N-terminal fold and C-terminal domain of ApoA-I stabilizes its lipid-bound conformation - Studies employing chemical cross-linking and mass spectrometry[J]. J Biol Chem, 2005, 280(38): 33 015-33 025.

[57] Gorshkova I N, Liu T, Kan H Y, et al. Structure and stability of apolipoprotein a-I in solution and in discoidal high-density lipoprotein probed by double charge ablation and deletion mutation[J]. Biochemistry, 2006, 45(4): 1 242-1 254.

[58] Martin D D, Budamagunta M S, Ryan R O, et al. Apolipoprotein A-I assumes a “looped belt” conformation on reconstituted high density lipoprotein[J]. J Biol Chem, 2006, 281(29): 20 418-20 426.

[59] Panagotopulos S E, Horace E M, Maiorano J N, et al. Apolipoprotein A-I adopts a belt-like orientation in reconstituted high density lipoproteins[J]. J Biol Chem, 2001, 276(46): 42 965-42 970.

[60] Li H H, Lyles D S, Thomas M J, et al. Structural determination of lipid-bound ApoA-I using fluorescence resonance energy transfer[J]. J Biol Chem, 2000, 275(47): 37 048-37 054.

[61] Li Y, Kijac A Z, Sligar S G, et al. Structural analysis of nanoscale self-assembled discoidal lipid bilayers by solid-state NMR spectroscopy[J]. Biophys J, 2006, 91(10): 3 819-3 828.

[62] Klon A E, Jones M K, Segrest J P, et al. Molecular belt models for the apolipoprotein A-I Paris and Milano mutations[J]. Biophys J, 2000, 79(3): 1 679-1 685.

[63] Segrest J P, Jones M K, Klon A E, et al. A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein
[J]. J Biol Chem, 1999, 274(45): 31 755-31 758.

[64] Cheung M C, Segrest J P, Albers J J, et al. Characterization of high density lipoprotein subspecies: structural studies by single vertical spin ultracentrifugation and immunoaffinity chromatography[J]. J Lipid Res, 1987, 28(8): 913-929.

[65] Bayburt T H, Sligar S G. Membrane protein assembly into Nanodiscs[J]. FEBS Lett, 2010, 584(9): 1 721-1 727.

[66] Bayburt T H, Sligar S G. Self-assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers[J]. Protein Sci, 2003, 12(11): 2 476-2 481.

[67] Civjan N R, Bayburt T H, Schuler M A, et al. Direct solubilization of heterologously expressed membrane proteins by incorporation into nanoscale lipid bilayers[J]. Biotechniques, 2003, 35(3): 556-560, 562-563.

[68] Sligar S G. Finding a single-molecule solution for membrane proteins[J]. Biochem Bioph Res Comm, 2003, 312(1): 115-119.

[69] Baas B J, Denisov I G, Sligar S G. Homotropic cooperativity of monomeric cytochrome P450 3A4 in a nanoscale native bilayer environment[J]. Arch Biochem Biophys, 2004, 430(2): 218-228.

[70] Duan H, Civjan N R, Sligar S G, et al. Co-incorporation of heterologously expressed Arabidopsis cytochrome P450 and P450 reductase into soluble nanoscale lipid bilayers[J]. Arch Biochem Biophys, 2004, 424(2): 141-153.

[71] Bayburt T H, Grinkova Y V, Sligar S G. Self-assembly of discoidal phospholipid bilayer nanoparticles with membrane scaffold proteins[J]. Nano Lett, 2002, 2(8): 853-856.

[72] Das A, Zhao J, Schatz G C, et al. Screening of type I and II drug binding to human Cytochrome P450-3A4 in Nanodiscs by localized surface plasmon resonance spectroscopy[J]. Anal Chem, 2009, 81(10): 3 754-3 759.

