Wakatsuki Laboratory

Publications

  1. Gabriele M. M. Stoffel, David Adrian Saez, Hasan DeMirci, Bastian Vögeli, Yashas Rao, Jan Zarzycki, Yasuo Yoshikuni, Soichi Wakatsuki, Esteban Vöhringer-Martinez, and Tobias J. Erb.Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases.PNAS June 26, 2019 https://doi.org/10.1073/pnas.1901471116
  2. Comerci CJ, Herrmann J, Yoon J, Jabbarpour F, Zhou X, Nomellini JF, Smit J, Shapiro L, Wakatsuki S, Moerner WE.Topologically-guided continuous protein crystallization controls bacterial surface layer self-assembly. Nat Commun.2019 Jun 21;10(1):2731. doi: 10.1038/s41467-019-10650-x. PubMed PMID: 31227690; PubMed Central PMCID: PMC6588578.
  3. Raub AG, Hwang S, Horikoshi N, Cunningham AD, Rahighi S, Wakatsuki S, Mochly-Rosen D. Small-Molecule Activators of Glucose-6-phosphate Dehydrogenase (G6PD) Bridging the Dimer Interface. ChemMedChem. 2019 Jun 11;. doi: 10.1002/cmdc.201900341. [Epub ahead of print] PubMed PMID: 31183991.
  4. I Ciftci H, G Sierra R, Yoon CH, Su Z, Tateishi H, Koga R, Kotaro K, Yumoto F, Senda T, Liang M, Wakatsuki S, Otsuka M, Fujita M, DeMirci H. Serial Femtosecond X-Ray Diffraction of HIV-1 Gag MA-IP6 Microcrystals at Ambient Temperature. Int J Mol Sci. 2019 Apr 3;20(7). doi: 10.3390/ijms20071675. PubMed PMID: 30987231; PubMed Central PMCID: PMC6479536.
  5. Sierra RG, Batyuk A, Sun Z, Aquila A, Hunter MS, Lane TJ, Liang M, Yoon CH, Alonso-Mori R, Armenta R, Castagna JC, Hollenbeck M, Osier TO, Hayes M, Aldrich J, Curtis R, Koglin JE, Rendahl T, Rodriguez E, Carbajo S, Guillet S, Paul R, Hart P, Nakahara K, Carini G, DeMirci H, Dao EH, Hayes BM, Rao YP, Chollet M, Feng Y, Fuller FD, Kupitz C, Sato T, Seaberg MH, Song S, van Driel TB, Yavas H, Zhu D, Cohen AE, Wakatsuki S, Boutet S. The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source. J Synchrotron Radiat. 2019 Mar 1;26(Pt 2):346-357. doi: 10.1107/S1600577519001577. Epub 2019 Feb 22. PubMed PMID: 30855242; PubMed Central PMCID: PMC6412173.
  6. Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA. 2018 Dec;24(12):1667-1676. doi: 10.1261/rna.067660.118. Epub 2018 Aug 23. PubMed PMID: 30139800; PubMed Central PMCID: PMC6239188.
  7. Hwang S, Mruk K, Rahighi S, Raub AG, Chen CH, Dorn LE, Horikoshi N, Wakatsuki S, Chen JK, Mochly-Rosen D. Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator. Nat Commun. 2018 Oct 2;9(1):4045. doi: 10.1038/s41467-018-06447-z. PubMed PMID: 30279493; PubMed Central PMCID: PMC6168459.
  8. Li PN, Herrmann J, Tolar BB, Poitevin F, Ramdasi R, Bargar JR, Stahl DA, Jensen GJ, Francis CA, Wakatsuki S, van den Bedem H. Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. ISME J. 2018 Oct;12(10):2389-2402. doi: 10.1038/s41396-018-0191-0. Epub 2018 Jun 13. PubMed PMID: 29899515; PubMed Central PMCID: PMC6155111.
  9. Tolar BB, Herrmann J, Bargar JR, van den Bedem H, Wakatsuki S, Francis CA. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea. Environ Microbiol Rep. 2017 Oct;9(5):484-491. doi: 10.1111/1758-2229.12567. Epub 2017 Jul 21. Review. PubMed PMID: 28677304.
  10. Cunningham AD, Mochly-Rosen D. Structural analysis of clinically relevant pathogenic G6PD variants reveals the importance of tetramerization for G6PD activity. Matters (Zur). 2017 Sep 14;2017. doi: 10.19185/matters.201705000008. PubMed PMID: 30148135; PubMed Central PMCID: PMC6105287.
  11. Rogov VV, Stolz A, Ravichandran AC, Rios-Szwed DO, Suzuki H, Kniss A, Löhr F, Wakatsuki S, Dötsch V, Dikic I, Dobson RC, McEwan DG. Structural and functional analysis of the GABARAP interaction motif (GIM). EMBO Rep. 2017 Aug;18(8):1382-1396. doi: 10.15252/embr.201643587. Epub 2017 Jun 27. PubMed PMID: 28655748; PubMed Central PMCID: PMC5538626.
  12. Herrmann J, Jabbarpour F, Bargar PG, Nomellini JF, Li PN, Lane TJ, Weiss TM, Smit J, Shapiro L, Wakatsuki S.Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer. Biophys J. 2017 May 9;112(9):1841-1851. doi: 10.1016/j.bpj.2017.04.003. PubMed PMID: 28494955; PubMed Central PMCID: PMC5425405.
