|Daisuke Kohda||Last modified date：2021.10.23|
Professor / Division of Structural Biology / Department of Molecular and Structural Biology / Medical Institute of Bioregulation
|1.||Daisuke Kohda, Glycoscience Applications and Basic Science: subtitle：Insights from Japan Consortium for Glycobiology and Glycotechnology
Chapter 2. Structural Biology of Glycans
2.5 Structural Study of Proteins in Glycoscience Field, Springer Nature Singapore, ISBN 978-981-13-5856-2, 2019.07, [URL].
|2.||Hidekazu Hiroaki, Daisuke Kohda, Protein-ligand interactions studied by NMR, Springer Singapore, 10.1007/978-981-10-5966-7_21, 579-600, 2017.11, Various solution NMR experiments for studying protein-ligand interactions have become indispensable techniques in both academia and industry. In general, solution NMR is superior to other physico-chemical methods, in terms of its spatial resolution and the fact that protein modifications are not required. The applications are loosely classified into two categories, "ligand-based approach" and "protein-based approach." Many unique experiments have been developed for the ligand-based approach, including STD, WaterLOGSY, DIRECTION, INPHARMA, ILOE, and trNOE. These experiments frequently comprise the important steps of a drug-discovery process, including ligand screening, pharmacophore mapping, and molecular design. This review provides a practicable classification of these experiments, to promote the selection of a suitable experiment depending on the purpose. In contrast, the variation of experiments in the protein-based approach is rather limited. The 1H-15N-HSQC-based NMR titration experiment and its variants are preferentially used for analyses of protein-ligand interactions. This review also discusses several practical aspects of the NMR titration experiment, including sample handling and data acquisition and analysis..|
|3.||Shunsuke Matsumoto, James Nyirenda, Daisuke Kohda, Structural biology of oligosaccharyltransferase (ost), Springer Japan, 10.1007/978-4-431-54841-6_44, 437-445, 2015.01, Asparagine-linked glycosylation of proteins is widespread not only in eukaryotes but also in archaea and some eubacteria. The oligosaccharyl transfer reaction is catalyzed by a membrane-bound enzyme, oligosaccharyltransferase (OST). The donor substrate is the lipid-linked oligosaccharide (LLO), and the acceptor is the asparagine residues in the N-glycosylation sequon (Asn-X-Ser/Thr, X 6¼ Pro). The catalytic subunit of OST consists of an N-terminal transmembrane region consisting of 13 TM helices and a C-terminal globular domain. The crystal structures of the eubacterial and archaeal catalytic subunits revealed the structural basis of the sequon recognition and activation. Two conserved motifs, termed DXDs, form a metal ion containing catalytic center that activates the side-chain carboxamide group of the acceptor Asn residue in the sequon. Other conserved motifs, WWDYG and DK/MI motifs, constitute a binding site for the Ser and Thr residues in the sequon. In addition to the crystallography, NMR and biochemical studies suggested that the flexibility of one long loop in the TM region and the Ser/Thr pocket in the C-terminal globular domain were both important for the enzymatic activity. It is likely that their dynamic nature facilitates the efficient scanning of a nascent polypeptide chain for the N-glycosylation sequons when coupled with ribosomal protein synthesis..|