Date of Award
2025
Document Type
Open Access Dissertation
Degree Name
Doctor of Philosophy in Chemistry (PhD)
Administrative Home Department
Department of Chemistry
Advisor 1
Christo Z. Christov
Committee Member 1
Tarun Dam
Committee Member 2
Lanrong Bi
Committee Member 3
Susanta Ghosh
Abstract
Enzymes catalyze complex biological transformations. Non-heme Fe(II)/2-oxoglutarate (2OG)–dependent enzymes are highly versatile catalysts capable of selective C–H oxidation, enabling transformations such as hydroxylation, halogenation, desaturation, demethylation, ring rearrangements, epoxidation, and electrophilic aromatic substitution. These enzymes are involved in various biological processes, including fatty acid metabolism, hypoxic signaling, collagen maturation, and transcriptional regulation. Computational Modeling provides detailed knowledge of the enzymes including atomistic details of the important catalytic species, conformational and electronic effects, which are crucial to enzyme engineering and drug design efforts. This dissertation implements advanced multi-scale molecular modelling techniques including Molecular dynamics and Quantum Mechanic / Molecular Mechanics calculations to comprehend the dynamics and catalytic reaction mechanisms of non-heme Fe(II)/2-oxoglutarate (2OG) dependent oxygenases. Chapter 2 describes the role of synergy between non-heme Fe(II) center, second coordination sphere (SCS) and long-range (LR) interactions in the catalytic mechanism of KDM6 family of enzymes, focusing on similarities and differences in dynamics and the reaction mechanism of KDM6A and KDM6B in the demethylation of tri-methylated H3 histone lysine. The results identified differences in the SCS interactions of the Fe-chelating glutamate influences the hydrogen atom transfer reactivity of KDM6A and KDM6B. Chapter 3 describes the mechanism of consecutive oxidations catalyzed by KDM6B enzyme with higher alkylated H3 Lysine substrates. The results identified the role of SCS residues N344 and Y239 in conformational positioning of different alkylation marks of the lysine substrate to access the Fe(IV)=O intermediate, thereby influencing the regio- and chemo-selectivity. Chapter 4 unravels the second branchpoint in the catalytic mechanism of ethylene forming enzyme, which determines the product distribution of ethylene and 3-hydroxypropionate (3HP). The results suggest that the propion-3-yl radical acts as the branchpoint between ethylene and 3HP rather than previously proposed carboxyethyl carbonato-Fe(II) intermediate. Chapter 5 explores the catalytic mechanism of Adev halogenases in achieving regio- and stereo-specific chlorination of nucleosides and determines the reactive intermediate among the two ferryl intermediates identified experimentally. The QM/MM reaction path calculations and Mossbauer calculations complements the experimental observation by suggesting the offline Fe(IV)=O as the reactive intermediate for C-H activation. Chapter 6 describes the reaction mechanism of free amino acid halogenase BesD and halogenase variants derived from homologous hydroxylase. The results suggest an isomerization pathway involving swapping of -OH and -Cl groups at the Cl-Fe(III)-OH intermediate which helps in achieving chlorination selectivity. Overall, the insights presented in this dissertation deepens the fundamental understanding of the catalysis by non-heme Fe(II)/2OG dependent enzymes, which could help in design of drugs and enzyme engineering efforts.
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Recommended Citation
Jaber Sathik Rifayee, Simahudeen Bathir, "MULTISCALE COMPUTATIONAL CHEMISTRY STUDIES OF THE CATALYTIC MECHANISMS OF NON-HEME FE(II)/2-OXOGLUTARATE-DEPENDENT OXYGENASES", Open Access Dissertation, Michigan Technological University, 2025.