  13. Rogov VV, Suzuki H, Marinković M, Lang V, Kato R, Kawasaki M, Buljubašić M, Šprung M, Rogova N, Wakatsuki S, Hamacher-Brady A, Dötsch V, Dikic I, Brady NR, Novak I. Phosphorylation of the mitochondrial autophagy receptor Nix enhances its interaction with LC3 proteins. Sci Rep. 2017 Apr 25;7(1):1131. doi: 10.1038/s41598-017-01258-6. PubMed PMID: 28442745; PubMed Central PMCID: PMC5430633.
  14. Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Batyuk A, Ciftci H, Guillet S, Hayes MJ, Hayes B, Lane TJ, Liang M, Lundström U, Koglin JE, Mgbam P, Rao Y, Rendahl T, Rodriguez E, Zhang L, Wakatsuki S, Boutet S, Holton JM, Hunter MS. Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin. Sci Data. 2017 Apr 25;4:170055. doi: 10.1038/sdata.2017.55. PubMed PMID: 28440794; PubMed Central PMCID: PMC5404608.
  15. Chiu W, Holton J, Langan P, Sauter NK, Schlichting I, Terwilliger T, Martin JL, Read RJ, Wakatsuki S. Responses to `Atomic resolution': a badly abused term in structural biology. Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):381-383. doi: 10.1107/S205979831700417X. Epub 2017 Mar 31. PubMed PMID: 28375150.
  16. Cunningham AD, Colavin A, Huang KC, Mochly-Rosen D. Coupling between Protein Stability and Catalytic Activity Determines Pathogenicity of G6PD Variants. Cell Rep. 2017 Mar 14;18(11):2592-2599. doi: 10.1016/j.celrep.2017.02.048. PubMed PMID: 28297664; PubMed Central PMCID: PMC5396575.
  17. Hunter MS, Yoon CH, DeMirci H, Sierra RG, Dao EH, Ahmadi R, Aksit F, Aquila AL, Ciftci H, Guillet S, Hayes MJ, Lane TJ, Liang M, Lundström U, Koglin JE, Mgbam P, Rao Y, Zhang L, Wakatsuki S, Holton JM, Boutet S. Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nat Commun. 2016 Nov 4;7:13388. doi: 10.1038/ncomms13388. PubMed PMID: 27811937; PubMed Central PMCID: PMC5097167.
  18. Suzuki N, Rohaim A, Kato R, Dikic I, Wakatsuki S, Kawasaki M. A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. FEBS J. 2016 Jun;283(11):2004-17. doi: 10.1111/febs.13734. Epub 2016 Apr 28. PubMed PMID: 27062441.
  19. Cunningham AD, Hwang S, Mochly-Rosen D. Glucose-6-Phosphate Dehydrogenase Deficiency and the Need for a Novel Treatment to Prevent Kernicterus. Clin Perinatol. 2016 Jun;43(2):341-54. doi: 10.1016/j.clp.2016.01.010. Epub 2016 Feb 28. Review. PubMed PMID: 27235212.
  20. Rahighi S, Braunstein I, Ternette N, Kessler B, Kawasaki M, Kato R, Matsui T, Weiss TM, Stanhill A, Wakatsuki S. Selective Binding of AIRAPL Tandem UIMs to Lys48-Linked Tri-Ubiquitin Chains. Structure. 2016 Mar 1;24(3):412-22. doi: 10.1016/j.str.2015.12.017. Epub 2016 Feb 11. PubMed PMID: 26876100; PubMed Central PMCID: PMC4775417.
  21. Boutet S, Cohen A, Wakatsuki S. The New Macromolecular Femtosecond Crystallography (MFX) Instrument at LCLS.Synchrotron Radiat News. 2016;29(1):23-28. doi: 10.1080/08940886.2016.1124681. Epub 2016 Feb 1. PubMed PMID: 28736484; PubMed Central PMCID: PMC5519296.
  22. Wakatsuki S. Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers . In: Synchrotron Light Sources and Free-Electron Lasers. Jaeschke E, Khan S, Schneider JR, Hastings JB, editors. Switzerland: Springer International Publishing; 2016. p.1-39.
  23. Martin JL, Read RJ, Wakatsuki S. Expanding beyond biological crystallography. Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):1. doi: 10.1107/S2059798315023761. Epub 2016 Jan 1. PubMed PMID: 26894528.
  24. Aquila A, Barty A, Bostedt C, Boutet S, Carini G, dePonte D, Drell P, Doniach S, Downing KH, Earnest T, Elmlund H, Elser V, Gühr M, Hajdu J, Hastings J, Hau-Riege SP, Huang Z, Lattman EE, Maia FR, Marchesini S, Ourmazd A, Pellegrini C, Santra R, Schlichting I, Schroer C, Spence JC, Vartanyants IA, Wakatsuki S, Weis WI, Williams GJ. The linac coherent light source single particle imaging road map. Struct Dyn. 2015 Jul;2(4):041701. doi: 10.1063/1.4918726. eCollection 2015 Jul. PubMed PMID: 26798801; PubMed Central PMCID: PMC4711616.
  25. Sakamoto H, Egashira S, Saito N, Kirisako T, Miller S, Sasaki Y, Matsumoto T, Shimonishi M, Komatsu T, Terai T, Ueno T, Hanaoka K, Kojima H, Okabe T, Wakatsuki S, Iwai K, Nagano T. Gliotoxin suppresses NF-κB activation by selectively inhibiting linear ubiquitin chain assembly complex (LUBAC). ACS Chem Biol. 2015 Mar 20;10(3):675-81. doi: 10.1021/cb500653y. Epub 2014 Dec 17. PubMed PMID: 25494483.
