Database Study on the Expression and Purification of Membrane Proteins

Author(s): Chen-Yan Zhang*, Shi-Qi Zhao, Shi-Long Zhang, Li-Heng Luo, Ding-Chang Liu, Wei-Hang Ding, Dong-Jie Fu, Xu-Dong Deng, Da-Chuan Yin*

Journal Name: Protein & Peptide Letters

Volume 28 , Issue 9 , 2021


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Abstract:

Membrane proteins are crucial for biological processes, and many of them are important to drug targets. Understanding the three-dimensional structures of membrane proteins are essential to evaluate their bio-function and drug design. High-purity membrane proteins are important for structural determination. Membrane proteins have low yields and are difficult to purify because they tend to aggregate. We summarized membrane protein expression systems, vectors, tags, and detergents, which have deposited in the Protein Data Bank (PDB) in recent four-and-a-half years. Escherichia coli is the most expression system for membrane proteins, and HEK293 cells are the most commonly cell lines for human membrane protein expression. The most frequently vectors are pFastBac1 for alpha-helical membrane proteins, pET28a for beta-barrel membrane proteins, and pTRC99a for monotopic membrane proteins. The most used tag for membrane proteins is the 6×His-tag. FLAG commonly used for alpha-helical membrane proteins, Strep and GST for beta- barrel and monotopic membrane proteins, respectively. The detergents and their concentrations used for alpha-helical, beta-barrel, and monotopic membrane proteins are different, and DDM is commonly used for membrane protein purification. It can guide the expression and purification of membrane proteins, thus contributing to their structure and bio function studying.

Keywords: Membrane protein, expression, purification, database, tags, detergent.

