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Nickel-substituted Rubredoxin as a Model Protein Scaffold for Hydrogen Production: A Handle Towards Understanding Biological Catalysis

Treviño, Regina Estefania
http://rave.ohiolink.edu/etdc/view?acc_num=osu1652063674268837

Abstract Details

2022, Doctor of Philosophy, Ohio State University, Chemistry.
The utilization of enzymes as bioelectrocatalysts is of increasing interest due to their advantages in chemical specificity and catalytic rates. Emphasis has been placed on hydrogen producing biocatalysts to overcome drawbacks of current heterogeneous catalysts, including limited availability and poor selectivity. Native enzymes, such as the [NiFe] hydrogenase, have demonstrated extreme proficiency as bi-directional catalysts for proton reduction and hydrogen oxidation, inspiring a variety of small molecule and protein mimics. The utilization of a robust and stable protein scaffold with a similar primary coordination environment as the native enzyme can result in similar activity. Previous reports have demonstrated that nickel-substituted rubredoxin (NiRd) serves as a structural, functional and mechanistic model of the [NiFe] hydrogenase, active towards proton reduction electrochemically and in solution, with an identical primary coordination sphere at the nickel center as the native enzyme. While the mechanism of proton reduction has been experimentally and computationally modeled to be similar to that of the native enzyme, key catalytic intermediates have not yet been isolated and characterized. This project aims to address some of the limitations of this current model, such as significant overpotential and lack of spectroscopic characterization of catalytically competent intermediates. Further, correlation between redox activity and protein structure are investigated by modification of the protein primary sphere coordination site. Primary sphere mutants demonstrate changes in the redox and catalytic behavior dependent on the cysteine site being modified. Drastic changes to the primary coordination sphere are explored using electrochemistry along with optical, multiwavelength resonance Raman, X-ray and electron paramagnetic resonance spectroscopies. This study demonstrates the ability to keep and shut off catalysis, aiding in the understanding of enzyme selectivity and its correlations to active site structure and geometry. Expanding beyond the primary coordination sphere, changes to the secondary sphere have resulted in drastic changes to the turnover frequencies of the enzyme, with modest changes in overpotential. Previous work using electrochemical analysis of a suite of secondary sphere mutants have shown dramatic variation in the catalytic rates and redox activity of NiRd, with some mutants demonstrating a change in the proton reduction mechanism. The observed differences in catalytic and redox activity are hypothesized to arise from changes in the protein structure, dynamics and H-bonding networks. A structural study of a suite of secondary and primary sphere mutants utilizing Nuclear Magnetic Resonance (NMR) spectroscopy directly provides solution-phase information on protein dynamics. The small size of Rd (5.2 kDa) makes it an ideal candidate for NMR interrogations. Additionally, due to the high spin (S=1) active site of the NiIIRd artificial enzyme, and the favorable relaxation properties of pseudo-tetrahedral four coordinate NiII, paramagnetic NMR spectroscopy can be used to gain further insight into the metal electronic structure and the H-bonding network. The information gathered will identify key factors that affect catalysis within a model protein scaffold, allowing for not only rational catalyst design and catalyst optimization, but the development of paramagnetic NMR methodology that allows to probe structural changes by NiRd under catalytically relevant conditions.
Hannah Shafaat (Advisor)
Yiying Wu (Committee Member)
Shiyu Zhang (Committee Member)
Anne Co (Committee Member)
321 p.
Chemistry
Rubredoxin, nickel, nickel-substituted rubredoxin, artificial enzyme, hydrogenase, hydrogen, proton reduction, rational design, primary sphere, secondary sphere, electrochemistry, optical spectroscopy, EPR, NMR, resonance Raman, spectroscopy

Recommended Citations

Citations

  • Treviño, R. E. (2022). Nickel-substituted Rubredoxin as a Model Protein Scaffold for Hydrogen Production: A Handle Towards Understanding Biological Catalysis [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1652063674268837

    APA Style (7th edition)

  • Treviño, Regina. Nickel-substituted Rubredoxin as a Model Protein Scaffold for Hydrogen Production: A Handle Towards Understanding Biological Catalysis. 2022. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1652063674268837.

    MLA Style (8th edition)

  • Treviño, Regina. "Nickel-substituted Rubredoxin as a Model Protein Scaffold for Hydrogen Production: A Handle Towards Understanding Biological Catalysis." Doctoral dissertation, Ohio State University, 2022. http://rave.ohiolink.edu/etdc/view?acc_num=osu1652063674268837

    Chicago Manual of Style (17th edition)

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This open access ETD is published by The Ohio State University and OhioLINK.
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