  26. Marinelli A, Ratner D, Lutman AA, Turner J, Welch J, Decker FJ, Loos H, Behrens C, Gilevich S, Miahnahri AA, Vetter S, Maxwell TJ, Ding Y, Coffee R, Wakatsuki S, Huang Z. High-intensity double-pulse X-ray free-electron laser. Nat Commun.2015 Mar 6;6:6369. doi: 10.1038/ncomms7369. PubMed PMID: 25744344; PubMed Central PMCID: PMC4366525.
  27. Takahashi T, Kojima K, Zhang W, Sasaki K, Ito M, Suzuki H, Kawasaki M, Wakatsuki S, Takahara T, Shibata H, Maki M.Structural analysis of the complex between penta-EF-hand ALG-2 protein and Sec31A peptide reveals a novel target recognition mechanism of ALG-2. Int J Mol Sci. 2015 Feb 6;16(2):3677-99. doi: 10.3390/ijms16023677. PubMed PMID: 25667979; PubMed Central PMCID: PMC4346919.
  28. McEwan DG, Popovic D, Gubas A, Terawaki S, Suzuki H, Stadel D, Coxon FP, Miranda de Stegmann D, Bhogaraju S, Maddi K, Kirchof A, Gatti E, Helfrich MH, Wakatsuki S, Behrends C, Pierre P, Dikic I. PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins. Mol Cell. 2015 Jan 8;57(1):39-54. doi: 10.1016/j.molcel.2014.11.006. Epub 2014 Dec 11. PubMed PMID: 25498145.
  29. Lutman AA, Decker FJ, Arthur J, Chollet M, Feng Y, Hastings J, Huang Z, Lemke H, Nuhn HD, Marinelli A, Turner JL, Wakatsuki S, Welch J, Zhu D. Demonstration of single-crystal self-seeded two-color x-ray free-electron lasers. Phys Rev Lett. 2014 Dec 19;113(25):254801. doi: 10.1103/PhysRevLett.113.254801. Epub 2014 Dec 18. PubMed PMID: 25554887.
  30. Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17122-7. doi: 10.1073/pnas.1418733111. Epub 2014 Oct 31. PubMed PMID: 25362050; PubMed Central PMCID: PMC4260607.
  31. Suzuki T, Makyio H, Ando H, Komura N, Menjo M, Yamada Y, Imamura A, Ishida H, Wakatsuki S, Kato R, Kiso M. Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing. Bioorg Med Chem. 2014 Apr 1;22(7):2090-101. doi: 10.1016/j.bmc.2014.02.023. Epub 2014 Feb 25. PubMed PMID: 24631362.
  32. Fujita H, Rahighi S, Akita M, Kato R, Sasaki Y, Wakatsuki S, Iwai K. Mechanism underlying IκB kinase activation mediated by the linear ubiquitin chain assembly complex. Mol Cell Biol. 2014 Apr;34(7):1322-35. doi: 10.1128/MCB.01538-13. Epub 2014 Jan 27. PubMed PMID: 24469399; PubMed Central PMCID: PMC3993567.
  33. Buchini S, Gallat FX, Greig IR, Kim JH, Wakatsuki S, Chavas LM, Withers SG. Tuning mechanism-based inactivators of neuraminidases: mechanistic and structural insights. Angew Chem Int Ed Engl. 2014 Mar 24;53(13):3382-6. doi: 10.1002/anie.201309675. Epub 2014 Mar 3. PubMed PMID: 24591206.
  34. Suzuki H, Tabata K, Morita E, Kawasaki M, Kato R, Dobson RC, Yoshimori T, Wakatsuki S. Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. Structure. 2014 Jan 7;22(1):47-58. doi: 10.1016/j.str.2013.09.023. Epub 2013 Nov 27. PubMed PMID: 24290141.
  35. Yamada Y, Chavas LM, Igarashi N, Hiraki M, Wakatsuki S, Matsugaki N. Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A. J Synchrotron Radiat. 2013 Nov;20(Pt 6):938-42. doi: 10.1107/S0909049513022875. Epub 2013 Oct 8. PubMed PMID: 24121344; PubMed Central PMCID: PMC3795560.
  36. Hiraki M, Yamada Y, Chavas LM, Wakatsuki S, Matsugaki N. Improvement of an automated protein crystal exchange system PAM for high-throughput data collection. J Synchrotron Radiat. 2013 Nov;20(Pt 6):890-3. doi: 10.1107/S0909049513021067. Epub 2013 Oct 1. PubMed PMID: 24121334; PubMed Central PMCID: PMC3795550.
  37. Rogov VV, Suzuki H, Fiskin E, Wild P, Kniss A, Rozenknop A, Kato R, Kawasaki M, McEwan DG, Löhr F, Güntert P, Dikic I, Wakatsuki S, Dötsch V. Structural basis for phosphorylation-triggered autophagic clearance of Salmonella. Biochem J.2013 Sep 15;454(3):459-66. doi: 10.1042/BJ20121907. PubMed PMID: 23805866.
  38. Liao JH, Ihara K, Kuo CI, Huang KF, Wakatsuki S, Wu SH, Chang CI. Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors. Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1395-402. doi: 10.1107/S0907444913008214. Epub 2013 Jul 13. PubMed PMID: 23897463.
