Abstract
The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)6 tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.
Similar content being viewed by others
References
Baneres JL, Martin A, Hullot P, Girard JP, Rossi JC, Parello J (2003) Structure-based analysis of GPCR function: conformational adaptation of both agonist and receptor upon leukotriene B4 binding to recombinant BLT1. J Mol Biol 329:801–814
Banères JL, Mesnier D, Martin A, Joubert L, Dumuis A, Bockaert J (2005) Molecular characterization of a purified 5-HT4 receptor: a structural basis for drug efficacy. J Biol Chem 280:20253–20260
Bennett M, Yeagle JA, Maciejewski M, Ocampo J, Yeagle PL (2004) Stability of loops in the structure of lactose permease. Biochemistry 43:12829–12837
Boyd D, Schierle C, Beckwith J (1998) How many membrane proteins are there? Protein Sci 7:201–205
Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318:1258–1265
Cohen LS, Arshava B, Estephan R, Englander J, Kim H, Hauser M, Zerbe O, Ceruso M, Becker JM, Naider F (2008) Expression and biophysical analysis of two double-transmembrane domain-containing fragments from a yeast G protein-coupled receptor. Biopolymers 90:117–130
Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302
Drew D, Froderberg L, Baars L, De Gier JW (2003) Assembly and overexpression of membrane proteins in Escherichia coli. Biochim Biophys Acta 1610:3–10
Drew D, Slotboom DJ, Friso G, Reda T, Genevaux P, Rapp M, Meindl-Beinker NM, Lambert W, Lerch M, Daley DO, Van Wijk KJ, Hirst J, Kunji E, De Gier JW (2005) A scalable, GFP-based pipeline for membrane protein overexpression screening and purification. Protein Sci 14:2011–2017
Engelman DM (2005) Membranes are more mosaic than fluid. Nature 438:578–580
Foord SM (2002) Receptor classification: post genome. Curr Opin Pharmacol 2:561–566
Getmanova E, Patel AB, Klein-Seetharaman J, Loewen MC, Reeves PJ, Friedman N, Sheves M, Smith SO, Khorana HG (2004) NMR spectroscopy of phosphorylated wild-type rhodopsin: mobility of the phosphorylated C-terminus of rhodopsin in the dark and upon light activation. Biochemistry 43:1126–1133
Glover KJ, Whiles JA, Wu G, Yu N, Deems R, Struppe JO, Stark RE, Komives EA, Vold RR (2001) Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules. Biophys J 81:2163–2171
Gohon Y, Dahmane T, Ruigrok RW, Schuck P, Charvolin D, Rappaport F, Timmins P, Engelman DM, Tribet C, Popot JL, Ebel C (2008) Bacteriorhodopsin/amphipol complexes: structural and functional properties. Biophys J 94:3523–3537
Grisshammer R, White JF, Trinh LB, Shiloach J (2005) Large-scale expression and purification of a G-protein-coupled receptor for structure determination–an overview. J Struct Funct Genomics 6:159–163
Harmar AJ (2001) Family-B G-protein-coupled receptors. Genome Biol 2:30131–3013.10
Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, Von Heijne G (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433:377–381
Hessa T, Meindl-Beinker NM, Bernsel A, Kim H, Sato Y, Lerch-Bader M, Nilsson I, White SH, von Heijne G (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450:1026–1030
Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727–730
Howell SC, Mesleh MF, Opella SJ (2005) NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system. Biochemistry 44:5196–5206
Huang KS, Bayley H, Liao MJ, London E, Khorana HG (1981) Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments. J Biol Chem 256:3802–3809
Jacoby E, Bouhelal R, Gerspacher M, Seuwen K (2006) The 7 TM G-protein-coupled receptor target family. Chem Med Chem 1:761–782
Kahn TW, Engelman DM (1992) Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five-helix fragment. Biochemistry 31:6144–6151
Katragadda M, Alderfer JL, Yeagle PL (2001a) Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin. Biophys J 81:1029–1036
