Study of the structure-function relations of hemicellulolytic enzymes using bioinformatics tools
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Date
2024
Authors
Παπαμίχος, Ηλίας
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Abstract
The boon of AI modelling technologies, coupled with the advancing capabilities of molecular dock-ing simulations has ushered in a new era for the field of bioinformatics. The growing need to explore the molecular capabilities of different enzymes in order to utilize them for degradation purposes of the many different biopolymers led to the advancement of this particular field. Biopolymers, such as cellu-loses and hemicelluloses are potent reservoirs of many monomers that exhibit certain properties pre-dominantly employed and useful in fields like biotechnology, food and drinks or even biofuels. This thesis dives into the concerted effort of AI protein folding modelling and Molecular Docking Simulations in order to explore the different modes of action of Glycoside Hydrolase 30 enzymes, sub-family 7 (GH30_7). These enzymes are efficient xylan degradation machines and doing so by exhibiting different modes of action, either endo action, exo-action or both. Xylan is a polysaccharide found in plant cell walls and is the major component of hemicellulose and its hydrolysis yields xylose and differ-ent XOS that present valuable platforms for the synthesis of many different products such as biofuels and pharmaceuticals. Thus understanding the structural basis of GH30_7 is key to optimizing their uti-lization. An obstacle that presents is the lack of experimental crystal structures for most GH30_7, only two have solved crystal structures, which makes the deciphering of their catalytic mechanism even more challenging. This gap is addressed by relying on computational techniques in order to delve into their mode of action. AlphaFold was used in order to construct the three-dimensional structure for all the eight characterized GH30_7 and Chimera to construct ligands that are natural products of xylan’s degradation by GH30_7. These models were used in Molecular Docking Simulations with SwissDock, in order to explore the interactions between the ligands and GH30_7. Such simulations visualize the pu-tative binding mechanism and interactions at the active site of enzymes with the different ligands. These simulations and comparisons helped shed light into the key residues and regions with putative implication in the function of GH30_7 xylanases such as the Arg residue responsible for endoglucu-ronoxylanase activity and a protruding loop at the active cleft that hinders the binding of xylan chain in the catalytic cleft. The results of this thesis will help elucidate the novelty of the aforementioned structural features and their importance on the mode of action. This thesis’ objective is to help infer such novel structure- function relations that could be applied for the rest of the uncharacterized GH30_7 enzymes while providing scientists with a platform to base their experimental work on and thus maximize the yield of certain products via enzymatic hydrolysis.
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Keywords
Glycoside hydrolase family 30, Xylan, AlphaFold, Molecular docking simulations, SwissDock, Protein structure modelling, Enzymatic hydrolysis, Enzymes, GH30_7