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The process of glycan biosynthesis is not fully understood, and while the biosynthesis of N-glycans in cells is somewhat understood, the quality control mechanisms and other O-glycans and proteoglycans are still under investigation. On the other hand, with the development of glycomics technology, it is possible to some extent to investigate the profile (glycome) of glycans using mass spectrometry, but there is still a need for technological development to investigate the details down to the glycosidic linkages. However, advances in information science technology and data standardization have made it possible to predict changes in cell behavior due to perturbations in the field of systems biology. Therefore, research and development of glycan biosynthesis simulation is being promoted; research especially on these processes in the Golgi apparatus has been advanced in recent years [1]. To perform glycan biosynthesis simulation analysis, mainly three steps are taken. The first is that information about the glycan-related enzymes (glycosyltransferases and glycosidases) expressed in the cell and the initial substrate glycan structure are necessary. Also, the substrate specificity of each enzyme and their reaction details are necessary, and for this, standardized nomenclature such as LiCoRR [2] is used. Based on this information, it is possible to predict the glycan structure that can be biosynthesized and to predict the biosynthesis pathway (Fig. 165.1) [3]. The second step is model creation. However, the details regarding what has been obtained as a pathway are just a prediction of the glycan structures to be synthesized, and the reaction conditions of the actual catalyzing enzyme are not yet included, so these parameters need to be set. To informatically express this model, the Systems Biology Markup Language (SBML) is used. Finally, the third step is to calculate the biosynthesis of the glycan structure quantitatively using the parameter values after the model is completed (Fig. 165.2). These three steps can be executed using the GlycoSim Web tool.

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Glycan Biosynthesis Simulation

  • 章节

  • 发表日期：

    2026年

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  • Kiyoko F. Aoki-Kinoshita

摘要

The process of glycan biosynthesis is not fully understood, and while the biosynthesis of N-glycans in cells is somewhat understood, the quality control mechanisms and other O-glycans and proteoglycans are still under investigation. On the other hand, with the development of glycomics technology, it is possible to some extent to investigate the profile (glycome) of glycans using mass spectrometry, but there is still a need for technological development to investigate the details down to the glycosidic linkages. However, advances in information science technology and data standardization have made it possible to predict changes in cell behavior due to perturbations in the field of systems biology. Therefore, research and development of glycan biosynthesis simulation is being promoted; research especially on these processes in the Golgi apparatus has been advanced in recent years [1]. To perform glycan biosynthesis simulation analysis, mainly three steps are taken. The first is that information about the glycan-related enzymes (glycosyltransferases and glycosidases) expressed in the cell and the initial substrate glycan structure are necessary. Also, the substrate specificity of each enzyme and their reaction details are necessary, and for this, standardized nomenclature such as LiCoRR [2] is used. Based on this information, it is possible to predict the glycan structure that can be biosynthesized and to predict the biosynthesis pathway (Fig. 165.1) [3]. The second step is model creation. However, the details regarding what has been obtained as a pathway are just a prediction of the glycan structures to be synthesized, and the reaction conditions of the actual catalyzing enzyme are not yet included, so these parameters need to be set. To informatically express this model, the Systems Biology Markup Language (SBML) is used. Finally, the third step is to calculate the biosynthesis of the glycan structure quantitatively using the parameter values after the model is completed (Fig. 165.2). These three steps can be executed using the GlycoSim Web tool.