Katragadda M, Chopra A, Bennett M, Alderfer JL, Yeagle PL, Albert AD (2001b) Structures of the transmembrane helices of the G-protein coupled receptor, rhodopsin. J Pept Res 58:79–89
Kay LE, Keifer P, Saarien T (1992) Pure absorption gradient enhanced heteronuclear single-quantum correlation sepctroscopy with improved sensitivity. J Am Chem Soc 114:10663–10665
Keeler J, Clowes RT, Davis AL, Laue ED (1994) Pulsed-field gradients: theory and practice. Methods Enzymol 239:145–207
Keller R (2004) The computer aided resonance assignment. CANTINA Verlag, Goldau
Kiefer H, Krieger J, Olszewski JD, Von Heijne G, Prestwich GD, Breer H (1996) Expression of an olfactory receptor in Escherichia coli: purification, reconstitution, and ligand binding. Biochemistry 35:16077–16084
Klammt C, Srivastava A, Eifler N, Junge F, Beyermann M, Schwarz D, Michel H, Dötsch V, Bernhard F (2007) Functional analysis of cell-free-produced human endothelin B receptor reveals transmembrane segment 1 as an essential area for ET-1 binding and homodimer formation. FEBS J 274:3257–3269
Klein-Seetharaman J, Reeves PJ, Loewen MC, Getmanova EV, Chung J, Schwalbe H, Wright PE, Khorana HG (2002) Solution NMR spectroscopy of [alpha-15N]lysine-labeled rhodopsin: The single peak observed in both conventional and TROSY-type HSQC spectra is ascribed to Lys-339 in the carboxyl-terminal peptide sequence. Proc Natl Acad Sci USA 99:3452–3457
Klein-Seetharaman J, Yanamala NV, Javeed F, Reeves PJ, Getmanova EV, Loewen MC, Schwalbe H, Khorana HG (2004) Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR. Proc Natl Acad Sci USA 101:3409–3413
Krüger-Koplin RD, Sorgen PL, Krüger-Koplin ST, Rivera-Torres IO, Cahill SM, Hicks DB, Grinius L, Krulwich TA, Girvin ME (2004) An evaluation of detergents for NMR structural studies of membrane proteins. J Biomol NMR 28:43–57
Lau TL, Partridge AW, Ginsberg MH, Ulmer TS (2008) Structure of the integrin beta3 transmembrane segment in phospholipid bicelles and detergent micelles. Biochemistry 47:4008–4016
Lee BK, Jung KS, Son C, Kim H, Verberkmoes NC, Arshava B, Naider F, Becker JM (2007) Affinity purification and characterization of a G-protein coupled receptor, Saccharomyces cerevisiae Ste2p. Prot Expr Purif 56:62–71
Lyukmanova EN, Shenkarev ZO, Paramonov AS, Sobol AG, Ovchinnikova TV, Chupin VV, Kirpichnikov MP, Blommers MJ, Arseniev AS (2008) Lipid-protein nanoscale bilayers: a versatile medium for NMR investigations of membrane proteins and membrane-active peptides. J Am Chem Soc 130:2140–2141
Ma D, Liu Z, Li L, Tang P, Xu Y (2005) Structure and dynamics of the second and third transmembrane domains of human glycine receptor. Biochemistry 44:8790–8800
Mackenzie KR, Prestegard JH, Engelman DM (1997) A transmembrane helix dimer—structure and implications. Science 276:131–133
Martin NP, Leavitt LM, Sommers CM, Dumont ME (1999) Assembly of G protein-coupled receptors from fragments: identification of functional receptors with discontinuities in each of the loops connecting transmembrane segments. Biochemistry 38:682–695
Massotte D (2003) G protein-coupled receptor overexpression with the baculovirus-insect cell system: a tool for structural and functional studies. Biochim Biophys Acta 1610:77–89
Miroux B, Walker JE (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol 260:289–298
Mobley CK, Myers JK, Hadziselimovic A, Ellis CD, Sanders CR (2007) Purification and initiation of structural characterization of human peripheral myelin protein 22, an integral membrane protein linked to peripheral neuropathies. Biochemistry 46:11185–11195
Murakami M, Kouyama T (2008) Crystal structure of squid rhodopsin. Nature 453:363–367
Musial-Siwek M, Kendall DA, Yeagle PL (2008) Solution NMR of signal peptidase, a membrane protein. Biochim Biophys Acta 1778:937–944
