Akitsugu Suga

RIKEN

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Yoshiki Yamaguchi

Tohoku Medical and Pharmaceutical University

Shinya Hanashima

Osaka University

Susumu Goto

Research Organization of Information and Systems

Masamichi Nagae

Osaka University

Yoshihiro Yamanishi

Kyushu Institute of Technology

Kosuke Hashimoto

Osaka Metropolitan University

Minoru Kanehisa

Kyoto University

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Kyoto University

Osaka University

RIKEN

RIKEN Advanced Science Institute

The University of Tokyo

Tokyo Institute of Technology

Joint Research Center

Kyoto University Institute for Chemical Research

Kyoto Bunkyo University

Instituto de Investigaciones Químicas

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Analysis of protein landscapes around N-glycosylation sites from the PDB repository for understanding the structural basis of N-glycoprotein processing and maturation

Glycobiology (2018)

Akitsugu Suga Masamichi Nagae Yoshiki Yamaguchi

Asparagine-linked glycans (N-glycans) are attached onto nascent glycoproteins in the endoplasmic reticulum (ER) and subsequently processed by a set of processing enzymes in the ER and Golgi apparatus. Accumulating evidence has shown that not all N-glycans on glycoproteins are uniformly processed into mature forms (hybrid and complex types in mammals) through the ER and Golgi apparatus, and a certain set of glycans remains unprocessed as an "immature" form (high-mannose type in mammals). Much attention has been paid to environmental factors regulating N-glycoprotein maturation, such as the expression levels of glycosyltransferases/glycosidases. On the other hand, the influence of the 3D structure of the carrier glycoprotein on N-glycan maturation has been investigated mostly using individual model glycoproteins. To obtain more insights into N-glycoprotein maturation, we herein analyze glycoprotein structures extracted from the Protein Data Bank. We confirm that site-specific N-glycan processing is largely explained by the solvent accessibility of the glycosylated Asn residue and of the conjugated N-glycan. Potential bias of protein structural features toward immature or mature forms was explored within a range of concentric circles of fully folded glycoproteins. There does appear to be bias in amino acid composition and secondary structure. Most notably, γ-branched amino acid residues (Asn+Asp+Leu) occur more frequently on unstructured loop regions of immature glycoproteins. Structural features of the protein surface around the N-glycosylated site do seem to affect N-glycan processing and maturation.

10.1093/glycob/cwy059

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Bisecting GlcNAc restricts conformations of branches in model N -glycans with GlcNAc termini

Carbohydrate Research (2017)

Shinya Hanashima Akitsugu Suga Yoshiki Yamaguchi

Glycosidic bond

Carbohydrate conformation

10.1016/j.carres.2017.12.002

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The 1st GLYCOINFO SYMPOSIUM Report

Trends in Glycoscience and Glycotechnology (2011)

Akitsugu Suga

this symposium from Soka University, was elected as the chair.To commence the symposium, Dr. Issaku Yamada from Noguchi institute introduced the Glyco Navigation System (http://glyconavi.org/) as a support system for glycan research.The Glyco Navigation System consists of 2 databases: a carbohydrate chemical database and a synthesis reaction database.The system enables researchers to search for the organic synthesis pathways of a particular glycan.Dr. Yamada also described CSEditor, a two-dimensional molecular drawing tool that enables researchers not only to draw the structures of chemical compounds but also to change the chemical structure of glycans into the monosaccharide symbols defined by the Consortium for Functional Glycomics.This software is currently available for Windows, and seems to be a valuable tool for glycan researchers.The Glyco Navigation System is linked with the Japan Consortium for Glycobiology and Glycotechnology Database (JCGGDB).

10.4052/tigg.23.158

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AN IMPROVED SCORING SCHEME FOR PREDICTING GLYCAN STRUCTURES FROM GENE EXPRESSION DATA

Akitsugu Suga Yoshihiro Yamanishi Kosuke Hashimoto Susumu Goto Minoru Kanehisa

The prediction of glycan structures from gene expression of glycosyltransferases (GTs) is a challenging new area in computational biology because the biosynthesis of glycan chains is under the control of GT expression. In this paper we developed a new method for predicting glycan structures from gene expression data. There are two main original aspects of the proposed method. First, we proposed to increase the number of predictable glycan structure candidates by estimating missing glycans from a global glycan structure map, which enables us to predict new glycan structures that are not stored in the database. Second, we proposed a more general scoring scheme based on real-valued gene expression intensity rather than converting it into binary information. In the result we applied the proposed method to predicting cancer-specific glycan structures from gene expression profiles for patients of acute lymphocytic leukemia (ALL) and acute myelocytic leukemia (AML). We confirmed that several of the predicted glycan structures successfully correspond to known cancer-specific glycan structures according to the literature, and our method outperforms the previous methods at a statistically significant level.

Expression (computer science)

10.1142/9781860949920_0023

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Citations (27)