Date of Award

5-16-2024

Publication Type

Dissertation

Degree Name

Ph.D.

Department

Chemistry and Biochemistry

Supervisor

James Gauld

Abstract

Understanding enzyme-related chemistry is essential for elucidating critical physiological processes, as well as providing medicinally and industrially relevant insights. Unfortunately, many of their reactions and roles remain unclear. In this dissertation, we have examined a number of critical questions related to enzymes and their roles. In chapter 1, a brief overview is provided of relevant enzyme chemistry related to the topics covered in this dissertation. Subsequently, in chapter 2 a summary of key foundational concepts of quantum chemistry is provided, along with those of the various computational methods used in this dissertation. Some sulfur containing biocompounds possess antioxidant properties due to their ability to reduce radicals which are known to potentially cause health problems. In chapter 3, we examine the effects of structure and chemical functionality on antioxidant properties. More specifically, we employ systematic series of disulfide and sulfur-nitrogen containing molecules based on experimentally known antioxidant biomolecules. However, key to any computational study on biomolecules is determining a suitably reliable and accurate DFT-based level of theory. We find that for sulfur-sulfur containing species, the ꞷB97XD method is preferred, while for sulfur-nitrogen containing species the ꞷB97XD or M06-2X methods are suitable. A range of DFT-methods, in combination with basis sets ranging from 6-31G(d) to 6-311+G(2df,p) were also examined. The sulfur-sulfur bond are sensitive to changes in basis set. However, their optimized bond lengths obtained using the 6-311G(2d,p) basis set showed best agreement with the benchmark level of theories (QCISD). Their key antioxidant-relevant properties were also examined within the context of their structure and functionality, including those related to hydrogen atom transfer (HAT), single electron transfer proton transfer (SETPT), and sequential proton and electron transfer (SPLET). Chapters 4 and 5 examine two different but related enzymes that catalyze amide bond formation. More specifically, the mechanisms of two different nonribosomal peptide synthetase domains are studied: the condensation domain from tyrocidine synthetase and cyclization domain from yersiniabactin synthetase. Multi-scale computational approaches (e.g., docking, molecular dynamics simulation (MD) and Quantum mechanics/Molecular Mechanics (QM/MM)) were complementarily applied in each study. The cyclization domain exhibits a distinctive structure, controlled by the dynamic behavior of its channels. Notably, during amide bond formation the two channels are open. However, during the heterocyclic ring formation reaction, one of the channels is closed to prevent any other substrates from being introduced to the active site. This transformation is unique and important since it can produce myriads of industrially important cyclic compounds. Ring formation as catalyzed by a cyclization domain from nonribosomal peptide synthetases is described in chapter 6 while the dynamic behaviour of the active site related to cyclization is studied in chapter 7. Enzymes are known for their selectivity and sensitivity towards certain substrates. For instance, however, the existence of structurally similar amino acids may interfere with the whole aminoacylation process. Aminoacyl tRNA can pick up the required amino acid with an average error rate is as low as 0.01%. To avoid this error, the whole process must undergo an editing process. However, Cysteinyl-tRNA synthetase can achieve high amino acid specificity without editing reaction. The reason behind this will be discussed in detail in chapter 8. The enzymes examined in this dissertation offer valuable insights into essential chemical reactions catalyzed by enzymes. By expanding upon these studies, the acquired knowledge can be applied to various systems. As a result, this will contribute to a deeper understanding of the chemical principles underlying the relationship between enzyme structure and activity, benefiting research in enzymology overall.

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