KinESim: Pre-equilibrium kinetic simulation of electrochemical reactions

John, Christopher W; Proshlyakov, Denis A.

doi:10.21105/joss.01532

Cited by 2 publications

(2 citation statements)

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“…Reference potentials ( E r ) in reduction and oxidation modes were +0.5 and −0.6 V, respectively, with a potential increment of 0.04 V. The potential pulse duration was 300 s, unless otherwise noted, with FTIR spectral acquisition (Equinox 55/S, Bruker) during the final 120 s (Figure S1). NPSV data were analyzed by a nonlinear global spectral regression (GSR) and kinetic simulations were performed using KinESim packages for Igor Pro …”

Section: Methodsmentioning

confidence: 99%

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

et al. 2019

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2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C−H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an in situ structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semiempirical computational methods, demonstrating that the Fe(III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between −127 mV for reduction of the ferric state and +171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox-difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

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Section: Methodsmentioning

confidence: 99%

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

et al. 2019

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“…Source code of the KinESim simulation package and demonstration Igor Pro experiment can be found on GitHub. 36…”

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confidence: 99%

Fourier Transform Infrared Spectrovoltammetry and Quantitative Modeling of Analytes in Kinetically Constrained Redox Mixtures

John

Proshlyakov

2019

Anal. Chem.

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Redox-active analytes that do not support direct electron transfer on the electrode, such as proteins with buried redox centers, pose challenges to characterization of their structural and thermodynamic properties. Investigations of indirect transitions in analytes supported by complex redox mixtures require a careful balance between kinetic limitations and spectral interference from the mediators. Using methylene green and thionine acetate as redox mediators and myoglobin as the analyte, we demonstrate that normal pulse spectrovoltammetry (NPSV) with Fourier transform infrared (FT-IR) detection and subsequent global spectral regression analysis can resolve structural and thermodynamic properties simultaneously with little a priori information. Both the E 1/2 and unbiased redox difference FT-IR spectra of the Fe(II)/Fe(III) redox couple of myoglobin in reduction and oxidation NPSV modes were in good agreement with those reported earlier by independent techniques. The thermodynamic and kinetic limitations of mediators/analyte interactions were investigated using comprehensive semiempirical kinetic simulation models. This modeling effort yielded a flexible computational tool capable of quantitatively predicting the redox response in mediated electrochemical studies and defining its limitations, thus greatly expanding the range and precision of the formal mediator/analyte concentration ratio rule.

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KinESim: Pre-equilibrium kinetic simulation of electrochemical reactions

Cited by 2 publications

References 4 publications

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

Fourier Transform Infrared Spectrovoltammetry and Quantitative Modeling of Analytes in Kinetically Constrained Redox Mixtures

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