MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES

Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps collagen degradation. Chapter 2 investigates the substrate selectivity and dynamics on the enzyme-substrate complexes of DNA repair enzymes, AlkB and FTO. Chapter 3 unravels the mechanisms and effects of dynamics on the demethylation of 3-methylcytosine substrate by AlkB and AlkBH2 enzymes. The results imply that the nature of DNA and conformational dynamics influence the electronic structure of the iron center during demethylation. Chapter 4 delineates how second-coordination and long-range residue mutations affect the oxidation of 5-methylcytosine substrate to 5-hydroxymethylcytosine by TET2 enzyme. The results reveal that mutations affect DNA binding/interactions and the energetic contributions of residues stabilizing key catalytic species. Chapter 5 describes the reparation of unnatural alkylated substrates by TET2, their effects on second-coordination interactions and long-range correlated motions in TET2. The study reveals that post-hydroxylation reactions occur in aqueous solution outside the enzyme environment. Chapter 6 establishes how applying external electric fields (EEFs) enhances specificity of KDM4E for C—H over N—H activation during dimethylated arginine substrate demethylation. The results reveal that applying positive EEFs parallel to Fe=O bond enhances C—H activation rate, while inhibiting the N—H one. Chapter 7 addresses the formation of catalytically competent MMP-1·THP complex of MMP-1. The studies reveal the role of MMP-1’s catalytic domain a-helices, the linker, and changes in coordination states of catalytic Zn(II) during the transition. Overall, the presented results contribute to the in-depth understanding of the fundamental mechanisms of the studied enzymes and provide a background for developing enzyme-specific inhibitors against the associated disorders and diseases