MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE DYNAMICS AND REACTION MECHANISMS OF NON-HEME IRON AND 2-OXOGLUTARATE DEPENDENT ENZYMES

Abstract

Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter 3 describes the use of combined quantum mechanics/molecular mechanics (QM/MM) and MD simulations to explore the reaction mechanism of histone lysine demethylases 7B (PHF8), including dioxygen activation, 2OG binding modes, and substrate demethylation steps. Importantly, the calculations imply the rearrangement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis, highlighting the dynamic nature of the non-heme Fe-center. Chapter 4 develops a computational framework for identifying second coordination sphere (SCS) and especially long range (LR) residues relevant for catalysis through dynamic cross correlation analysis (DCCA) using the PHF8 as a model oxygenase and explores their effects on the rate determining hydrogen atom transfer step. The results from the QM/MM calculations suggest that DCCA can identify non-active site residues relevant to catalysis. Chapter 5 explores the unique catalytic mechanism of EFE. In particular, the study elucidates the atomic and electronic structure determinants that distinguish between ethylene formation and L-Arg hydroxylation reaction mechanisms in the EFE. The results indicated that synergy between the conformation of L-Arg and the coordination mode of 2OG directs the reaction toward ethylene formation or L-Arg hydroxylation. Chapter 6 demonstrates that applying an external electric field (EEF) along the Fe-O bond in the EFE·Fe(III)·OO.-·2OG·L-Arg complex can switch the EFE reactivity between L-Arg hydroxylation and ethylene generation. Overall, applying an EEF on EFE indicates that making the intrinsic electric field of EFE less negative and stabilizing the off-line binding of 2OG might increase ethylene generation while reducing L-Arg hydroxylation. Chapter 7 probes the role of the protein environment in modulating the dioxygen diffusion and binding and thus ultimately contributing to the diverging reactivities of PHF8 and EFE. Overall, the results of this dissertation together highlight the several catalytic strategies utilized by the non-heme Fe(II) and 2OG dependent enzymes for achieving their reaction outcomes. In the longer term, the results can be used to modulate the activities of these enzymes either through enzyme redesign or the generation of enzyme-selective inhibitors.