Selective capture of histidine-tagged proteins from cell lysates using TEM grids modified with NTA-graphene oxide

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Benjamin, Christopher J ^a   Wright, Kyle J ^a   Bolton, Scott C ^a   Hyun, Seok Hee ^a   Krynski, Kyle ^a   Grover, Mahima ^a   Yu, Guimei ^b   Guo, Fei ^b   Kinzer Ursem, Tamara L ^c   Jiang, Wen ^c   Thompson, David H ^a,b,d  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

^d Purdue University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2-N,N-BIS(CARBOXYMETHYL)LYSINE; 4 AMINOBENZOIC ACID; CHAPERONIN 60; ESCHERICHIA COLI PROTEIN; FUSION PROTEIN; GRAPHITE; HIS-HIS-HIS-HIS-HIS-HIS; HISTIDINE; LYSINE; OLIGOPEPTIDE; OXIDE; PROTEIN BINDING;

ANALOGS AND DERIVATIVES; ARTIFICIAL MEMBRANE; CHEMISTRY; CRYOELECTRON MICROSCOPY; DEVICES; ENTEROBACTERIA PHAGE T7; ESCHERICHIA COLI; GENETICS; METABOLISM; TRANSMISSION ELECTRON MICROSCOPY; ULTRASTRUCTURE;

4-AMINOBENZOIC ACID; BACTERIOPHAGE T7; CHAPERONIN 60; CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GRAPHITE; HISTIDINE; LYSINE; MEMBRANES, ARTIFICIAL; MICROSCOPY, ELECTRON, TRANSMISSION; OLIGOPEPTIDES; OXIDES; PROTEIN BINDING; RECOMBINANT FUSION PROTEINS;

EID: 84992740854     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep32500     Document Type: Article

References (38)

