Date on Master's Thesis/Doctoral Dissertation

12-2021

Document Type

Doctoral Dissertation

Degree Name

Ph. D.

Department

Chemistry

Degree Program

Chemistry, PhD

Committee Chair

Kozlowski, Pawel M.

Committee Member

Grapperhaus, Craig A.

Committee Member

Thompson, Lee M.

Committee Member

Narayanan, Badri

Author's Keywords

QM/MM; TDDFT; DFT; Co-C bond; Cobalamin; Vitamin B12

Abstract

The vitamin B12 derivates, otherwise known as cobalamin (Cbl), are ubiquitous organometallic cofactors. The biologically active forms of Cbl, such as methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), act as cofactors in different physiological reactions for both prokaryotes and eukaryotes. A crucial aspect of the Cbl-mediated systems is the activation of the organometallic Co-C bond that plays a critical role in its catalytic activity. One of the most remarkable features of this Co-C bond is its unusual activation in AdoCbl-dependent enzymatic reactions, where a trillion-fold rate acceleration of the Co-C bond cleavage is observed inside the enzyme compared to the isolated AdoCbl. Although several hypotheses have been proposed previously, none can fully explain the trillion-fold rate acceleration that is observed for the Co-C bond cleavage. Thus, the factor(s) responsible for the unusual activation of the Co-C bond in the AdoCbl-dependent enzyme remains elusive. Nonetheless, this Co-C bond of MeCbl and AdoCbl cofactors is also known for its unique ability to be activated both thermally and photolytically within the enzymatic environment as well as in solutions. Even though the photochemistry of Cbl-dependent systems has been known for almost five decades, it has recently received a lot of attention due to its potential role in light-activated drug delivery, biomimetic catalysis, and a variety of other applications. Therefore, with these applications in mind, understanding the mechanistic insight into the activation of the Co-C bond is paramount for gaining a comprehensive knowledge of these reactions. In this dissertation, the mechanistic details of the activation of the Co-C in the photolysis and native catalysis of MeCbl and AdoCbl-dependent systems have been investigated using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, density functional theory (DFT), and time-dependent density functional theory (TD-DFT) methodologies. Overall, this dissertation is divided into six chapters. Chapter one gives an introduction, a historical overview of B12 chemistry, and possible applications in therapeutics and optogenetics. Chapters two and three discuss the photoactivation of the Co-C bond in MeCbl-dependent methionine synthase (MetH) and explore the role of the enzymatic environment on photoreaction. The photochemical data of isolated MeCbl cofactor in solution were also discussed and compared with the enzymatic environment to understand the effect of protein binding on the photolysis of Co-C bonds. The influence of mutation on the photolysis of Co-C is discussed in chapter three. Overall, in these two chapters, it was shown that the enzymatic environment affects the photolysis of the Co-C bond by modulating the electronically excited state. Chapter four provides an in-depth insight into the aerobic photolysis of MeCbl, with emphasis placed on the mechanistic details of the insertion of O2 in the activated Co-C bond. It was shown that the photochemical properties of MeCbl can also be modulated in the presence of molecular oxygen, i.e., in aerobic conditions. While chapters two to four cover the light-activation of the Co-C bond, chapter five focused on the activation of the Co-C bond during the native catalysis of AdoCbl-dependent methylmalonyl CoA mutase (MCM). The QM/MM methodology has been used to investigate the factor(s) responsible for the unusual activation of the Co-C bond that is observed in the enzyme as compared to AdoCbl in solution. While there are at least three previously reported hypotheses for the activation of the Co-C bond including, substrate-induced conformational changes, electrostatic interaction between the Ado group and the enzyme, and involvement of tyrosine residue, none of these can explain this unusual activation. Thus, how the arrival of the substrate triggers the activation of the Co-C bond remains an open issue.

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