[1]
Lacapère, J.J.; Pebay-Peyroula, E.; Neumann, J.M.; Etchebest, C. Determining membrane protein structures: still a challenge! Trends Biochem. Sci., 2007, 32(6), 259-270.[http://dx.doi.org/10.1016/j.tibs.2007.04.001] [PMID: 17481903]
[2]
Wise, A.; Gearing, K.; Rees, S. Target validation of G-protein coupled receptors. Drug Discov. Today, 2002, 7(4), 235-246.[http://dx.doi.org/10.1016/S1359-6446(01)02131-6] [PMID: 11839521]
[3]
Chayen, N.E.; Saridakis, E. Protein crystallization: from purified protein to diffraction-quality crystal. Nat. Methods, 2008, 5(2), 147-153.[http://dx.doi.org/10.1038/nmeth.f.203] [PMID: 18235435]
[4]
McPherson, A. Protein crystallization. Methods Mol. Biol., 2017, 1607, 17-50.[http://dx.doi.org/10.1007/978-1-4939-7000-1_2] [PMID: 28573568]
[5]
Cuéllar-Cruz, M.; Schneider, D.K.; Stojanoff, V.; Islas, S.R.; Sanchez-Puig, N.; Arreguin-Espinosa, R.; Delgado, J.M.; Moreno, A. Formation of crystalline silica-carbonate biomorphs of alkaline earth metals (Ca, Ba, Sr) from ambient to low temperatures: chemical implications during the primitive earth’s life. Cryst. Growth Des., 2020, 20, 1186-1195.[http://dx.doi.org/10.1021/acs.cgd.9b01473]
[6]
Botha, S.; Baitan, D.; Jungnickel, K.E.J.; Oberthür, D.; Schmidt, C.; Stern, S.; Wiedorn, M.O.; Perbandt, M.; Chapman, H.N.; Betzel, C. De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography. IUCrJ, 2018, 5(Pt 5), 524-530.[http://dx.doi.org/10.1107/S2052252518009223] [PMID: 30224955]
[7]
Seddon, A.M.; Curnow, P.; Booth, P.J. Membrane proteins, lipids and detergents: not just a soap opera. Biochim. Biophys. Acta, 2004, 1666(1-2), 105-117.[http://dx.doi.org/10.1016/j.bbamem.2004.04.011] [PMID: 15519311]
[8]
Zhou, Z.R.; Huang, W.; Liu, K.J.; Lin, F.L.; Wang, X.L.; Wang, F.; Jiang, R. Soluble expression, one-step purification and characterization of recombinant human growth hormone fused with ompA3 in Escherichia coli. Protein Pept. Lett., 2021, 28(5), 533-542.[http://dx.doi.org/10.2174/0929866527666201110123426] [PMID: 33172365]
[9]
Braiman, M.S.; Stern, L.J.; Chao, B.H.; Khorana, H.G. Structure-function studies on bacteriorhodopsin. IV. Purification and renaturation of bacterio-opsin polypeptide expressed in Escherichia coli. J. Biol. Chem., 1987, 262(19), 9271-9276.[http://dx.doi.org/10.1016/S0021-9258(18)48076-3] [PMID: 3298254]
[10]
Fukuda, M.; Eshdat, Y.; Tarone, G.; Marchesi, V.T. Isolation and characterization of peptides derived from the cytoplasmic segment of band 3, the predominant intrinsic membrane protein of the human erythrocyte. J. Biol. Chem., 1978, 253(7), 2419-2428.[http://dx.doi.org/10.1016/S0021-9258(17)38090-0] [PMID: 632277]
[11]
Carpenter, E.P.; Beis, K.; Cameron, A.D.; Iwata, S. Overcoming the challenges of membrane protein crystallography. Curr. Opin. Struct. Biol., 2008, 18(5), 581-586.[http://dx.doi.org/10.1016/j.sbi.2008.07.001] [PMID: 18674618]
[12]
Lyons, J.A.; Shahsavar, A.; Paulsen, P.A.; Pedersen, B.P.; Nissen, P. Expression strategies for structural studies of eukaryotic membrane proteins. Curr. Opin. Struct. Biol., 2016, 38, 137-144.[http://dx.doi.org/10.1016/j.sbi.2016.06.011] [PMID: 27362979]
[13]
Rosano, G.L.; Morales, E.S.; Ceccarelli, E.A. New tools for recombinant protein production in Escherichia coli: A 5-year update. Protein Sci., 2019, 28(8), 1412-1422.[http://dx.doi.org/10.1002/pro.3668] [PMID: 31219641]
[14]
Ahmad, M.; Hirz, M.; Pichler, H.; Schwab, H. Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production. Appl. Microbiol. Biotechnol., 2014, 98(12), 5301-5317.[http://dx.doi.org/10.1007/s00253-014-5732-5] [PMID: 24743983]