Neumoin A, Arshava B, Becker J, Zerbe O, Naider F (2007) NMR studies in dodecylphosphocholine of a fragment containing the seventh transmembrane helix of a G-protein-coupled receptor from Saccharomyces cerevisiae. Biophys J 93:467–482
Noggle JH, Schirmer RE (1971) The nuclear overhauser effect—chemical applications. Academic Press, New York
O’Hara PJ, Sheppard PO, Thogersen H, Venezia D, Haldeman BA, Mcgrane V, Houamed KM, Thomsen C, Gilbert TL, Mulvihill ER (1993) The ligand-binding domain in metabotropic glutamate receptors is related to bacterial periplasmic binding proteins. Neuron 11:41–52
Oxenoid K, Kim HJ, Jacob J, Sonnichsen FD, Sanders CR (2004) NMR assignments for a helical 40 kDa membrane protein. J Am Chem Soc 126:5048–5049
Page RC, Moore JD, Nguyen HB, Sharma M, Chase R, Gao FP, Mobley CK, Sanders CR, Ma L, Sönnichsen FD, Lee S, Howell SC, Opella SJ, Cross TA (2006) Comprehensive evaluation of solution nuclear magnetic resonance spectroscopy sample preparation for helical integral membrane proteins. J Struct Func Genom 7:51–64
Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739–745
Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP (2008) Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454:183–187
Pervushin K, Riek R, Wider G, Wüthrich K (1997) 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. Proc Natl Acad Sci USA 94:12366–12371
Poget SF, Girvin ME (2007) Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but sometimes bigger is better. Biochim Biophys Acta 1768:3098–3106
Popot JL, Engelman DM (1990) Membrane protein folding and oligomerization: the two-stage model. Biochemistry 29:4031–4037
Popot JL, Engelman DM (2000) Helical membrane protein folding, stability, and evolution. Annu Rev Biochem 69:881–922
Rastogi VK, Girvin ME (1999) Structural changes linked to proton translocation by subunit c of the ATP synthase. Nature 402:263–268
Ridge KD, Lee SS, Yao LL (1995) In vivo assembly of rhodopsin from expressed polypeptide fragments. Proc Natl Acad Sci USA 92:3204–3208
Rosenbaum DM, Cherezov V, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Yao XJ, Weis WI, Stevens RC, Kobilka BK (2007) GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function. Science 318:1266–1273
Salzmann M, Pervushin K, Wider G, Senn H, Wüthrich K (1998) TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc Natl Acad Sci USA 95:13585–13590
Salzmann M, Wider G, Pervushin K, Senn H, Wüthrich K (1999) TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins. J Am Chem Soc 121:844–848
Sanders CR, Oxenoid K (2000) Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins. Biochim Biophys Acta 1508:129–145
Sanders CR, Sönnichsen F (2006) Solution NMR of membrane proteins: practice and challenges. Magn Reson Chem 44:S24–S40
Sanders C, Kuhn Hoffmann A, Gray D, Keyes M, Ellis CD (2004) French swimwear for membrane proteins. ChemBioChem 5:423–426
Sarramegna V, Talmont F, Demange P, Milon A (2003) Heterologous expression of G-protein-coupled receptors: comparison of expression systems fron the standpoint of large-scale production and purification. Cell Mol Life Sci 60:1529–1546
Sarramegn V, Muller I, Milon A, Talmont F (2006) Recombinant G protein-coupled receptors from expression to renaturation: a challenge towards structure. Cell Mol Life Sci 63:1149–1164
Schubert M, Kolbe M, Kessler B, Oesterhelt D, Schmieder P (2002) Heteronuclear multidimensional NMR spectroscopy of solubilized membrane proteins: resonance assignment of native bacteriorhodopsin. ChemBioChem 3:1019–1023
Shan X, Gardner K, Muhandiram D, Rao NS, Arrowsmith C, Kay LE (1996) Assignment of N-15, C-13(alpha), C-13(beta), and HN resonances in an N-15, C-13, H-2 labeled 64 kDa trp repressor-operator complex using triple-resonance NMR spectroscopy and H-2-decoupling. J Am Chem Soc 118:6570–6579
Stevens TJ, Arkin IT (2000) Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins 39:417–420
