Our group has been focusing on the in silico simulation of glycosylation and related pathways.
We have been successful in modeling the N-glycan biosynthesis pathway in Drosophila embryo, using Michaelis-Menten kinetic parameter estimation, to predict the glycome of Drosophila embryo. Moreover, we could perform knock-out gene simulations with this model to produce glycomes that reflect what has already been reported in the literature.
We are currently expanding our work to O-glycan biosynthesis in CHO cells using various combinations of glycosyltransferases, as well as development of a Web tool to allow researchers to easily perform these simulations over the Web. Our Web tool, called GlycoSim, will soon be available, allowing researchers to select their glycosyltransferases of interest, generate the biosynthesis pathway, set and estimate the necessary reaction parameters, and perform simulations to predict the generated glycome.
In collaboration with various proteomics and glycomics researchers, we aim to provide a useful tool and model to aid in the better understanding of glycan biosynthesis. This could be applied to glyco-engineering of various cells, as well as identification of important key glycosyltransferases in various pathologies. We also hope to expand our simulations from glycan biosynthesis to signaling and other relevant metabolic pathways.
This work has been funded by the JST Mirai Program.