Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Shimada Atsushi Last modified date:2021.10.04

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

1. Hanawa-Suetsugu K, Itoh Y, Ab Fatah M, Nishimura T, Takemura K, Takeshita K, Kubota S, Miyazaki N, Wan Mohamad Noor WNI, Inaba T, Nguyen NTH, Hamada-Nakahara S, Oono-Yakura K, Tachikawa M, Iwasaki K, Kohda D, Yamamoto M, Kitao A, Shimada A, Suetsugu S., Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7, Nature Communications, 10.1038/s41467-019-12738-w, 10, 4763, 2019.10, Phagocytosis is a cellular process for internalization of micron-sized large particles including pathogens. The Bin-Amphiphysin-Rvs167 (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, impose specific morphologies on lipid membranes. Most BAR domain proteins are thought to form membrane invaginations or protrusions by assembling into helical submicron-diameter filaments, such as on clathrin-coated pits, caveolae, and filopodia. However, the mechanism by which BAR domain proteins assemble into micron-scale phagocytic cups was unclear. Here, we show that the two-dimensional sheet-like assembly of Growth Arrest-Specific 7 (GAS7) plays a critical role in phagocytic cup formation in macrophages. GAS7 has the F-BAR domain that possesses unique hydrophilic loops for two-dimensional sheet formation on flat membranes. Super-resolution microscopy reveals the similar assemblies of GAS7 on phagocytic cups and liposomes. The mutations of the loops abolishes both the membrane localization of GAS7 and phagocytosis. Thus, the sheet-like assembly of GAS7 plays a significant role in phagocytosis..
2. Siqin Bala, Shoko Shinya, Arpita Srivastava, Marie Ishikawa, Atsushi Shimada, Naohiro Kobayashi, Chojiro Kojima, Florence Tama, Osamu Miyashita, Daisuke Kohda, Crystal contact-free conformation of an intrinsically flexible loop in protein crystal
Tim21 as the case study, Biochimica et Biophysica Acta - General Subjects, 10.1016/j.bbagen.2019.129418, 2019.01, Background: In protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to characterize the structural and dynamic properties of intrinsically flexible loops of protein molecules. Methods: We designed an intended crystal contact-free space (CCFS) in protein crystals, and arranged the flexible loop of interest in the CCFS. The yeast Tim 21 protein was chosen as the model protein, because one of the loops (loop 2) is distorted by crystal contacts in the conventional crystal. Results: Yeast Tim21 was fused to the MBP protein by a rigid α-helical linker. The space created between the two proteins was used as the CCFS. The linker length provides adjustable freedom to arrange loop 2 in the CCFS. We re-determined the NMR structure of yeast Tim21, and conducted MD simulations for comparison. Multidimensional scaling was used to visualize the conformational similarity of loop 2. We found that the crystal contact-free conformation of loop 2 is located close to the center of the ensembles of the loop 2 conformations in the NMR and MD structures. Conclusions: Loop 2 of yeast Tim21 in the CCFS adopts a representative, dominant conformation in solution. General significance: No single powerful technique is available for the characterization of flexible structures in protein molecules. NMR analyses and MD simulations provide useful, but incomplete information. CCFS crystallography offers a third route to this goal..
3. Shunsuke Matsumoto, Yuya Taguchi, Atsushi Shimada, Mayumi Igura, Daisuke Kohda, Tethering an N-Glycosylation Sequon-Containing Peptide Creates a Catalytically Competent Oligosaccharyltransferase Complex., 10.1021/acs.biochem.6b01089, 56, 4, 602-611, 2017.01, Oligosaccharyltransferase (OST) transfers an oligosaccharide chain to the Asn residue in the Asn-X-Ser/Thr sequon in proteins, where X is not proline. A sequon was tethered to an archaeal OST enzyme via a disulfide bond. The positions of the cysteine residues in the OST protein and the sequon-containing acceptor peptide were selected by reference to the eubacterial OST structure in a noncovalent complex with an acceptor peptide. We determined the crystal structure of the cross-linked OST-sequon complex. The Ser/Thr-binding pocket recognizes the Thr residue in the sequon, and the catalytic structure termed the "carboxylate dyad" interacted with the Asn residue. Thus, the recognition and the catalytic mechanism of the sequon are conserved between the archaeal and eubacterial OSTs. We found that the tethered peptides in the complex were efficiently glycosylated in the presence of the oligosaccharide donor. The stringent requirements are greatly relaxed in the cross-linked state. The two conserved acidic residues in the catalytic structure were each dispensable, although the double mutation abolished the activity. A Gln residue at the Asn position in the sequon functioned as an acceptor, and the hydroxy group at position +2 was not required. In the standard assay using short free peptides, strong amino acid preferences were observed at the X position, but the preferences, except for Pro, completely disappeared in the cross-linked state. By skipping the initial binding process and stabilizing the complex state, the catalytically competent cross-linked complex offers a unique system for studying the oligosaccharyl transfer reaction..
4. Rei Matsuoka, Atsushi Shimada, Yasuaki Komuro, Yuji Sugita, Daisuke Kohda, Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules., Protein Sci., 25, 3, 754-768, 2016.03.