  39. Makyio H, Takeuchi T, Tamura M, Nishiyama K, Takahashi H, Natsugari H, Arata Y, Kasai K, Yamada Y, Wakatsuki S, Kato R.Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6.Glycobiology. 2013 Jul;23(7):797-805. doi: 10.1093/glycob/cwt017. Epub 2013 Mar 12. PubMed PMID: 23481096.
  40. Uejima T, Ihara K, Sunada M, Kawasaki M, Ueda T, Kato R, Nakano A, Wakatsuki S. Direct metal recognition by guanine nucleotide-exchange factor in the initial step of the exchange reaction. Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):345-51. doi: 10.1107/S0907444912047294. Epub 2013 Feb 16. PubMed PMID: 23519409.
  41. Hiraki M, Yamada Y, Chavas L, Matsugaki N, Igarashi N, Wakatsuki S. Current status and future prospects of an automated sample exchange system PAM for protein crystallography. J. Phys.: Conf. Ser.. 2013; 425.
  42. Yamada Y, Matsugaki N, Chavas L, Hiraki M, Igarashi N, Wakatsuki S. Data Management System at the Photon Factory Macromolecular Crystallography Beamline. J. Phys.: Conf. Ser.. 2013; 425.
  43. Chavas L, Matsugaki N, Yamada Y, Hiraki M, Igarashi N, Suzuki M, Wakatsuki S. 10 years of protein crystallography at AR-NW12A beamline. J. Phys.: Conf. Ser.. 2013; 425.
  44. Ihara K, Fujiwara N, Yamaguchi Y, Torigoe H, Wakatsuki S, Taniguchi N, Suzuki K. Structural switching of Cu,Zn-superoxide dismutases at loop VI: insights from the crystal structure of 2-mercaptoethanol-modified enzyme. Biosci Rep. 2012 Dec;32(6):539-48. doi: 10.1042/BSR20120029. PubMed PMID: 22804629; PubMed Central PMCID: PMC3497728.
  45. Ascone I, Asakura K, George GN, Wakatsuki S. International Workshop on Improving Data Quality and Quantity for XAFS Experiments (Q2XAFS 2011). J Synchrotron Radiat. 2012 Nov;19(Pt 6):849-50. doi: 10.1107/S0909049512043506. Epub 2012 Oct 23. PubMed PMID: 23093741.
  46. Hasnain SS, Wakatsuki S. Frontiers and challenges of biophysical methods: from computational biology to X-ray free electron laser. Curr Opin Struct Biol. 2012 Oct;22(5):591-3. doi: 10.1016/j.sbi.2012.09.005. Epub 2012 Oct 1. PubMed PMID: 23036819.
  47. Nakamura K, Man Z, Xie Y, Hanai A, Makyio H, Kawasaki M, Kato R, Shin HW, Nakayama K, Wakatsuki S. Structural basis for membrane binding specificity of the Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin-2 determined by Arl1 GTPase. J Biol Chem. 2012 Jul 20;287(30):25478-89. doi: 10.1074/jbc.M112.365783. Epub 2012 Jun 7. PubMed PMID: 22679020; PubMed Central PMCID: PMC3408144.
  48. Makyio H, Ohgi M, Takei T, Takahashi S, Takatsu H, Katoh Y, Hanai A, Ueda T, Kanaho Y, Xie Y, Shin HW, Kamikubo H, Kataoka M, Kawasaki M, Kato R, Wakatsuki S, Nakayama K. Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis. EMBO J. 2012 May 30;31(11):2590-603. doi: 10.1038/emboj.2012.89. Epub 2012 Apr 20. PubMed PMID: 22522702; PubMed Central PMCID: PMC3365427.
  49. Ru H, Zhao L, Ding W, Jiao L, Shaw N, Liang W, Zhang L, Hung LW, Matsugaki N, Wakatsuki S, Liu ZJ. S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS. Acta Crystallogr D Biol Crystallogr. 2012 May;68(Pt 5):521-30. doi: 10.1107/S0907444912004490. Epub 2012 Apr 17. PubMed PMID: 22525750; PubMed Central PMCID: PMC3335285.
  50. Chavas LM, Matsugaki N, Yamada Y, Hiraki M, Igarashi N, Suzuki M, Wakatsuki S. Beamline AR-NW12A: high-throughput beamline for macromolecular crystallography at the Photon Factory. J Synchrotron Radiat. 2012 May;19(Pt 3):450-4. doi: 10.1107/S0909049512009727. Epub 2012 Mar 31. PubMed PMID: 22514184.
  51. Okazaki S, Kato R, Uchida Y, Taguchi T, Arai H, Wakatsuki S. Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2. Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):117-23. doi: 10.1107/S0907444911051626. Epub 2012 Jan 13. PubMed PMID: 22281740.
  52.  Fujihashi M, Hiraki M, Ueno G, Baba S, Murakami H, et al. Crystal-sample pins and a storage cassette system compatible with the protein crystallography beamlines at both the Photon Factory and SPring-8. Journal of applied crystallography. 2012; 45:1156-61.
  53. Uchida Y, Hasegawa J, Chinnapen D, Inoue T, Okazaki S, et al. Intracellular phosphatidylserine is essential for retrograde membrane traffic through endosomes. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15846-51. PubMed PMID: 21911378; PubMed Central PMCID: PMC3179068.
