Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer

Petrenko, Alexander; Stein, Matthias

doi:10.20944/preprints201701.0029.v2

Cited by 3 publications

(3 citation statements)

References 16 publications

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“… 36 Recent density functional theory calculations suggest that this is because electrons pass between the outer surface of the protein and the distal cluster via a precise molecular route that terminates at the His ligand ( Supplementary Figure 1 ). 37 , 38 Variants HyaA-K189N and HyaA-Y191E, which mimic differences in this surface-to-histidine route in O 2 -tolerant and O 2 -sensitive [NiFe]-hydrogenases ( Figure 1 ), are generated to investigate the role of residues along this route in tuning E dist .…”

Section: Introductionmentioning

confidence: 99%

Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site

et al. 2017

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The redox chemistry of the electron entry/exit site in Escherichia coli hydrogenase-1 is shown to play a vital role in tuning biocatalysis. Inspired by nature, we generate a HyaA-R193L variant to disrupt a proposed Arg–His cation−π interaction in the secondary coordination sphere of the outermost, “distal”, iron–sulfur cluster. This rewires the enzyme, enhancing the relative rate of H2 production and the thermodynamic efficiency of H2 oxidation catalysis. On the basis of Fourier transformed alternating current voltammetry measurements, we relate these changes in catalysis to a shift in the distal [Fe4S4]2+/1+ redox potential, a previously experimentally inaccessible parameter. Thus, metalloenzyme chemistry is shown to be tuned by the second coordination sphere of an electron transfer site distant from the catalytic center.

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Section: Introductionmentioning

confidence: 99%

Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site

et al. 2017

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“…389 DFT calculations demonstrated that substitution of the histidine ligand to a cysteine in Df [NiFe]hydrogenase does not change the reorganization energy of the distal [4Fe-4S] cluster. 390 The calculated rate of electron transfer was, however, reduced by three orders of magnitude, resulting from a change in electronic donor−acceptor coupling including histidine H184 and phenylalanine F193 (F197 in DvMF). These results indicated that the protein environment is tuned for efficient electron transfer.…”

Section: Medial and Distal Clustersmentioning

confidence: 96%

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

et al. 2022

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Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in “green” energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

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“…The works of Petrenko and Stein 24 , 25 are rare examples of FO DFT calculations where the wave functions of individual fragments are considered explicitly in the H AB computations. The authors calculate electronic coupling matrix elements for the biological ET process that involves iron–sulfur clusters.…”

Section: Introductionmentioning

confidence: 99%

How the Donor/Acceptor Spin States Affect the Electronic Couplings in Molecular Charge-Transfer Processes?

Kubas

2021

J. Chem. Theory Comput.

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The electronic coupling matrix element H AB is an essential ingredient of most electron-transfer theories. H AB depends on the overlap between donor and acceptor wave functions and is affected by the involved states’ spin. We classify the spin-state effects into three categories: orbital occupation, spin-dependent electron density, and density delocalization. The orbital occupancy reflects the diverse chemical nature and reactivity of the spin states of interest. The effect of spin-dependent density is related to a more compact electron density cloud at lower spin states due to decreased exchange interactions between electrons. Density delocalization is strongly connected with the covalency concept that increases the spatial extent of the diabatic state’s electron density in specific directions. We illustrate these effects with high-level ab initio calculations on model direct donor–acceptor systems relevant to metal oxide materials and biological electron transfer. Obtained results can be used to benchmark existing methods for H AB calculations in complicated cases such as spin-crossover materials or antiferromagnetically coupled systems.

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Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer

Cited by 3 publications

References 16 publications

Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site

Retuning the Catalytic Bias and Overpotential of a [NiFe]-Hydrogenase via a Single Amino Acid Exchange at the Electron Entry/Exit Site

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

How the Donor/Acceptor Spin States Affect the Electronic Couplings in Molecular Charge-Transfer Processes?

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