MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES
Author | : |
Publisher | : |
Total Pages | : 0 |
Release | : 2023 |
Genre | : |
ISBN | : |
Download MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES Book in PDF, ePub and Kindle
Abstract : 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.