  54.  Oveisi H, Rahighi S, Jiang X, Agawa Y, Beitollahi A, et al. Improved Inactivation Effect of Bacteria: Fabrication of Mesoporous Anatase Films with Fine Ag Nanoparticles Prepared by Coaxial Vacuum Arc Deposition. Chemistry letters. 2011; 40(4):420-422.
  55.  Ikeda F, Rahighi S, Wakatsuki S, Dikic I. Selective binding of linear ubiquitin chains to NEMO in NF-kappaB activation. Adv Exp Med Biol. 2011;691:107-14. PubMed PMID: 21153314.
  56. Chavas LM, Yamada Y, Hiraki M, Igarashi N, Matsugaki N, et al. UV LED lighting for automated crystal centring. J Synchrotron Radiat. 2011 Jan;18(1):11-5. PubMed PMID: 21169682; PubMed Central PMCID: PMC3004245.
  57.  Uejima T, Ihara K, Goh T, Ito E, Sunada M, et al. GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5·Vps9 system. J Biol Chem. 2010 Nov 19;285(47):36689-97. PubMed PMID: 20833725; PubMed Central PMCID: PMC2978598.
  58. Hasnain SS, Wakatsuki S. Advances in biophysical methods: characterisation and visualization of molecules, cells and organism. Curr Opin Struct Biol. 2010 Oct;20(5):584-6. PubMed PMID: 20884198
  59.  Suzuki N, Hiraki M, Yamada Y, Matsugaki N, Igarashi N, et al. Crystallization of small proteins assisted by green fluorescent protein. Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1059-66. PubMed PMID: 20944239.
  60.  Satoh T, Sakata E, Yamamoto S, Yamaguchi Y, Sumiyoshi A, et al. Crystal structure of cyclic Lys48-linked tetraubiquitin. Biochem Biophys Res Commun. 2010 Sep 24;400(3):329-33. PubMed PMID: 20728431.
  61. Oveisi H, Rahighi S, Jiang X, Nemoto Y, Beitollahi A, et al. Unusual antibacterial property of mesoporous titania films: drastic improvement by controlling surface area and crystallinity. Chem Asian J. 2010 Sep 3;5(9):1978-83. PubMed PMID: 20665652.
  62. Inuzuka T, Suzuki H, Kawasaki M, Shibata H, Wakatsuki S, et al. Molecular basis for defect in Alix-binding by alternatively spliced isoform of ALG-2 (ALG-2DeltaGF122) and structural roles of F122 in target recognition. BMC Struct Biol. 2010 Aug 6;10:25. PubMed PMID: 20691033; PubMed Central PMCID: PMC2927601.
  63. Wakatsuki S, Yamada Y, Chavas LM, Igarashi N, Kawasaki M, et al. [Advancement of synchrotron radiation protein crystallography in the targeted protein research program: beamline developments at the photon factory]. Yakugaku Zasshi. 2010 May;130(5):631-40. PubMed PMID: 20460857.
  64. Chavas LM, Kato R, Suzuki N, von Itzstein M, Mann MC, et al. Complexity in influenza virus targeted drug design: interaction with human sialidases. J Med Chem. 2010 Apr 8;53(7):2998-3002. PubMed PMID: 20222714.
  65. Nishio M, Kamiya Y, Mizushima T, Wakatsuki S, Sasakawa H, et al. Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency. Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4034-9. PubMed PMID: 20142513; PubMed Central PMCID: PMC2840101.
  66. Kudo N, Kumagai K, Matsubara R, Kobayashi S, Hanada K, et al. Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer. J Mol Biol. 2010 Feb 19;396(2):245-51. PubMed PMID: 20036255.
  67. Sakata E, Satoh T, Yamamoto S, Yamaguchi Y, Yagi-Utsumi M, et al. Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates. Structure. 2010 Jan 13;18(1):138-47. PubMed PMID: 20152160.
  68. Hiraki M, Watanabe S, Chavas L, Yamada Y, Matsugaki N, et al. Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes. AIP conference proceedings. 2010;
  69. Yamada Y, Hiraki M, Sasajima K, Matsugaki N, Igarashi N, et al. AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory. AIP conference proceedings. 2010;
  70. Dikic I, Wakatsuki S, Walters KJ. Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol. 2009 Oct;10(10):659-71. PubMed PMID: 19773779.
  71. Wakatsuki S, Yamamoto M, Tanaka I, Miki K, Nakagawa A. [Development of beam line X-ray crystallography targeting multiprotein complexes: Overview]. Tanpakushitsu Kakusan Koso. 2009 Sep;54(12 Suppl):1476. PubMed PMID: 21089573.
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  73. Rahighi S, Ikeda F, Kawasaki M, Akutsu M, Suzuki N, et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell. 2009 Mar 20;136(6):1098-109. PubMed PMID: 19303852.
  74. Nagae M, Nishi N, Murata T, Usui T, Nakamura T, et al. Structural analysis of the recognition mechanism of poly-N- acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology. 2009 Feb;19(2):112-7. PubMed PMID: 18977853.
  75. Suzuki H, Kawasaki M, Inuzuka T, Okumura M, Kakiuchi T, et al. The mechanism of Ca2+-dependent recognition of Alix by ALG-2: insights from X-ray crystal structures. Biochem Soc Trans. 2009 Feb;37(Pt 1):190-4. PubMed PMID: 19143629.