5. Atsushi Shimada, Atsuko Yamaguchi, Daisuke Kohda, Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain., Sci. Rep., 29, 6, 19565, 2016.01.
6. Nobuaki Takahashi, Sayaka Hamada-Nakahara, Yuzuru Itoh, Kazuhiro Takemura, Atsushi Shimada, Yoshifumi Ueda, Manabu Kitamata, Rei Matsuoka, Kyoko Hanawa-Suetsugu, Yosuke Senju, Masayuki X. Mori, Shigeki Kiyonaka, Daisuke Kohda, Akio Kitao, Yasuo Mori, Shiro Suetsugu, TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P2, Nature Communications, 10.1038/ncomms5994, 5, Article number: 4994, 2014.06.
7. Shunsuke Matsumoto, Atsushi Shimada, Daisuke Kohda, Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases, BMC STRUCTURAL BIOLOGY, 10.1186/1472-6807-13-11, 13, 2013.07.
8. Machaidze, G., Sokoll, A., Shimada, A., Lustig, A., Mazur, A., Wittinghofer, A., Aebi, U. and Mannherz, H.G., Actin filament bundling and different nucleating effects of mouse Diaphanous-related formin FH2 domains on Actin/ADF and Actin/Cofilin complexes, J. Mol. Biol., 403, 4, 529-545, 2010.10.
9. Shimada, A., Takano, K., Shirouzu, M., Hanawa-Suetsugu, K., Terada, T., Toyooka, K., Umehara, T., Yamamoto, M., Yokoyama, S. and Suetsugu, S., Mapping of the basic amino-acid residues responsible for tabulation and cellular protrusion by EFC/F-BAR domain of pacsin2/Syndapin II, FEBS Lett., 584, 6, 1111-1118, 2010.03.
10. Shimada, A., Niwa, H., Tsujita, K., Suetsugu, S., Nitta, K., Hanawa-Suetsugu, K., Akasaka, R., Nishino, Y., Toyama, M., Chen, L., Liu, Z.J., Wang, B.C., Yamamoto, M., Terada, T., Miyazawa, A., Tanaka, A., Sugano, S., Shirouzu, M., Nagayama, K., Takenawa, T. and Yokoyama, S. , Curved EFC/F-BAR domain dimers are joined end to end into a filament for membrane invagination in endocytosis
, Cell, 129, 4, 761-772, 2007.05.
11. Hirose, E., Mukai, M., Shimada, A., Nishitani, H., Shibata, Y. and Nishimoto, T., Loss of RanGEF/Pim1 activity abolishes the orchestration of Ran-mediated mitotic cellular events in S.Pombe, Genes Cells, 11, 1, 29-46, 2006.01.
12. Shimada, A., Nyitrai, M., Vetter, I.R., Kuhlmann, D., Bugyi, B., Narumiya, S., Geeves, M.A. and Wittinghofer, A., The core FH2 domain of diaphanous-related formins is an elongated actin binding protein that inhibits polymerization
, Mol. Cell, 13, 4, 511-522, 2004.02.
13. Fukai, S., Nureki, O., Sekine, S., Shimada, A., Vassylyev, D.G. and Yokoyama, S., Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase, RNA, 9, 1, 100-111, 2003.01.
14. Shimada, A., Nureki, O., Goto, M., Takahashi, S. and Yokoyama S, Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase
, Proc. Natl. Acad. Sci. USA, 98, 24, 13537-13542, 2001.11.
15. Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G. and Yokoyama S, Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase, Nat. Struct. Biol., 8, 3, 203-206, 2001.03.
16. Sekine, S., Shimada, A., Nureki, O., Cavarelli, J., Moras, D., Vassylyev, D.G. and Yokoyama, S., Crucial role of the HIGH-loop lysine for the catalytic activity of arginyl-tRNA synthetase, J. Biol. Chem., 276, 6, 3723-3726, 2001.02.
17. Shimada, A., Nureki, O., Dohmae, N., Takio, K. and Yokoyama, S., Gene cloning, expression, crystallization and preliminary X-ray analysis of Thermus thermophilus arginyl-tRNA synthetase
, Acta Crystallogr. D Biol. Crystallogr., 57 (Pt2), 272-275, 2001.02.
18. Fukai, S., Nureki, O., Sekine, S., Shimada, A., Tao, J., Vassylyev, D.G. and Yokoyama, S., Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase, Cell, 103, 5, 793-803, 2000.11.
19. Sugiura, I., Nureki, O., Ugaji-Yoshikawa, Y., Kuwabara, S., Shimada, A., Tateno, M., Lorber, B., Giege, R., Moras, D., Yokoyama, S. and Konno, M., The 2.0 Å crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules
, Structure, 8, 2, 197-208, 2000.02.
20. Nureki, O., Vassylyev, D.G., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T.L., Schimmel, P. and Yokoyama, S., Enzyme structure with two catalytic sites for double-sieve selection of substrate, Science, 280, 5363, 578-582, 1998.04.