[15]
Yang, Z.; Zhang, Z. Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: a review. Biotechnol. Adv., 2018, 36(1), 182-195.[http://dx.doi.org/10.1016/j.biotechadv.2017.11.002] [PMID: 29129652]
[16]
Gottesman, M.M. Chinese hamster ovary cells. Methods Enzymol., 1987, 151, 3-8.[http://dx.doi.org/10.1016/S0076-6879(87)51004-7] [PMID: 3431446]
[17]
Arena, T.A.; Chou, B.; Harms, P.D.; Wong, A.W. An anti-apoptotic HEK293 cell line provides a robust and high titer platform for transient protein expression in bioreactors. MAbs, 2019, 11(5), 977-986.[http://dx.doi.org/10.1080/19420862.2019.1598230] [PMID: 30907238]
[18]
Brödel, A.K.; Sonnabend, A.; Kubick, S. Cell-free protein expression based on extracts from CHO cells. Biotechnol. Bioeng., 2014, 111(1), 25-36.[http://dx.doi.org/10.1002/bit.25013] [PMID: 24018795]
[19]
Gagoski, D.; Polinkovsky, M.E.; Mureev, S.; Kunert, A.; Johnston, W.; Gambin, Y.; Alexandrov, K. Performance benchmarking of four cell-free protein expression systems. Biotechnol. Bioeng., 2016, 113(2), 292-300.[http://dx.doi.org/10.1002/bit.25814] [PMID: 26301602]
[20]
Studier, F.W.; Moffatt, B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol., 1986, 189(1), 113-130.[http://dx.doi.org/10.1016/0022-2836(86)90385-2] [PMID: 3537305]
[21]
Rosenberg, A.H.; Lade, B.N.; Chui, D.S.; Lin, S.W.; Dunn, J.J.; Studier, F.W. Vectors for selective expression of cloned DNAs by T7 RNA polymerase. Gene, 1987, 56(1), 125-135.[http://dx.doi.org/10.1016/0378-1119(87)90165-X] [PMID: 3315856]
[22]
Studier, F.W.; Rosenberg, A.H.; Dunn, J.J.; Dubendorff, J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol., 1990, 185, 60-89.[http://dx.doi.org/10.1016/0076-6879(90)85008-C] [PMID: 2199796]
[23]
Zhang, X.; Yao, Z.; Duan, Y.; Zhang, X.; Shi, J.; Xu, Z. Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope. Biochem. J., 2018, 475(1), 319-328.[http://dx.doi.org/10.1042/BCJ20170616] [PMID: 29187520]
[24]
Wang, W.; Li, Y.; Wang, Y.; Shi, C.; Li, C.; Li, Q.; Linhardt, R.J. Bacteriophage T7 transcription system: an enabling tool in synthetic biology. Biotechnol. Adv., 2018, 36(8), 2129-2137.[http://dx.doi.org/10.1016/j.biotechadv.2018.10.001] [PMID: 30290194]
[25]
Shang, H.; Garretson, T.A.; Kumar, C.M.S.; Dieter, R.F.; Cheng, X.W. Improved pFastBac™ donor plasmid vectors for higher protein production using the Bac-to-Bac® baculovirus expression vector system. J. Biotechnol., 2017, 255, 37-46.[http://dx.doi.org/10.1016/j.jbiotec.2017.06.397] [PMID: 28645582]
[26]
Goehring, A.; Lee, C.H.; Wang, K.H.; Michel, J.C.; Claxton, D.P.; Baconguis, I.; Althoff, T.; Fischer, S.; Garcia, K.C.; Gouaux, E. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies. Nat. Protoc., 2014, 9(11), 2574-2585.[http://dx.doi.org/10.1038/nprot.2014.173] [PMID: 25299155]
[27]
Hochuli, E.; Döbeli, H.; Schacher, A. New metal chelate adsorbent selective for proteins and peptides containing neighbouring histidine residues. J. Chromatogr. A, 1987, 411, 177-184.[http://dx.doi.org/10.1016/S0021-9673(00)93969-4] [PMID: 3443622]
[28]
Abdullah, N.; Chase, H.A. Removal of poly-histidine fusion tags from recombinant proteins purified by expanded bed adsorption. Biotechnol. Bioeng., 2005, 92(4), 501-513.[http://dx.doi.org/10.1002/bit.20633] [PMID: 16080185]
[29]
Tovar, C.N.; Odunuga, O.O. Size of Protein is a major factor that affects retention on preparative IMAC columns. Protein J., 2019, 38(1), 76-82.[http://dx.doi.org/10.1007/s10930-018-9803-9] [PMID: 30448899]