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  77. Kawasaki M, Wakatsuki S. [Structural biology of vesicular transport]. Tanpakushitsu Kakusan Koso. 2008 Dec;53(16 Suppl):2071-7. PubMed PMID: 21038587.
  78. Wada J, Honda Y, Nagae M, Kato R, Wakatsuki S, et al. 1,2-alpha-l-Fucosynthase: a glycosynthase derived from an inverting alpha-glycosidase with an unusual reaction mechanism. FEBS Lett. 2008 Nov 12;582(27):3739-43. PubMed PMID: 18845150.
  79. Suzuki H, Kawasaki M, Kakiuchi T, Shibata H, Wakatsuki S, et al. Crystallization and X-ray diffraction analysis of N- terminally truncated human ALG-2. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Nov 1;64(Pt 11):974-7. PubMed PMID: 18997320; PubMed Central PMCID: PMC2581688.
  80. Chavas LM, Ihara K, Kawasaki M, Torii S, Uejima T, et al. Elucidation of Rab27 recruitment by its effectors: structure of Rab27a bound to Exophilin4/Slp2-a. Structure. 2008 Oct 8;16(10):1468-77. PubMed PMID: 18940603.
  81. Suzuki H, Kawasaki M, Inuzuka T, Okumura M, Kakiuchi T, et al. Structural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism. Structure. 2008 Oct 8;16(10):1562-73. PubMed PMID: 18940611.
  82. Hasnain SS, Wakatsuki S. Biophysical methods: structure, function and dynamics studies of macromolecular assemblies using electrons, lasers, neutrons and X-rays. Curr Opin Struct Biol. 2008 Oct;18(5):577-80. PubMed PMID: 18801436.
  83. Kato R, Nagae M, Wakatsuki S. [Molecular basis of sugar-protein interaction]. Tanpakushitsu Kakusan Koso. 2008 Sep;53(12 Suppl):1670-5. PubMed PMID: 21089386.
  84. Chavas LM, Ihara K, Kawasaki M, Kato R, Izumi T, et al. Purification, crystallization and preliminary X-ray crystallographic analysis of Rab27a GTPase in complex with exophilin4/Slp2-a effector. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1;64(Pt 7):599-601. PubMed PMID: 18607085; PubMed Central PMCID: PMC2443971.
  85. Murakami K, Stewart M, Nozawa K, Tomii K, Kudou N, et al. Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T. Proc Natl Acad Sci U S A. 2008 May 20;105(20):7200-5. PubMed PMID: 18483193; PubMed Central PMCID: PMC2438227.
  86. Yousef MS, Kamikubo H, Kataoka M, Kato R, Wakatsuki S. Miranda cargo-binding domain forms an elongated coiled- coil homodimer in solution: implications for asymmetric cell division in Drosophila. Protein Sci. 2008 May;17(5):908- 17. PubMed PMID: 18369190; PubMed Central PMCID: PMC2327284.
  87. Miyoshi T, Igarashi N, Matsugaki N, Yamada Y, Hirano K, et al. Development of an X-ray HARP-FEA detector system for high-throughput protein crystallography. J Synchrotron Radiat. 2008 May;15(Pt 3):281-4. PubMed PMID: 18421159; PubMed Central PMCID: PMC2394816.
  88. Igarashi N, Ikuta K, Miyoshi T, Matsugaki N, Yamada Y, et al. X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory. J Synchrotron Radiat. 2008 May;15(Pt 3):292-5. PubMed PMID: 18421162; PubMed Central PMCID: PMC2394782.
  89. Yamada Y, Phonda N, Matsugaki N, Igarashi N, Hiraki M, et al. Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines. J Synchrotron Radiat. 2008 May;15(Pt 3):296-9. PubMed PMID: 18421163; PubMed Central PMCID: PMC2394808.
  90. Hiraki M, Watanabe S, Phonda N, Yamada Y, Matsugaki N, et al. High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines. J Synchrotron Radiat. 2008 May;15(Pt 3):300-3. PubMed PMID: 18421164; PubMed Central PMCID: PMC2394784.
  91. Wakatsuki S, Kato R, Kawasaki M, Igarashi N, Masahiko H. [Structural and functional biology for post translational modification and transport in eukaryotes]. Tanpakushitsu Kakusan Koso. 2008 Apr;53(5):628-31. PubMed PMID: 18409553.
  92. Kudo N, Kumagai K, Tomishige N, Yamaji T, Wakatsuki S, et al. Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):488-93. PubMed PMID: 18184806; PubMed Central PMCID: PMC2206563.
  93. Nagae M, Nishi N, Nakamura-Tsuruta S, Hirabayashi J, Wakatsuki S, et al. Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue. J Mol Biol. 2008 Jan 4;375(1):119-35. PubMed PMID: 18005988.
  94. Das M, Kobayashi M, Yamada Y, Sreeramulu S, Ramakrishnan C, et al. Design of disulfide-linked thioredoxin dimers and multimers through analysis of crystal contacts. J Mol Biol. 2007 Oct 5;372(5):1278-92. PubMed PMID: 17727880.
  95. Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, et al. Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36. J Biol Chem. 2007 Sep 21;282(38):28246-55. PubMed PMID: 17652092.
  96. Inoue M, Shiba T, Ihara K, Yamada Y, Hirano S, et al. Molecular basis for autoregulatory interaction between GAE domain and hinge region of GGA1. Traffic. 2007 Jul;8(7):904-13. PubMed PMID: 17506864.
