Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase - PubMed (original) (raw)

. 2024 Mar 27;15(16):5916-5928.

doi: 10.1039/d4sc00023d. eCollection 2024 Apr 24.

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Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase

Luke C Lewis et al. Chem Sci. 2024.

Abstract

The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.

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Conflict of interest statement

There are no conflicts to declare.

Figures

Fig. 1

Fig. 1. Proposed catalytic cycle for CO oxidation and CO2 reduction at the C-cluster of CODH showing two different hypothesized structures for Cred2. Amino acid numbering is from CODH IICh. Structures in gray indicate intermediate states that are not well-characterized.

Fig. 2

Fig. 2. CW X-band EPR spectra (ν = 9.37 GHz, _P_μw = 20 mW, T = 8.0 K) of natural abundance (colored traces) and 61Ni-isotopically labelled (gray traces) samples of (A) NiFdred, (B) NiFd–CN, and (C) NiFd–CO. (Insets) Zoomed in views of low-field turning points highlight 61Ni-induced broadening. * indicates residual NiFdred that remains after exposure to CO.

Fig. 3

Fig. 3. CW EPR spectra (ν = 9.37 GHz, _P_μw = 20 mW) of (A) NiFd–CN and (B) NiFd–CO at the indicated temperatures. Spectra were normalized to temperature using a standard Curie dependence [I × _T_]. * denotes small (<5%) amount of contaminating S = 1/2 [Fe4S4]–CN Fd.

Fig. 4

Fig. 4. Resonance Raman spectra of [Fe3S4]0 Fd (gray), NiFdred (green), NiFd–CN (orange), and NiFd–CO (blue). Samples were collected at 77 K using an excitation wavelength of 407 nm, P = 8 mW. Residual features corresponding to buffer are indicated with an *. Bands arising from buffer, DT, and quartz were subtracted after collection. (Inset) High frequency region of the resonance Raman spectra of NiFd–CO prepared with natural abundance CO (dark blue) and 13CO (light blue), shown offset from the difference spectrum (gray). The band at 1906 cm−1 is present in both samples and independent of the CO isotope.

Fig. 5

Fig. 5. (A) Ni K-edge XANES of the four isolated forms of NiFd. (Inset) Zoom in on the pre-edge region. (B) Fe K-edge XANES of the four isolated forms of NiFd. (Inset) Zoom in on the pre-edge region. (C) Derivative of the Ni K-edge XANES from the traces in A. (D) Derivative of the Fe K-edge XANES from the traces in B.

Fig. 6

Fig. 6. Ni K-edge EXAFS of the four isolated forms of NiFd. (A) Comparison of experimental Fourier transform (FT) EXAFS data (solid) for the four different forms of NiFd overlaid with the best fit (gray). (B) Comparison of experimental k3 EXAFS data (solid) for the four different forms of NiFd overlaid with the best fit (gray).

Fig. 7

Fig. 7. Experimental pre-edge Ni K-edge XANES spectra of NiFdred (green), NiFdox (black), and NiFd–CO (blue) with calculated TD-DFT contributions using the DFT geometry-optimized structures of the NiFd species (inset). Dominant contributing orbital to the indicated transition for each species shown at an isosurface value of 0.03 with distribution over Ni and the Fe atoms indicated.

Fig. 8

Fig. 8. Proposed electronic and geometric structures of the (A) NiFdox, NiFdred, NiFd–CO, and NiFd–CN species with key experimental metrics indicated that have been obtained from this work, and (B) analogous Cox, Cred1, Cred1-CO, and Cred1-CN states of CODH with spectroscopic metrics obtained from ref. , and .

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