Date on Master's Thesis/Doctoral Dissertation
5-2020
Document Type
Doctoral Dissertation
Degree Name
Ph. D.
Department
Chemistry
Degree Program
Chemistry, PhD
Committee Chair
Kozlowski, Pawel M.
Committee Co-Chair (if applicable)
Grapperhaus, Craig
Committee Member
Grapperhaus, Craig
Committee Member
Thompson, Lee
Committee Member
Sathithsuksanoh, Noppadon
Committee Member
Jaroszynska-Wolinska, Justyna
Author's Keywords
vitamin B12; AdoCbl; ethanolamine ammonia lyase; glutamate mutase; QM/MM; DFT
Abstract
Vitamin B12 is a complex organometallic molecule, the derivatives of which such as adenosylcobalamin (AdoCbl) and methylcobalamin (CH3Cbl) act as a cofactor in numerous enzymatic reactions. These two biologically active cofactors contain a unique organometallic Co-C σ bond. Important feature of this Co-C bond is that it can be activated by both thermally and photolytically inside the enzymatic environment as well as in the solution. In the case of enzymatic reactions where AdoCbl molecule act as a cofactor, the cleavage of the Co-C bond constitutes the key catalytic step. The most intriguing features of this cleavage is that upon binding with a substrate the cleavage of the Co-C bond is 1012-fold rate accelerated inside enzyme compared to the isolated cofactor. There are number of factors responsible behind this trillion-fold rate acceleration which are still under investigation. Alternatively, the Co-C bond in AdoCbl can also be cleaved by light to generate the same radical pair (RP) as in the case of enzymatic catalysis. The light sensitivity of these cobalamins was known for more than five decades only until recently it has been associated with controlled reactivity, namely optogenetic regulation and light-activated drug delivery. Moreover, the ability to probe photolytic cleavage of the Co−C bond for enzyme bound AdoCbl is of particular relevance in enzymatic catalysis. Herein this study the photolysis and native catalysis mechanism for vitamin B12-dependent enzymes will be investigated using a combined quantum mechanics/molecular mechanics (QM/MM) approach. According to our studies, it appears that the enzymatic environment controls the cleavage of Co-C bond by exerting an electrostatic interaction. In addition, the enzymatic environment controls the generated Ado radical path by providing a cage. This ultimately effects the formation of the product in native catalysis as well as in photolysis.Finally, I will be discussing a plausible connection between photolysis and native catalysis mechanism in vitamin B12-dependent enzymes based on the idea that the protein environment reduces the cofactor. The reaction mechanism based on the reduced cofactor in native catalysis was found to be similar with the photo-dissociation mechanism.
Recommended Citation
Mamun, Abdullah Al, "Computational modeling of photolysis and catalysis reactions in vitamin b12-dependent enzymes." (2020). Electronic Theses and Dissertations. Paper 3406.
https://doi.org/10.18297/etd/3406