  97. Chavas LM, Torii S, Kamikubo H, Kawasaki M, Ihara K, et al. Structure of the small GTPase Rab27b shows an unexpected swapped dimer. Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):769-79. PubMed PMID: 17582168.
  98. Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, et al. Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. J Biol Chem. 2007 Jun 22;282(25):18497- 509. PubMed PMID: 17459873.
  99. Hirano K, Miyoshi T, Igarashi N, Takeda T, Wu J, et al. X-ray phase imaging of biological soft tissue using a direct- sensing x-ray HARP tube camera. Phys Med Biol. 2007 May 7;52(9):2545-52. PubMed PMID: 17440251.
  100. Igarashi N, Matsugaki N, Yamada Y, Hiraki M, Koyama A, et al. BL-17A, A New Protein Micro-Crystallography Beam Line of the Photon Factory. AIP conference proceedings. 2007; 879:812-815.
  101. Gaponov YA, Matsugaki N, Honda N, Sasajima K, Igarashi N, et al. Development of Control Applications for High- Throughput Protein Crystallography Experiments. AIP conference proceedings. 2007; 879:1932-1935.
  102. Hiraki M, Watanabe S, Yamada Y, Matsugaki N, Igarashi N, et al. Automated Sample Exchange Robots for the Structural Biology Beam Lines at the Photon Factory. AIP conference proceedings. 2007; 879:1924-1927.
  103. Matsugaki N, Yamada Y, Igarashi N, Wakatsuki S. Design and Construction of the High-speed Network Connecting All the Protein Crystallography Beam Lines at the Photon Factory. AIP conference proceedings. 2007; 879:1936-1939.
  104. Nagae M, Nishi N, Murata T, Usui T, Nakamura T, et al. Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition. J Biol Chem. 2006 Nov 24;281(47):35884-93. PubMed PMID: 16990264.
  105. Yogosawa S, Kawasaki M, Wakatsuki S, Kominami E, Shiba Y, et al. Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability. Biochem Biophys Res Commun. 2006 Nov 10;350(1):82-90. PubMed PMID: 16996030.
  106. Shiba T, Kakuda S, Ishiguro M, Morita I, Oka S, et al. Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope. Proteins. 2006 Nov 1;65(2):499-508. PubMed PMID: 16897771.
  107. Hirano S, Suzuki N, Slagsvold T, Kawasaki M, Trambaiolo D, et al. Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain. Nat Struct Mol Biol. 2006 Nov;13(11):1031-2. PubMed PMID: 17057714.
  108. Shiba T, Koga H, Shin HW, Kawasaki M, Kato R, et al. Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1. Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15416-21. PubMed PMID: 17030804; PubMed Central PMCID: PMC1622838.
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  110. Kubota T, Shiba T, Sugioka S, Furukawa S, Sawaki H, et al. Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10). J Mol Biol. 2006 Jun 9;359(3):708-27. PubMed PMID: 16650853.
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  112. Hirano S, Kawasaki M, Ura H, Kato R, Raiborg C, et al. Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat Struct Mol Biol. 2006 Mar;13(3):272-7. PubMed PMID: 16462748.
  113. Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, et al. Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. PubMed PMID: 16273103; NIHMSID: NIHMS5617; PubMed Central PMCID: PMC1790907.
  114. Kawasaki M, Nakayama K, Wakatsuki S. Membrane recruitment of effector proteins by Arf and Rab GTPases. Curr Opin Struct Biol. 2005 Dec;15(6):681-9. PubMed PMID: 16289847.
  115. Nakayama K, Wakatsuki S. [GGAs: structure and function of a novel family of clathrin adaptors involved in membrane trafficking between the TGN and endosomes]. Seikagaku. 2005 Nov;77(11):1367-81. PubMed PMID: 16370355.
  116. Akutsu M, Kawasaki M, Katoh Y, Shiba T, Yamaguchi Y, et al. Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. FEBS Lett. 2005 Oct 10;579(24):5385-91. PubMed PMID: 16199040.
  117. Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, et al. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell. 2005 Sep 2;19(5):655-66. PubMed PMID: 16167380
  118. Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, et al. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell. 2005 Aug 12;122(3):351-63. PubMed PMID: 16096056.
  119. Chang CI, Ihara K, Chelliah Y, Mengin-Lecreulx D, Wakatsuki S, et al. Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition. Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10279-84. PubMed PMID: 16006509; PubMed Central PMCID: PMC1174924.
  120. Kawasaki M, Shiba T, Shiba Y, Yamaguchi Y, Matsugaki N, et al. Molecular mechanism of ubiquitin recognition by GGA3 GAT domain. Genes Cells. 2005 Jul;10(7):639-54. PubMed PMID: 15966896.
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  122. Yamada Y, Inoue M, Shiba T, Kawasaki M, Kato R, et al. Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic. Acta Crystallogr D Biol Crystallogr. 2005 Jun;61(Pt 6):731-6. PubMed PMID: 15930630.
  123. Slagsvold T, Aasland R, Hirano S, Bache KG, Raiborg C, et al. Eap45 in mammalian ESCRT-II binds ubiquitin via a phosphoinositide-interacting GLUE domain. J Biol Chem. 2005 May 20;280(20):19600-6. PubMed PMID: 15755741.
  124. Shiba T, Kakuda S, Oka S, Ishiguro M, Kawasaki T, et al. [Molecular mechanisms in acceptor substrate recognition of a human glucuronyltransferase, GlcAT-P, an enzyme critical in the biosynthesis of the carbohydrate epitope HNK-1]. Seikagaku. 2005 Feb;77(2):153-8. PubMed PMID: 15786744.