[30]
Kutyshenko, V.P.; Mikoulinskaia, G.V.; Chernyshov, S.V.; Yegorov, A.Y.; Prokhorov, D.A.; Uversky, V.N. Effect of C-terminal His-tag and purification routine on the activity and structure of the metalloenzyme, l-alanyl-d-glutamate peptidase of the bacteriophage T5. Int. J. Biol. Macromol., 2019, 124, 810-818.[http://dx.doi.org/10.1016/j.ijbiomac.2018.11.219] [PMID: 30500497]
[31]
Sayari, A.; Mosbah, H.; Verger, R.; Gargouri, Y. The N-terminal His-tag affects the enantioselectivity of staphylococcal lipases: a monolayer study. J. Colloid Interface Sci., 2007, 313(1), 261-267.[http://dx.doi.org/10.1016/j.jcis.2007.04.053] [PMID: 17532333]
[32]
Terpe, K. Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl. Microbiol. Biotechnol., 2003, 60(5), 523-533.[http://dx.doi.org/10.1007/s00253-002-1158-6] [PMID: 12536251]
[33]
Schmidt, T.G.M.; Koepke, J.; Frank, R.; Skerra, A. Molecular interaction between the Strep-tag affinity peptide and its cognate target, streptavidin. J. Mol. Biol., 1996, 255(5), 753-766.[http://dx.doi.org/10.1006/jmbi.1996.0061] [PMID: 8636976]
[34]
Schmidt, T.G.M.; Skerra, A. The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins. Nat. Protoc., 2007, 2(6), 1528-1535.[http://dx.doi.org/10.1038/nprot.2007.209] [PMID: 17571060]
[35]
Hopp, T.P.; Prickett, K.S.; Price, V.L.; Libby, R.T.; March, C.J.; Cerretti, D.P.; Urdal, D.L.; Conlon, P.J. A short polypeptide marker sequence useful for recombinant protein identification and purification. Bio-Biotechnol., 1988, 6, 1204-1210.[http://dx.doi.org/10.1038/nbt1088-1204]
[36]
Smith, D.B.; Johnson, K.S. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene, 1988, 67(1), 31-40.[http://dx.doi.org/10.1016/0378-1119(88)90005-4] [PMID: 3047011]
[37]
Wang, X.; Guo, T.; Chen, J.; Li, X.; Zhou, Y.; Pan, Z. Covalent and selective immobilization of GST fusion proteins with fluorophosphonate-based probes. Chem. Commun. (Camb.), 2018, 54(37), 4661-4664.[http://dx.doi.org/10.1039/C7CC08888D] [PMID: 29542741]
[38]
Wolfe, A.J.; Gugel, J.F.; Chen, M.; Movileanu, L. Detergent desorption of membrane proteins exhibits two kinetic phases. J. Phys. Chem. Lett., 2018, 9(8), 1913-1919.[http://dx.doi.org/10.1021/acs.jpclett.8b00549] [PMID: 29595981]
[39]
Le Bon, C.; Della Pia, E.A.; Giusti, F.; Lloret, N.; Zoonens, M.; Martinez, K.L.; Popot, J.L. Synthesis of an oligonucleotide-derivatized amphipol and its use to trap and immobilize membrane proteins. Nucleic Acids Res., 2014, 42(10), e83.[http://dx.doi.org/10.1093/nar/gku250] [PMID: 24744236]
[40]
Giusti, F.; Kessler, P.; Hansen, R.W.; Della Pia, E.A.; Le Bon, C.; Mourier, G.; Popot, J.L.; Martinez, K.L.; Zoonens, M. Synthesis of a polyhistidine-bearing amphipol and its use for immobilizing membrane proteins. Biomacromolecules, 2015, 16(12), 3751-3761.[http://dx.doi.org/10.1021/acs.biomac.5b01010] [PMID: 26492302]
[41]
Le Bon, C.; Marconnet, A.; Masscheleyn, S.; Popot, J.L.; Zoonens, M. Folding and stabilizing membrane proteins in amphipol A8-35. Methods, 2018, 147, 95-105.[http://dx.doi.org/10.1016/j.ymeth.2018.04.012] [PMID: 29678587]
[42]
Denisov, I.G.; Sligar, S.G. Nanodiscs for structural and functional studies of membrane proteins. Nat. Struct. Mol. Biol., 2016, 23(6), 481-486.[http://dx.doi.org/10.1038/nsmb.3195] [PMID: 27273631]
[43]
Nollert, P. Membrane protein crystallization in amphiphile phases: practical and theoretical considerations. Prog. Biophys. Mol. Biol., 2005, 88(3), 339-357.[http://dx.doi.org/10.1016/j.pbiomolbio.2004.07.006] [PMID: 15652249]
