Abstract
Understanding the mechanisms and kinetics of enzymatic reactions is essential for studies of life science and for bioengineering. Here the different reaction states in the catalytic cycle of formate dehydrogenase have been distinguished by their characteristic conductances, using the scanning tunnelling microscope break-junction technique, and these conductances have been further exploited as markers to monitor the catalytic mechanism of formate dehydrogenase from Candida boidinii. Combined with multiscale simulations, we demonstrate that the bound reduced form of nicotinamide adenine dinucleotide (NADH) converts to nicotinamide adenine dinucleotide (NAD+) directly via a hydride-transfer reaction in situ during the catalytic cycle of formate dehydrogenase. This conversion does not proceed via the apoenzyme state invoked in the conventional, generally accepted Theorell–Chance mechanism. This work provides intriguing insight into the mechanism of formate dehydrogenase and highlights the potential of the single-molecule technique in revealing the catalytic mechanism of NADH/NAD+-dependent oxidoreductases.
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Data availability
All data that support the findings of this study are available within this Article and its Supplementary Information. Source data are provided with this paper.
Code availability
The data analysis of conductance measurements in this work was performed using our open-source code XME analysis, which is available at Github (https://github.com/Pilab-XMU/XMe_DataAnalysis) and Zenodo (https://doi.org/10.5281/zenodo.6578853). The code used for data processing in this study is available from the website: https://github.com/JChonpca/Algorithm_for_STM-based_Single_Molecule_Enzymology_Time_Series_Data.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (grant numbers 21978245, B.F.; 22122305, B.W.; 22250003, 21722305, W.H.), the National Key R&D Program of China (grant number 2017YFA0204902, W.H.), and the National Postdoctoral Program for Innovative Talents (grant number BX20200197, A.Z.). W.H. thanks Y. Zhang (Xiamen University) for discussion on the catalytic mechanism of oxidoreductase. B.W. thanks Y. Zhao (Xiamen University) for discussion on the electron transfer mechanism.
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B.F., W.H. and B.W. designed the experiments and co-supervised the project. B.F. conceived the idea and discussed with W.H. to probe the FDH catalytic cycle at the single-molecule level. A.Z. and B.W. wrote the manuscript with inputs from all authors. X.Z. was responsible for molecular synthesis and characterization. X.Z. and A.Z. carried out the BJ experiments and analysed the data. J.L. performed the theoretical modelling. J.H. performed the data processing method based on artificial intelligence. L.L and Y.T. carried out the data-clustering analysis. S.Z. and R.L. built the electrical measurement instrument. All authors participated in discussion of the work.
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Supplementary Discussion, Figs. 1–33 and Tables 1–5.
Supplementary Data 1
The Cartesian coordinates of the truncated PDB (solvation waters 3 Å away from the protein are removed) of all species involved in the catalytic cycle (Fig. 3) from MD and QM/MM metadynamics.
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Zhang, A., Zhuang, X., Liu, J. et al. Catalytic cycle of formate dehydrogenase captured by single-molecule conductance. Nat Catal 6, 266–275 (2023). https://doi.org/10.1038/s41929-023-00928-1
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DOI: https://doi.org/10.1038/s41929-023-00928-1
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