Ni-NTA

The term Ni-NTA (Nickel NTA) refers to a nickel²⁺ ion that has been coupled Nitrilotriacetic acid (NTA). Ni-NTA can then be coupled to agarose resin or magnetic beads for IMAC (Immobilized Metal Chelate Affinity Chromatography). This is a purification method to obtain functional His tagged protein. The size of the used agarose resin beads or magnetic beads influences the flow rated and the protein yield.

Overview of Cube Biotech's Ni-NTA products for His tag protein purification.

Ni-NTA agarose (40 µm)	Ni-NTA agarose (40 µm) Cartridge	Ni-NTA Magnetic Beads
Ni-NTA agarose (100 µm)	Ni-NTA agarose (40 µm) COMPACT Cartridge	Ni-NTA MagBeads XL
Ni-NTA agarose XL	Ni-NTA agarose (100 µm) Cartridge
	Ni-NTA agarose (100 µm) COMPACT Cartridge

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Features

Usage	Specific binding and purification of 6x his-tagged proteins
Specifity	Affinity to His-tagged proteins
Binding capacity	>80 mg/mL
Chelator stability	Stable in buffer containing 10 mM DTT and 1 mM EDTA
Bead Ligand	Ni-NTA

 

Ni-NTA products by Cube Biotech were used in the following publications:

 