[44]
Lee, Y.C.; Bååth, J.A.; Bastle, R.M.; Bhattacharjee, S.; Cantoria, M.J.; Dornan, M.; Gamero-Estevez, E.; Ford, L.; Halova, L.; Kernan, J.; Kürten, C.; Li, S.; Martinez, J.; Sachan, N.; Sarr, M.; Shan, X.; Subramanian, N.; Rivera, K.; Pappin, D.; Lin, S.H. Impact of detergents on membrane protein complex isolation. J. Proteome Res., 2018, 17(1), 348-358.[http://dx.doi.org/10.1021/acs.jproteome.7b00599] [PMID: 29110486]
[45]
Opitz, S.; Hannika, F.; Krüger, T.; Rhode, H. The removal of Triton X-100 by dialysis is feasible! Anal. Bioanal. Chem., 2015, 407(4), 1107-1118.[http://dx.doi.org/10.1007/s00216-014-8333-3] [PMID: 25424179]
[46]
le Maire, M.; Arnou, B.; Olesen, C.; Georgin, D.; Ebel, C.; Møller, J.V. Gel chromatography and analytical ultracentrifugation to determine the extent of detergent binding and aggregation, and stokes radius of membrane proteins using sarcoplasmic reticulum Ca2+-ATPase as an example. Nat. Protoc., 2008, 3(11), 1782-1795.[http://dx.doi.org/10.1038/nprot.2008.177] [PMID: 18974737]
[47]
Gorka, J.; Rohmer, M.; Bornemann, S.; Papasotiriou, D.G.; Baeumlisberger, D.; Arrey, T.N.; Bahr, U.; Karas, M. Perfusion reversed-phase high-performance liquid chromatography for protein separation from detergent-containing solutions: an alternative to gel-based approaches. Anal. Biochem., 2012, 424(2), 97-107.[http://dx.doi.org/10.1016/j.ab.2012.02.021] [PMID: 22370273]
[48]
Ehsan, M.; Du, Y.; Mortensen, J.S.; Hariharan, P.; Qu, Q.; Ghani, L.; Das, M.; Grethen, A.; Byrne, B.; Skiniotis, G.; Keller, S.; Loland, C.J.; Guan, L.; Kobilka, B.K.; Chae, P.S. Self-assembly behavior and application of terphenyl-cored trimaltosides for membrane-protein studies: impact of detergent hydrophobic group geometry on protein stability. Chemistry, 2019, 25(49), 11545-11554.[http://dx.doi.org/10.1002/chem.201902468] [PMID: 31243822]
[49]
Anandan, A.; Vrielink, A. Detergents in membrane protein purification and crystallisation. Adv. Exp. Med. Biol., 2016, 922, 13-28.[http://dx.doi.org/10.1007/978-3-319-35072-1_2] [PMID: 27553232]
[50]
Bechara, C.; Bolbach, G.; Bazzaco, P.; Sharma, K.S.; Durand, G.; Popot, J.L.; Zito, F.; Sagan, S. MALDI-TOF mass spectrometry analysis of amphipol-trapped membrane proteins. Anal. Chem., 2012, 84(14), 6128-6135.[http://dx.doi.org/10.1021/ac301035r] [PMID: 22703540]
[51]
Burton-Smith, R.N.; Watanabe, A.; Tokutsu, R.; Song, C.; Murata, K.; Minagawa, J. Structural determination of the large photosystem II-light-harvesting complex II supercomplex of Chlamydomonas reinhardtii using nonionic amphipol. J. Biol. Chem., 2019, 294(41), 15003-15013.[http://dx.doi.org/10.1074/jbc.RA119.009341] [PMID: 31420447]
[52]
Hagn, F.; Nasr, M.L.; Wagner, G. Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR. Nat. Protoc., 2018, 13(1), 79-98.[http://dx.doi.org/10.1038/nprot.2017.094] [PMID: 29215632]
[53]
Yeh, V.; Lee, T.Y.; Chen, C.W.; Kuo, P.C.; Shiue, J.; Chu, L.K.; Yu, T.Y. Highly efficient transfer of 7TM membrane protein from native membrane to covalently circularized nanodisc. Sci. Rep., 2018, 8(1), 13501.[http://dx.doi.org/10.1038/s41598-018-31925-1] [PMID: 30201976]


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Article Details

VOLUME: 28
ISSUE: 9
Year: 2021
Published on: 15 April, 2021
Page: [972 - 982]
Pages: 11
DOI: 10.2174/0929866528666210415120234
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