Abstract
Objectives
To better understand the unique inhibitory behavior of a non-natural cofactor preferred formaldehyde dehydrogenase (FalDH) mutant 9B2.
Results
We described our serendipitous observation that 9B2 was reversibly inhibited by residual imidazole introduced during protein preparation, while the wild-type enzyme was not sensitive to imidazole. Kinetic analysis showed that imidazole was a competitive inhibitor of formaldehyde with a Ki of 16 μM and an uncompetitive inhibitor of Nicotinamide Cytosine Dinucleotide for 9B2, indicating that formaldehyde and imidazole were combined in the same position. Molecular docking results of 9B2 showed that imidazole could favorably bind very close to the nicotinamide moiety of the cofactor, where formaldehyde was expected to reside for catalysis, which was in line with a competitive inhibition.
Conclusion
The mutant 9B2 can be competitively inhibited by imidazole, suggesting that cautions should be taken to evaluate activities as protein mutants might attain unexpected sensitivity to a component in buffers for purification or activity assays.
Graphical abstract
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
Data will be made available on request.
References
Achi F, Bourouina-Bacha S, Bourouina M, Amine A (2015) Mathematical model and numerical simulation of inhibition based biosensor for the detection of Hg(II). Sens Actuator B-Chem 207:413–423. https://doi.org/10.1016/j.snb.2014.10.033
Barber RD, Rott MA, Donohue TJ (1996) Characterization of a glutathione-dependent formaldehyde dehydrogenase from Rhodobacter sphaeroides. J Bacteriol 178:1386–1393. https://doi.org/10.1128/jb.178.5.1386-1393.1996
Barbosa J, Sivaraman J, Li YG, Larocque R, Matte A, Schrag JD, Cygler M (2002) Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Proc Natl Acad Sci USA 99:1859–1864. https://doi.org/10.1073/pnas.022476199
Caramia S, Gatius AGM, Dal Piaz F, Gaja D, Hochkoeppler A (2017) Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis) β-glucosidase. Biochem Biophys Rep 10:137–144. https://doi.org/10.1016/j.bbrep.2017.03.007
Chen NH, Counago RM, Djoko KY, Jennings MP, Apicella MA, Kobe B, McEwan AG (2013) A glutathione-dependent detoxification system Is required for formaldehyde resistance and optimal survival of Neisseria meningitidis in biofilms. Antioxid Redox Signal 18:743–755. https://doi.org/10.1089/ars.2012.4749
Collins PA, Hanes CS, Wong JT (1978) Parallelism between ethanol and imidazole interactions with horse liver alcohol-dehydrogenase. Can J Biochem 56:1016–1020. https://doi.org/10.1139/o78-160
Dahl KH, McKinleymckee JS (1981) The imidazole-promoted inactivation of horse-liver alcohol-dehydrogenase. Eur J Biochem 120:451–459. https://doi.org/10.1111/j.1432-1033.1981.tb05723.x
Daraji DG, Prajapati NP, Patel HD (2019) Synthesis and applications of 2-substituted imidazole and its derivatives: a review. J Heterocycl Chem 56:2299–2317. https://doi.org/10.1002/jhet.3641
Field RA, Haines AH, Chrystal EJT, Luszniak MC (1991) Histidines, histamines and imidazoles as glycosidase inhibitors. Biochem J 274:885–889. https://doi.org/10.1042/bj2740885
Guo XJ, Liu YX, Wang Q, Wang XY, Li Q, Liu WJ, Zhao ZK (2020) Non-natural cofactor and formate-driven reductive carboxylation of pyruvate. Angew Chem-Int Edit 59:3143–3146. https://doi.org/10.1002/anie.201915303
Ito K, Takahashi M, Yoshimoto T, Tsuru D (1994) Cloning and high-level expression of the glutathione-independent formaldehyde dehydrogenase gene from Pseudomonas putida. J Bacteriol 176:2483–2491. https://doi.org/10.1128/JB.176.9.2483-2491.1994
Ji DB, Wang L, Hou SH, Liu WJ, Wang JX, Wang Q, Zhao ZK (2011) Creation of bioorthogonal redox systems depending on nicotinamide flucytosine dinucleotide. J Am Chem Soc 133:20857–20862. https://doi.org/10.1021/ja2074032
Liteplo RG, Meek ME (2003) Inhaled formaldehyde: exposure estimation, hazard characterization, and exposure-response analysis. J Toxicol Env Health-Pt b-Crit Rev 6:85–114. https://doi.org/10.1080/10937400306480