[73] Davydov D R, Fernando H, Baas B J, et al. Kinetics of dithionite-dependent reduction of cytochrome P450 3A4: heterogeneity of the enzyme caused by its oligomerization[J]. Biochemistry, 2005, 44(42): 13 902-13 913.

[74] Denisov I G, Grinkova Y V, Baas B J, et al. The ferrous-dioxygen intermediate in human cytochrome P450 3A4. Substrate ependence of formation and decay kinetics[J]. J Biol Chem, 2006, 281(33): 23 313-23 318.

[75] Leitz A J, Bayburt T H, Barnakov A N, et al. Functional reconstitution of beta(2)-adrenergic receptors utilizing self-assembling Nanodisc technology[J]. Biotechniques, 2006, 40(5): 601-602, 604, 606.

[76] Hiller S, Ibraghimov I, Wagner G, et al. Coupled decomposition of four-dimensional NOESY spectra[J]. J Am Chem Soc, 2009, 131(36): 12 970-12 978.

[77] Lyukmanova E N, Shenkarev Z O, Paramonov A S, et al. Lipid-protein nanoscale bilayers: a versatile medium for NMR investigations of membrane proteins and membrane-active peptides[J]. J Am Chem Soc, 2008, 130(7): 2 140-2 141.

[78] Raschle T, Hiller S, Yu T Y, et al. Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer Nanodiscs[J]. J Am Chem Soc, 2009, 131(49): 17 777-17 779.

[79] Raschle T, Hiller S, Etzkorn M, et al. Nonmicellar systems for solution NMR spectroscopy of membrane proteins[J]. Curr Opin Struct Biol, 2010, 20(4): 471-479.

[80] Yoshiura C, Kofuku Y, Ueda T, et al. NMR analyses of the interaction between CCR5 and its ligand using functional reconstitution of CCR5 in lipid bilayers[J]. J Am Chem Soc, 2010, 132(19): 6 768-6 777.

[81] Katzen F, Peterson T C, Kudlicki W. Membrane protein expression: no cells required[J]. Trends Biotechnol, 2009, 27(8): 455-460.

[82] Shimizu Y, Kuruma Y, Ying B W, et al. Cell-free translation systems for protein engineering[J]. FEBS J, 2006, 273(18): 4 133-4 140.

[83] Katzen F, Chang G, Kudlicki W. The past, present and future of cell-free protein synthesis[J]. Trends Biotechnol, 2005, 23(3): 150-156.

[84] Farrokhi N, Hrmova M, Burton R A, et al. Heterologous and cell free protein expression systems[J]. Method Mol Biol, 2009, 513: 175-198.

[85] Luirink J, von Heijne G, Houben E, et al. Biogenesis of inner membrane proteins in Escherichia coli[J]. Annu Rev Microbiol, 2005, 59: 329-355.

[86] Andersson H, Vonheijne G. Membrane-protein topology-effects of delta-Mu(H)+ on the translocation of charged residues explain the positive inside rule[J]. Embo J, 1994, 13(10): 2 267-2 272.

[87] Cappuccio J A, Blanchette C D, Sulchek T A, et al. Cell-free Co-expression of functional membrane proteins and apolipoprotein, forming soluble nanolipoprotein particles[J]. Mol Cell Proteomics, 2008, 7(11): 2 246-2 253.

[88] Katzen F, Fletcher J E, Yang J P, et al. Insertion of membrane proteins into discoidal membranes using a cell-free protein expression approach[J]. J Proteome Research, 2008, 7(8): 3 535-3 542.

[89] Alami M, Dalal K, Lelj-Garolla B, et al. Nanodiscs unravel the interaction between the SecYEG channel and its cytosolic partner SecA[J]. Embo J, 2007, 26(8): 1 995-2 004.

[90] Frias J C, Williams K J, Fisher E A, et al. Recombinant HDL-like nanoparticles: a specific contrast agent for MRI of atherosclerotic plaques[J]. J Am Chem Soc, 2004, 126(50): 16 316-16 317.