1. Bartesaghi, A. et al. 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor. Science 348, 1147-1151, doi: 10.1126/science.aab1576 (2015).
2. Banerjee, S. et al. 2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 351, 871-875, doi: 10.1126/science.aad7974 (2016).
3. Cheng, Y., Grigorieff, N., Penczek, Pawel A. & Walz, T. A primer to single-particle cryo-electron microscopy. Cell 161, 438-449, doi: 10.1016/j.cell.2015.03.050 (2015).
4. Russo, C. J. & Passmore, L. A. Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas. Nature Methods 11, 649-652, doi: 10.1038/nmeth.2931 (2014).
5. Meyerson, J. R. et al. Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports. Scientific Reports 4, 7084, doi: 10.1038/srep07084 (2014).
6. Russo, C. J. & Passmore, L. A. Ultrastable gold substrates: Properties of a support for high-resolution electron cryomicroscopy of biological specimens. Journal of Structural Biology 193, 33-44, doi: 10.1016/j.jsb.2015.11.006 (2016).
7. Kelly, D. F., Dukovski, D. & Walz, T. Monolayer purification: a rapid method for isolating protein complexes for single-particle electron microscopy. Proceedings of the National Academy of Sciences of the United States of America 105, 4703-4708, doi: 10.1073/ pnas.0800867105 (2008).
8. Kelly, D. F., Dukovski, D. & Walz, T. Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy. Journal of Molecular Biology 400, 675-681, doi: 10.1016/j.jmb.2010.05.045 (2010).
9. Kutsay, O. et al. Surface properties of amorphous carbon films. Diamond and Related Materials 17, 1689-1691, doi: 10.1016/j. diamond.2008.02.020 (2008).
10. Kelly, D. F., Abeyrathne, P. D., Dukovski, D. & Walz, T. The affinity grid: a pre-fabricated EM grid for monolayer purification. Journal of Molecular Biology 382, 423-433, doi: 10.1016/j.jmb.2008.07.023 (2008).
11. Kubalek, E. W., Le Grice, S. F. & Brown, P. O. Two-dimensional crystallization of histidine-tagged, HIV-1 reverse transcriptase promoted by a novel nickel-chelating lipid. Journal of Structural Biology 113, 117-123, doi: 10.1006/jsbi.1994.1039 (1994).
12. Schmitt, L., Dietrich, C. & Tampe, R. Synthesis and characterization of chelator-lipids for reversible immobilization of engineered proteins at self-assembled lipid interfaces. Journal of the American Chemical Society 116, 8485-8491, doi: 10.1021/ja00098a008 (1994).
13. Barklis, E. et al. Structural analysis of membrane-bound retrovirus capsid proteins. The EMBO Journal 16, 1199-1213, doi: 10.1093/ emboj/16.6.1199 (1997).
14. Thompson, D. H., Zhou, M., Grey, J. & Kim, H.-k. Design, synthesis, and performance of NTA-modified lipids as templates for histidine-tagged protein crystallization. Chemistry Letters 36, 956-975, doi: 10.1246/cl.2007.956 (2007).
15. Benjamin, C. J. et al. Nonfouling NTA-PEG-based TEM grid coatings for selective capture of histidine-tagged protein targets from cell lysates. Langmuir 32, 551-559, doi: 10.1021/acs.langmuir.5b03445 (2016).
16. Marcano, D. C. et al. Improved synthesis of graphene oxide. ACS Nano 4, 4806-4814, doi: 10.1021/nn1006368 (2010).
17. Zhang, J., Yu, J. G., Jaroniec, M. & Gong, J. R. Noble metal-free reduced graphene oxide-ZnxCd1-xS nanocomposite with enhanced solar photocatalytic H-2-production performance. Nano Letters 12, 4584-4589, doi: 10.1021/Nl301831h (2012).
18. Wang, G. X. et al. Synthesis of enhanced hydrophilic and hydrophobic graphene oxide nanosheets by a solvothermal method. Carbon 47, 68-72, doi: 10.1016/j.carbon.2008.09.002 (2009).
19. Paredes, J. I., Villar-Rodil, S., Martínez-Alonso, A. & Tascón, J. M. D. Graphene oxide dispersions in organic solvents. Langmuir 24, 10560-10564, doi: 10.1021/la801744a (2008).
20. Gengler, R. Y. et al. Large-yield preparation of high-electronic-quality graphene by a Langmuir-Schaefer approach. Small 6, 35-39, doi: 10.1002/smll.200901120 (2010).
21. Kim, J. et al. Graphene oxide sheets at interfaces. Journal of the American Chemical Society 132, 8180-8186, doi: 10.1021/ja102777p (2010).
22. Cote, L. J. et al. Graphene oxide as surfactant sheets. Pure and Applied Chemistry 83, 95-110, doi: 10.1351/Pac-Con-10-10-25 (2011).
23. Cote, L. J., Kim, F. & Huang, J. Langmuir-Blodgett assembly of graphite oxide single layers. Journal of the American Chemical Society 131, 1043-1049, doi: 10.1021/ja806262m (2009).
24. Kim, J., Cote, L. J. & Huang, J. Two dimensional soft material: new faces of graphene oxide. Accounts of Chemical Research 45, 1356-1364, doi: 10.1021/ar300047s (2012).
25. Zheng, Q. et al. Structure control of ultra-large graphene oxide sheets by the Langmuir-Blodgett method. RSC Advances 3, 4680-4691, doi: 10.1039/C3RA22367A (2013).
26. Ni, Z. H. et al. Graphene thickness determination using reflection and contrast spectroscopy. Nano Letters 7, 2758-2763, doi: 10.1021/nl071254m (2007).
27. Wilson, N. R. et al. Graphene oxide: structural analysis and application as a highly transparent support for electron microscopy. ACS Nano 3, 2547-2556, doi: 10.1021/Nn900694t (2009).
28. Pan, S. Y. & Aksay, I. A. Factors controlling the size of graphene oxide sheets produced via the graphite oxide route. ACS Nano 5, 4073-4083, doi: 10.1021/Nn200666r (2011).
29. Song, J. P., Qiao, J., Shuang, S. M., Guo, Y. J. & Dong, C. Synthesis of neutral red covalently functionalized graphene nanocomposite and the electrocatalytic properties toward uric acid. Journal of Materials Chemistry 22, 602-608, doi: 10.1039/C1jm13233d (2012).
30. Ema, T., Miyazaki, Y., Koyama, S., Yano, Y. & Sakai, T. A bifunctional catalyst for carbon dioxide fixation: cooperative double activation of epoxides for the synthesis of cyclic carbonates. Chemical Communications 48, 4489-4491, doi: 10.1039/c2cc30591g (2012).
31. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J of Structural Biology 157, 38-46, doi: 10.1016/j.jsb.2006.05.009 (2007).
32. Ludtke, S. J., Jakana, J., Song, J. L., Chuang, D. T. & Chiu, W. A 11.5 A single particle reconstruction of GroEL using EMAN. Journal of Molecular Biology 314, 253-262, doi: 10.1006/jmbi.2001.5133 (2001).
33. Ludtke, S. J., Chen, D. H., Song, J. L., Chuang, D. T. & Chiu, W. Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure 12, 1129-1136, doi: 10.1016/j.str.2004.05.006 (2004).
34. Ludtke, S. J. et al. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16, 441-448, doi: 10.1016/j.str.2008.02.007 (2008).
35. Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25, 1605-1612, doi: 10.1002/jcc.20084 (2004).
36. Cote, L. J., Kim, J., Zhang, Z., Sun, C. & Huang, J. X. Tunable assembly of graphene oxide surfactant sheets: wrinkles, overlaps and impacts on thin film properties. Soft Matter 6, 6096-6101, doi: 10.1039/C0sm00667j (2010).
37. Suloway, C. et al. Automated molecular microscopy: the new Leginon system. Journal of Structural Biology 151, 41-60, doi: 10.1016/j.jsb.2005.03.010 (2005).
38. Lander, G. C. et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. Journal of Structural Biology 166, 95-102, doi: 10.1016/j.jsb.2009.01.002 (2009).