Liu YX, Guo XJ, Liu WJ, Wang JT, Zhao ZK (2021) Structural insights into malic enzyme variants favoring an unnatural redox cofactor. ChemBioChem 22:1765–1768. https://doi.org/10.1002/cbic.202000800
Mayer KM, Arnold FH (2002) A colorimetric assay to quantify dehydrogenase activity in crude cell lysates. J Biomol Screen 7:135–140. https://doi.org/10.1089/10870570252906594
Mishra R, Ganguly S (2012) Imidazole as an anti-epileptic: an overview. Med Chem Res 21:3929–3939. https://doi.org/10.1007/s00044-012-9972-6
Morellato AE, Umansky C, Pontel LB (2021) The toxic side of one-carbon metabolism and epigenetics. Redox Biol. https://doi.org/10.1016/j.redox.2020.101850
Morgan KT, Jiang XZ, Starr TB, Kerns WD (1986) More precise localization of nasal tumors associated with chronic exposure of F-344 rats to formaldehyde gas. Toxicol Appl Pharmacol 82:264–271. https://doi.org/10.1016/0041-008X(86)90201-2
Singh RK, Singh R, Sivakumar D, Kondaveeti S et al (2018) Insights into cell-free conversion of CO2 to chemicals by a multienzyme cascade reaction. ACS Catal 8:11085–11093. https://doi.org/10.1021/acscatal.8b02646
Tanaka N, Kusakabe YK, Yoshimoto T, Nakamura KT (2002) Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases. J Mol Biol 324:519–533. https://doi.org/10.1016/S0022-2836(02)01066-5
Tao RR, Liao MH, Wang YX, Wang H et al (2022) In situ imaging of formaldehyde in live mice with high spatiotemporal resolution reveals aldehyde dehydrogenase-2 as a potential target for alzheimer’s disease treatment. Anal Chem 94:1308–1317. https://doi.org/10.1021/acs.analchem.1c04520
Teiserskyte V, Urbonavicius J, Ratautas D (2021) A direct electron transfer formaldehyde dehydrogenase biosensor for the determination of formaldehyde in river water. Talanta. https://doi.org/10.1016/j.talanta.2021.122657
Wang JT, Guo XJ, Wan L, Liu YX, Xue HZ, Zhao ZK (2022) Engineering formaldehyde dehydrogenase from Pseudomonas putida to favor nicotinamide cytosine dinucleotide. Chem Biochem. https://doi.org/10.1002/cbic.202100697
Wang L, Ji DB, Liu YX, Wang Q, Wang XY, Zhou YJ, Zhang YX, Liu WJ, Zhao ZK (2017) Synthetic cofactor-linked metabolic circuits for selective energy transfer. ACS Catal 7:1977–1983. https://doi.org/10.1021/acscatal.6b03579
Wani SR, Jain V (2022) Molecular dissection of a dedicated formaldehyde dehydrogenase from Mycobacterium smegmatis. Protein Sci 31:628–638. https://doi.org/10.1002/pro.4258
Zhang L, Peng XM, Damu GLV, Geng R-X, Zhou CH (2014) Comprehensive review in current developments of imidazole-based medicinal chemistry. Med Res Rev 34:340–437. https://doi.org/10.1002/med.21290
Zhang WL, Chen S, Liao YP, Wang DL, Ding JF, Wang YM, Ran XY, Lu DR, Zhu HX (2013) Expression, purification, and characterization of formaldehyde dehydrogenase from Pseudomonas aeruginosa. Protein Expr Purif 92:208–213. https://doi.org/10.1016/j.pep.2013.09.017
Funding
This work was supported by the National Key R&D Program of China (Grand No. 2018YFA0900300); the National Natural Science Foundation of China (Grand Nos. 21907092, 32001028); and Dalian Institute of Chemical Physics, CAS (No. DICP I202020).
Author information
Authors and Affiliations
Contributions
XW developed the idea for the study. XW, ZKZ. conceived the project. JW performed most experiments and drafted the manuscript. LW analyzed the structure and performed the molecular docking. XG helped with experiments. XW, ZKZ, LW, XG, and JW revised the manuscript. All authors contributed to the discussion of results and comments on this paper.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Ethical approval
This article does not contain any studies with human participants or animals.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Wang, J., Wan, L., Guo, X. et al. Competitive inhibition of a non-natural cofactor dependent formaldehyde dehydrogenase by imidazole. Biotechnol Lett 45, 679–687 (2023). https://doi.org/10.1007/s10529-023-03372-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10529-023-03372-0