Protein	Year	Author	Ni-NTA product
Plasmodium falciparum 6- phosphogluconate dehydrogenase	2018	Haeussler, K., Fritz-Wolf, K., Reichmann, M., Rahlfs, S., & Becker, K. 1	Ni-NTA agarose (40 µm)
mCherry protein	2018	Wang, X., Liu, Y., Liu, J., & Chen, Z. 2	Ni-NTA agarose (40 µm)
Channelrhodopsin 2	2017	Volkov, O., Kovalev, K., Polovinkin, V., Borshchevskiy, V., Bamann, C., Astashkin, R., & Büldt, G. 3	Ni-NTA agarose (40 µm)
Geobacillus sp. Manganese catalase	2017	Li, H. C., Yu, Q., Wang, H., Cao, X. Y., Ma, L., & Li, Z. Q. 4	Ni-NTA agarose (40 µm)
Diacylglycerol kinase	2016	Rues, R. B., Henrich, E., Boland, C., Caffrey, M., & Bernhard, F. 5	Ni-NTA agarose (40 µm)
Glutamyl (aspartyl) specific aminopeptidase	2016	Stressler, T., Ewert, J., Merz, M., Funk, J., Claaßen, W., Lutz-Wahl, S., & Fischer, L. 6	Ni-NTA agarose (40 µm)
Histidine kinase domain of Ethylene Response Sensor 1	2016	Hsieh, Y. L., Lu, C. F., Chiang, B. Y., Liao, S. C., Chen, R. P. Y., Lin, C. S., ... & Yang, C. C. 7	Ni-NTA agarose (40 µm)
Arylsulfatase from Kluyveromyces lactis	2018	Stressler, T., Reichenberger, K., Glück, C., Leptihn, S., Pfannstiel, J., Swietalski, P., & Fischer, L. 8	Ni-NTA agarose (40 µm)
PepA from Lactobacillus delbrueckii	2017	Ewert, J., Glück, C., Strasdeit, H., Fischer, L., & Stressler, T. 9	Ni-NTA agarose (40 µm)
CagL	2019	Buß M., Tegtmeyer., Schnieder J., Dong X., Li J., Springer T.A., Backert S., Niemann H.H.10	Ni-NTA agarose (40 µm)
eIF3B2; eIF4A2; eIFiso4G1 and eIFiso4G2	2018	Cho H.-Y., Lu M.-Y. J., Shih M-C.11	Ni-NTA agarose (40 µm)
PvG6PD	2019	Haessler K., Berneburg I., Jortzik E., Hahn J., Rahbari M., Schulz N., Preuss J., Zapol'skii V.A., Bode L., Pinkerton A.B., Kaufmann D.E., Rahlfs S., Becker K.,12	Ni-NTA agarose (40 µm)
flavin-dependent tryptophan 6-halogenase Thal	2018	Moritzer A.-C., Minges H., Prior T., Frese M., Seewald N., Niemann H.H.13	Ni-NTA agarose (40 µm)
HrpII	2017	Bauer W.S., Richardson K.A., Adams N.M., Ricks K.M., Gasperino D.J., Ghionea S.J., Rosen M., Nichols K.P., Weigl B.H., Haselton F.R., Wright D.W., 14	Ni-NTA agarose (40 µm)
Human serotonin transporter	2019	Worms D., Maertens B., Kubicek J., Subhramanyam U.K.T., Labahn J.15	Ni-NTA agarose (40 µm)
CagL variants	2019	Buß M., Tegtmeyer N., Schnieder J., Dong X., Li J., Springer T.A., Backert S., Niemann H.H.16	Ni-NTA agarose (40 µm)
AtEDS1	2019	Voß M., Tölzer C., Bhandari D., Parker J., Niefind K.17	Ni-NTA agarose (40 µm)
PMMoV-CP	2019	Phatsaman T., Hongprayoon R., Wasee S.17	Ni-NTA agarose (40 µm)
Metal Binding Phages	2019	Matys S., Schönberger N., Lederer F., Pollmann K.18	Ni-NTA agarose (40 µm)
EH1	2018	Coscolín C., Beloqui A., Martínez-Martínez M., Bergiela., Santiago G., Blanco R-M., Delaittre G., Márquez-Álvarez C., Ferrer M., 19	Ni-NTA MagBeads
HRP2	2017	Bauer W-S., Kimmel D-W., Adams N-M., Gibson L-E., Scharr T-F., Richardson K-A., Conrad J-A., Matakala H-K., Haselton F-R., Wright D-W., 20	Ni-NTA MagBeads
HFITC	2016	Scherr T-F., Ryskoski H-B., Adithya S., Ricks K-M., Adams, N-M., Wright D.-W., Haselton F-R.,21	Ni-NTA MagBeads
Several Proteins	2019	Yang M.; Yang S-X.; Liu Z-M.; Li N-N.; Li L.; Mou Hai-Jin.23	Ni-NTA (40µm) Cartridge
PepA	2017	Ewert J., Glück C., Strasdeit H., Fischer L., Stressler T.24	Ni-NTA (40µm) Cartridge
Arylsulfatase variants	2018	Stressler T., Reichenberger K., Glück C., Lephtin S., Pfannstiel J., Swietalski P., Kuhn A., Seitl I., Fischer L.25	Ni-NTA (40µm) Cartridge
recombinant alginate lyase	2019	Yang M., Li N., Yang S., Yu Y., Han Z., Li L., Mou H.26	Ni-NTA (40µm) Cartridge
Phosphorylated Tau protein	2020	Wang H., Zhang J., Dou F., Zhijun C.27	Ni-NTA (40µm) Cartridge
AofleA	2020	Tian D., Zhang L., Zhang S., Kong X., Sheng K., Wang J., Zhang M., Wang Y.28	Ni-NTA (40µm) Cartridge

Different metal ions confer different binding affinity and specificity

Fig. 1: Depending on which metal ion is coupled to NTA the balance between protein yield and purification specificity shifts. Nickel is a very balanced choice between the two extremes.

His tag purification is based on ionic interactions of a the coupled metal ion and the Poly His tag. Therefore other metal ions can also fullfill the function of Nickel. Figure 1 shows the most frequently used metal ions for His tag purification. Depending on the used metal ion the balance between the specificity and the affinity of the metal ion to the His tag shifts. Nickel is a balanced choice between both extremes. Copper has the highest affinity, but Cobalt is the choice for the most pure His tag purifications.

 

Fig. 2: Over 20% more yield obtained with PureCube Ni-NTA Agarose. SDS-PAGE of GFP expressed in E. coli and purified in gravity columns with PureCube Ni-NTA Agarose and Ni-NTA resin from Competitor Q. 80 mg/mL protein yield was obtained with PureCube Ni-NTA Agarose (E1–E4, Cube) compared to 65 and 48 mg/mL, respectively, with the widely used alternative resins G and Q (E1–E4, Competitor G / Competitor Q).

