Date of Award


Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy in Chemistry (PhD)

Administrative Home Department

Department of Chemistry

Advisor 1

Tatyana G. Karabencheva-Christova

Committee Member 1

Tarun K. Dam

Committee Member 2

Paul Charlesworth

Committee Member 3

Parisa Pour Shahid Saeed Abadi


Enzymes are biological macromolecules, typically proteins, that efficiently accelerate the rate of chemical reactions. Their remarkable catalytic power plays a vital role in essential processes across all kingdoms of life. Nowadays, computational chemistry methods provide valuable insights into enzymatic functions aiding our understanding of biological processes and providing advancements in fields such as biomedical sciences, biomimetic catalysis, drug design and biotechnology. This dissertation employs multilevel computational chemistry methods to investigate the structure-function relationships and the catalytic mechanisms of two metalloenzymes -Zn(II)-dependent matrix metalloproteinase-1 (MMP-1) and non-heme Fe(II)/2-oxoglutarate (2OG) dependent fat-mass and obesity-associated (FTO) enzyme. Chapter 2 explores the role of catalytic and structural Zn(II) ions in the long-range dynamics and overall stability of the MMP-1•triple-helical peptide (THP) ES complex. The results identified catalytic (CAT) domain residues arginine195 (R195) and methionine217 (M217) as crucial for preserving the integrity of the active site. Additionally, the studies show that both Zn(II) ions are critical to maintain effective communication between the exosite of the hemopexin (HPX) domain and the specificity loop (extensive target for drug design) of the CAT domain. Chapter 3 discusses the impact of the removal of THP substrate from MMP-1 ES complex and the effect of in silico replacement of the catalytic Zn(II) ion by Co(II) on the geometry of catalytic site, the overall structure, and dynamics of MMP-1•THP complex. The results highlight that the removal of THP induces slightly increased flexibility in the CAT domain and along with the catalytic Zn(II), influences the stabilizing interactions of the subsite of MMP-1. Chapter 4 is focused on the catalytic mechanism of MMP-1 catalyzed collagenolysis. Our proposed mechanism involves the participation of an additional water molecule (wat2) in the catalytic site that aids in catalysis. The results reveal that the rate-determining step is the water-mediated nucleophilic attack. Furthermore, the calculations show the consecutive and concerted route for the following hydrogen-bond rearrangement and proton transfer steps. Chapter 5 delineates the catalytic mechanism of FTO with pentanucleotide single-stranded RNA (ssRNA) with N6-methyladenine (m6A) substrate and the effects of clinically relevant mutations Arginine316Glutamine (R316Q) and Serine319Phenylalanine (S319F) on the second-coordination sphere (SCS) interactions, dynamics and different stages of the catalytic cycle. The results reveal the different networks of residues that stabilize the TS of the rate-determining hydrogen atom transfer (HAT) step. Additionally, the mutations R316Q and S319F were identified to influence the interactions of the jelly-roll motif and various loops in FTO and, in particular, the S319F affects the pentanucleotide ssRNA(m6A) binding by FTO. Overall, the results of this dissertation provide advanced insights into the intricate relationship between the enzyme structure and function and contribute to an in-depth understanding of the enzymatic mechanism of MMP-1 and FTO. These insights serve as valuable guidelines in enzyme redesign or selective design of inhibitors.

Available for download on Wednesday, December 04, 2024