Tian C, Breyer RM, Kim HJ, Karra MD, Friedman DB, Karpay A, Sanders CR (2005) Solution NMR spectroscopy of the human vasopressin V2 receptor, a G protein-coupled receptor. J Am Chem Soc 127:8010–8011
Tian C, Vanoye CG, Kang C, Welch RC, Kim HJ, George AL, Sanders CR (2007) Preparation, functional characterization, and NMR studies of human KCNE1, a voltage-gated potassium channel accessory subunit associated with deafness and long QT syndrome. Biochemistry 46:11459–11472
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, Mckusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, Mccawley S, Mcintosh T, Mcmullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, Mcdaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) The sequence of the human genome. Science 291: 1304–1351
Vold RR, Prosser RS, Deese AJ (1997) Isotropic solutions of phospholipid bicelles—a new membrane mimetic for high-resolution NMR studies of polypeptides. J Biomol NMR 9:329–335
Warne T, Serrano-Vega MJ, Baker J, Moukhametzianov R, Edwards P, Henderson R, Leslie A, Tate C, Schertler G (2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454:486–491
Wedekind A, O’malley MA, Niebauer RT, Robinson AS (2006) Optimization of the human adenosine A2a receptor yields in Saccharomyces cerevisiae. Biotechnol Prog 22:1249–1255
Weigelt J (1998) Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments. J Am Chem Soc 120:10778–10779
Werner K, Richter C, Klein-Seetharaman J, Schwalbe H (2008) Isotope labeling of mammalian GPCRs in HEK293 cells and characterization of the C-terminus of bovine rhodopsin by high resolution liquid NMR spectroscopy. J Biomol NMR 40:49–53
White SH, Wimley WC (1999) Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 28:319–365
Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171–180
Wishart D, Sykes B, Richards F (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311–333
Wittekind M, Mueller L (1993) HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha-carbon and beta-carbon resonances in proteins. J Magn Reson Ser B 101:201–205
Wrubel W, Stochaj U, Ehring R (1994) Construction and in vivo analysis of new split lactose permeases. FEBS Lett 349:433–438
Yamazaki T, Lee W, Arrowsmith C, Muhandiram D, Kay LE (1994) A suite of triple-resonance NMR experiments for the backbone assignment of N-15, C-13, H2-labeled proteins with high sensitivity. J Am Chem Soc 116:11655–11666
Yeagle PL, Salloum A, Chopra A, Bhawsar N, Ali L, Kuzmanovski G, Alderfer JL, Albert AD (2000) Structures of the intradiskal loops and amino terminus of the G-protein receptor, rhodopsin. J Pept Res 55:455–465
Yin D, Gavi S, Shumay E, Duell K, Konopka JB, Malbon CC, Wang HY (2005) Successful expression of a functional yeast G-protein-coupled receptor (Ste2) in mammalian cells. Biochem Biophys Res Commun 329:281–287
Zheng H, Zhao J, Sheng W, Xie XQ (2006) A transmembrane helix-bundle from G-protein coupled receptor CB2: biosynthesis, purification, and NMR characterization. Biopolymers 83:46–61
Zoonens M, Catoire LJ, Giusti F, Popot JL (2005) NMR study of a membrane protein in detergent-free aqueous solution. Proc Natl Acad Sci USA 102:8893–8898
Zou C, Kumaran S, Markovic S, Walser R, Zerbe O (2008) Studies of the structure of the N-terminal domain from the Y4 receptor, a G-protein coupled receptor, and its interaction with hormones from the NPY family. ChemBioChem 9:2276–2284
Acknowledgements
We would like to thank for financial support from the Swiss National Science Foundation (grant No. 3100A0-11173 to CZ), from the Alfred Werner Legat (to OZ) and from the National Institutes of Health (GM22086 to FN).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Zou, C., Naider, F. & Zerbe, O. Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR. J Biomol NMR 42, 257–269 (2008). https://doi.org/10.1007/s10858-008-9281-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10858-008-9281-z