 

High yield and purity

Our unique production process yields a Ni-NTA Agarose that exhibits a protein binding capacity >20% higher than that of two leading competitor products. Figure 1 shows the SDS-PAGE of GFP expressed in E. coli and purified in gravity colums with PureCube Ni-NTA Agarose and the Ni-NTA resin from Competitor G and Competitor Q. The protein yield in 4 elutions (E1-E4, Cube) was 80 mg/mL, compared to 65 and 48 mg/mL obtained with the alternative resins (E1-E4, Competitor G, Competitor Q). Similar results (10-18% higher binding capacity; data not shown here) were obtained comparing the purification of JNK1 (Kinase, 48 kDa) on PureCube Ni-NTA and the Ni-NTA of leading providers.

 

Fig. 3: NTA is robust in the presence of reducing and chelating agents. GFP-His was purified on gravity columns containing PureCube Ni-NTA Agarose after exposing the resin for 1 h to 3 concentrations of DTT or EDTA. NTA exhibits a shallow decay rate in binding capacity.

 

Superior DTT and EDTA stability

PureCube Ni-NTA Agarose is very robust in the presence of DTT and EDTA. In a stability test, PureCube Ni-NTA Agarose was exposed to increasing concentrations of DTT or EDTA for 1 h. Thereafter, the resins were used to purify E. coli-expressed GFP-His in gravity columns. The binding capacity of the resin decreased in the presence of both DTT and EDTA but the decay rate was shallow. In presence of DTT, PureCube Ni-NTA Agarose lost on average 8% binding capacity with each increase in DTT concentration, resulting in an overall decay of 22% at 10 mM. Even at 1.5 mM EDTA, the resin still exihibits 54% of its maximum binding capacity (Fig. 2).

 

Fig. 4: PureCube Ni-NTA Agarose is robust against oxidation and regenerable. PureCube Ni-NTA Agarose was exposed to 5mM DTT for 1 h (A). After demonstrating that it could still bind GFP (B), the resin was washed, stripped (C), and reloaded with Ni2+ (D) following standard Cube protocol (see Cube Protocols & Datasheets).

 

Robust against oxidation and regenerable

PureCube Ni-NTA Agarose retains its color and function after exposure to as much as 10 mM DTT. Figure 3 shows a photo series of the resin after a 1 h exposure to 5 mM DTT. Unlike other resins, PureCube Ni-NTA Agarose did not turn brown (A). The resin was still able to bind GFP (B), with a measured binding capacity of 65 mg/mL (see Fig. 2). The resin could then be regenerated by stripping the NTA, turning the resin white (C), and reloading it with nickel ions (D). The protocol for regenerating PureCube Ni-NTA Agarose can be downloaded.

References:

