Kyushu University Academic Staff Educational and Research Activities Database
List of Presentations
Daisuke Kohda Last modified date:2021.10.23

Professor / Division of Structural Biology / Department of Molecular and Structural Biology / Medical Institute of Bioregulation


Presentations
1. Daisuke Kohda, The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states: Thermodynamic analysis using the NMR signals as residue-specific probes, Annual Taiwan Magnetic Resonance Society Meeting, 2019.12.
2. Yuki Kawasaki, Hirotaka Ariyama, Daisuke Fujinami, Hajime Motomura, Ashutosh Srivastava, Florence Tama, Daisuke Noshiro, Toshio Ando, Kouta Mayanagi, Daisuke Kohda, Integrative Analysis Combining AFM, NMR, and EM Revealed Two-State Conformational Exchange of a Single-subunit Oligosaccharyltransferase from Archaeoglobus fulgidus, Thermophiles 2019, 2019.09.
3. Daisuke Kohda, The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states , 8th Asia-Pacific NMR Symposium 2019, 2019.07.
4. Daisuke Fujinami, Abdullah-Al-Mahin, Khaled M. Elsayed, Jun-ichi Nagao, Takeshi Zendo, Kenji Sonomoto, Daisuke Kohda, The lantibiotic Nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states, XXVIIIth International Conference on Magnetic Resonance in Biological Systems (ICMRBS), 2018.08.
5. Daisuke Kohda, Integrative Structural Biology Approach to Understand the Structural and Dynamic Basis of Asn-Glycosylation, The Japanese Biochemical Society Bio-Frontier Symposium, International symposium on ER stress, glycosylation, homeostasis and diseases, 2018.03.
6. Daisuke Kohda, Integrative Structural Biology Approach to Understand the Structural and Dynamic Basis of Asn-Glycosylation, 2nd Joint International Symposium of NSRRC and IPR, 2017.12.
7. Yuya Taguchi, Daisuke Fujinami, Daisuke Kohda, Archaeal Glycobiology by MS and NMR, 2017 Taiwan-Japan Biomedical Symposium on Magnetic Resonance, 2017.10.
8. Daisuke Kohda, Integrative Structural Biology Approach to Understand the Structural and Dynamic Basis of Asn-Glycosylation, The 10th Anniversary of Protein & Peptide Conference (PepCon-2017), 2017.03.
9. Daisuke Kohda, Integrative structural biology approach to decipher the molecular mechanism of Asn-glycosylation , The 42nd Naito Conference, “In the Vanguard of Structural Biology: Revolutionizing Life Sciences”, 2016.10.
10. Daisuke Kohda, Application of “crystal contact-free space” to the study of protein dynamics, The 25th Hot Spring Harbor International Symposium, 2015.11.
11. Daisuke Kohda, Crystal contact-free space for analyzing spatial distribution of protein internal motions, 第53回日本生物物理学会年会, 2015.09.
12. Daisuke Kohda, Integrative structural biology approach to understand the structural and dynamic basis of Asn-glycosylation, 6th Asia-Pacific NMR Symposium, 2015.06, Asparagine-linked glycosylation of proteins is the most ubiquitous protein modification. The oligosaccharyl transfer of an oligosaccharide chain to the Asn residues in the N-glycosylation sequon (Asn-X-Ser/Thr) is catalyzed by a membrane-bound enzyme, oligosaccharyltransferase (OST) 1. The catalytic subunit of the OST enzyme is a polypeptide chain referred to as STT3 in eukaryotes, AglB in archaea, and PglB in eubacteria. The archaeal OST is a single subunit enzyme consisting only of the AglB protein, and thus suitable for structural studies.
We determined the crystal structures of the full-length AglB from a hyperthermophilic archaeon, Archaeoglobus fulgidus2. The AglB consists of an N-terminal transmembrane region, which contains the catalytic center consisting of conserved acidic residues and a divalent metal ion, and a C-terminal globular domain, which contains a binding site for the Ser and Thr residues in the N-glycosylation sequon. NMR and biochemical studies suggested the essential flexibility of the Ser/Thr pocket in the C-terminal globular domain for the enzymatic activity3. It is likely that the dynamic nature of the Ser/Thr-binding pocket facilitates the efficient scanning of a nascent polypeptide chain for the N-glycosylation sequons when coupled with ribosomal protein synthesis. Recently, we started EM single particle analysis and high-speed AFM studies of the AglB protein embedded in nanodiscs to elucidate the precise structure and dynamics in the lipid-bilayer environment. The preliminary 3D reconstruction of the AglB-nanodisc particles suggested a more open conformation of the AglB protein in the lipid bilayers.
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13. Daisuke Kohda, Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation, Progress 100: Kyushu-U and Stanford-U Joint Research and Education Program, First Symposium: From Genes to Human Diseases, 2015.03.
14. Daisuke Kohda, Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation , 2014 SFG & JSCR joint annual meeting, 2014.11.
15. Daisuke Kohda, Crystal structures of oligosaccharyltransferase provide insights into the sequon recognition and activation of N-linked protein glycosylation, 第87回日本生化学会大会シンポジウム, 2014.10.
16. Daisuke Kohda, Structural and dynamic basis for mitochondrial presequence recognition by Tom20, ISN 2014 Special Neurochemistry Conference, 2014.09.
17. Daisuke Kohda, Intentional creation of crystal-contact free space for analyzing large amplitude motions in protein crystals , International Symposium between Kyushu U. Post Global COE and School of Biomedical Sciences, Monash U., 2014.02.
18. Daisuke Kohda, Intentional creation of crystal-contact free space for monitoring large amplitude motions of ligands in protein crystals (workshop, “transient macromolecular complexes involved in multilevel biological phenomena”), 第51回日本生物物理学会, 2013.10.
19. Daisuke Kohda, Crystal structure of an archaeal oligosaccharyltransferase, a membrane enzyme that catalyzes the transfer of sugar chains to asparagine residues of glycoproteins, Post-GCOE Symposium & Retreat in Singapore with NUS and TLL, 2013.03.
20. 神田 大輔, Intentional creation of crystal-contact free space for monitoring large amplitude motions of proteins and ligands in protein crystals, 第85回日本生化学会年会, 2012.12.
21. 神田 大輔, Structural biology of the N-glycosylation reaction, The 20th Anniversary of the Mizutani Foundation for Glycosciences, 2012.11.
22. Cracking of the targeting signal embedded in mitochondrial presequences by NMR and crystallography
Daisuke Kohda
CREST international symposium, Frontier of Biologcal NMR Spectroscopy.
23. From structure to function of PX domains in the NADPH oxidase system
Daisuke Kohda
11th Hot Spring Harbor Symposium of Medical Institute of Bioregulation.
24. Molecular mechanisms of recognition of arrested replication forks by PriA protein in E. coli
T. Tanaka, T. Mizukoshi, C. Taniyama, K. Arai, D. Kohda, H. Masai
25th Annual Meeting of the Japan Society of Molecular Biology.
25. Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67phox, Grb2, and Pex13p
Keiichiro Kami, Ryu Takeya, Hideki Sumimoto , Daisuke Kohda
XXth ICMRBS (International conference on magnetic resonance in biological systems).
26. Structure and Function of PX and SH3 Domains in the NAPDH Oxidase System
Daisuke Kohda
the 2nd Tsinghua International Conference of Protein Science
Tsinghua University, Beijing, China.