1. Haeussler, Kristina, et al. "Characterization of Plasmodium falciparum 6-phosphogluconate dehydrogenase as an antimalarial drug target." Journal of molecular biology 430.21 (2018): 4049-4067.
2. Wang, Xiaoliang, et al. "Protein–Polymer Microcapsules for PCR Technology." ChemBioChem 19.10 (2018): 1044-1048.
3. Volkov, Oleksandr, et al. "Structural insights into ion conduction by channelrhodopsin 2." Science 358.6366 (2017): eaan8862.
4. Li, Hai-Chao, et al. "A New Homo-Hexamer Mn-Containing Catalase from Geobacillus sp. WCH70." Catalysts 7.9 (2017): 277.
5. Rues, Ralf-Bernhardt, et al. "Cell-free production of membrane proteins in Escherichia coli lysates for functional and structural studies." Heterologous Expression of Membrane Proteins. Humana Press, New York, NY, 2016. 1-21.
6. Stressler, Timo, et al. "A novel glutamyl (aspartyl)-specific aminopeptidase A from Lactobacillus delbrueckii with promising properties for application." PloS one 11.3 (2016): e0152139.
7. Hsieh, Yi-Lin, et al. "Molecular Characterization of Ethylene Response Sensor 1 (BoERS1) in Bambusa oldhamii." Plant molecular biology reporter 34.2 (2016): 387-398.
8. Stressler, Timo, et al. "A natural variant of arylsulfatase from Kluyveromyces lactis shows no formylglycine modification and has no enzyme activity." Applied microbiology and biotechnology102.6 (2018): 2709-2721.
9. Ewert, Jacob, et al. "Influence of the metal ion on the enzyme activity and kinetics of PepA from Lactobacillus delbrueckii." Enzyme and microbial technology 110 (2018): 69-78.
10. Ewert, Jacob, et al. "Buß, Maren et al.(2019). Specific high affinity interaction of Helicobacter pylori CagL with integrin α V β 6 promotes type IV secretion of CagA into human cells. The FEBS Journal. 10.1111/febs.14962." Enzyme and microbial technology 110 (2018): 69-78.
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12. Haeussler, Kristina et al.(2019). Glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase: Characterization of the Plasmodium vivax enzyme and inhibitor studies. Malaria Journal. 18. 10.1186/s12936-019-2651-z.
13. Moritzer, Ann-Christin et al. (2018). Structure-based switch of regioselectivity in the flavin-dependent tryptophan 6-halogenase Thal. Journal of Biological Chemistry. 294. jbc.RA118.005393. 10.1074/jbc.RA118.005393.
14. Bauer, Westley S et al. “Rapid concentration and elution of malarial antigen histidine-rich protein II using solid phase Zn(II) resin in a simple flow-through pipette tip format.” Biomicrofluidics vol. 11,3 034115. 2 Jun. 2017, doi:10.1063/1.4984788
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16. Buß et al. (2019). Specific high affinity interaction of Helicobacter pylori CagL with integrin α V β 6 promotes type IV secretion of CagA into human cells. The FEBS Journal. 10.1111/febs.14962.
17. Voß M. et al.(2019). Arabidopsis immunity regulator EDS1 in a PAD4/SAG101-unbound form is a monomer with an inherently inactive conformation. Journal of Structural Biology. 10.1016/j.jsb.2019.09.007.
18. Matys, S. et al. (2019). Characterization of specifically metal-binding phage clones for selective recovery of cobalt and nickel. Journal of Environmental Chemical Engineering. 103606. 10.1016/j.jece.2019.103606.
19. Coscolín, Cristina et al. (2018). Controlled manipulation of enzyme specificity through immobilization-induced flexibility constraints. Applied Catalysis A: General. 565. 10.1016/j.apcata.2018.08.003.
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23. Yang, M. et al. (2019). Rational Design of Alginate Lyase from Microbulbifer sp. Q7 to Improve Thermal Stability. Marine Drugs. 17. 378. 10.3390/md17060378.
24. Ewert, J. et al. (2017). Influence of the metal ion on the enzyme activity and kinetics of PepA from Lactobacillus delbrueckii. Enzyme and Microbial Technology. 110. 10.1016/j.enzmictec.2017.10.002.
25. Stressler, T. et al. (2018). A natural variant of arylsulfatase from Kluyveromyces lactis shows no formylglycine modification and has no enzyme activity. Applied Microbiology and Biotechnology. 102. 10.1007/s00253-018-8828-5.
26. Yang, M. et al.(2019). Study on expression and action mode of recombinant alginate lyases based on conserved domains reconstruction. Applied Microbiology and Biotechnology. 103. 10.1007/s00253-018-9502-7.
27. Wag et al. (2020). A near-infrared fluorescent probe quinaldine red lights up the β-sheet structure of amyloid proteins in mouse brain. Biosensors and Bioelectronics. 153. doi.org/10.1016/j.bios.2020.112048
28. Tian, Dongrui, et al. "Heterologous expression and molecular binding properties of AofleA, a fucose-specific lectin from nematophagous fungus Arthrobotrys oligospora." International Journal of Biological Macromolecules (2020).