  125. Chavas LM, Tringali C, Fusi P, Venerando B, Tettamanti G, et al. Crystal structure of the human cytosolic sialidase Neu2 Evidence for the dynamic nature of substrate recognition. J Biol Chem. 2005 Jan 7;280(1):469-75. PubMed PMID: 15501818.
  126. Shiba T, Kakuda S, Oka S, Ishiguro M, Kawasaki T, et al. Unique sugar substrate recognition mechanism of a GlcAT-P, a glycosyltransferase responsible for biosynthesis of HNK-1 oligosaccharide. Seikagaku. The Journal of Japanese Biochemical Society. 2005; 77(2):153-158.
  127. Wakatsuki S. Synchrotron Protein X-ray crystallography in the era of structural proteomics. Journal of the Crystallographic Society of Japan. 2005; 47(6).
  128. Wakatsuki S, Hiraki M, Gaponov Y, Suzuki M, Igarashi N, et al. [The Photon Factory, a synchrotron radiation facility]. Tanpakushitsu Kakusan Koso. 2004 Aug;49(11 Suppl):1816-20. PubMed PMID: 15377022.
  129. Shiba T, Kametaka S, Kawasaki M, Shibata M, Waguri S, et al. Insights into the phosphoregulation of beta-secretase sorting signal by the VHS domain of GGA1. Traffic. 2004 Jun;5(6):437-48. PubMed PMID: 15117318.
  130. Kakuda S, Shiba T, Ishiguro M, Tagawa H, Oka S, et al. Structural basis for acceptor substrate recognition of a human glucuronyltransferase, GlcAT-P, an enzyme critical in the biosynthesis of the carbohydrate epitope HNK-1. J Biol Chem. 2004 May 21;279(21):22693-703. PubMed PMID: 14993226.
  131. Gaponov YA, Igarashi N, Hiraki M, Sasajima K, Matsugaki N, et al. Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments. AIP conference proceedings. 2004 May 12; 705:1213-1216.
  132. Matsugaki N, Igarashi N, Suzuki M, Hiraki M, Wakatsuki S. Structural biology using PF-AR NW12 beam line of Photon Factory. Journal of the Japanese Society for Synchrotron Radiation Research. 2004 May; 17(3):144-152.
  133. Shiba Y, Katoh Y, Shiba T, Yoshino K, Takatsu H, et al. GAT (GGA and Tom1) domain responsible for ubiquitin binding and ubiquitination. J Biol Chem. 2004 Feb 20;279(8):7105-11. PubMed PMID: 14660606.
  134. Suzuki M, Igarashi N, Matsugaki N, Wakatsuki S. 5. The Protein Crystallography Beamlines at Photon Factory. Genomics and Proteomics, Toward the Analysis and Application of Biological Information. 2004; :612-617.
  135. Wakatsuki S, Hiraki M, Gaponov Y, Matsugaki N, Igarashi N, et al. 6. Automation in X-ray diffraction experiment of protein crystal. Genomics and Proteomics, Toward the Analysis and Application of Biological Information. 2004; :618- 622.
  136. Gaponov Y, Igarashi N, Hiraki M, Sasajima K, Matsugaki N, et al. Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments. J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):17-20. PubMed PMID: 14646123.
  137. Nakayama K, Wakatsuki S. The structure and function of GGAs, the traffic controllers at the TGN sorting crossroads. Cell Struct Funct. 2003 Oct;28(5):431-42. PubMed PMID: 14745135.
  138. Shiba T, Kawasaki M, Takatsu H, Nogi T, Matsugaki N, et al. Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport. Nat Struct Biol. 2003 May;10(5):386-93. PubMed PMID: 12679809.
  139. Wakatsuki S. Structural Biology of Protein Transport. Journal of the Crystallographic Society of Japan. 2003 March; 45:26-31.
  140. Wakatsuki S. Impact of insertion devices on macromolecular crystallography. Undulators, Wigglers and Their Applications by Taylor & Francis Inc.. 2003; :293-321.
  141. Wakatsuki S. Structural Genomics of intracellular transport and post-translational transport. Science & Technology Journal. 2002 August; 11(8):26-27.
  142. Nogi T, Shiba Y, Kawasaki M, Shiba T, Matsugaki N, et al. Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain. Nat Struct Biol. 2002 Jul;9(7):527-31. PubMed PMID: 12042876.
  143. Shiba T, Takatsu H, Nogi T, Matsugaki N, Kawasaki M, et al. Structural basis for recognition of acidic-cluster dileucine sequence by GGA1. Nature. 2002 Feb 21;415(6874):937-41. PubMed PMID: 11859376.
  144. Oshima T, Nishimura Y, Kuramitsu S, Yokoyama S, Wakatsuki S, et al. What are the goals of structural proteomics? Round table discussion. Tanpakushitsu-Kakusan-Koso. 2002; 47(8):865-881.
  145. Dumon-Seignovert L, Matsumuto T, Monaco-Malbet S, Tomizaki T, Sato M, et al. Purification, crystallization and preliminary X-ray diffraction analysis of the yeast Sec12Deltap protein, a guanine nucleotide-exchange factor involved in vesicle transport. Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):893-5. PubMed PMID: 11375521.
  146. Tsukihara T, Miki K, Tanokura M, Wakatsuki S, Tanaka I. The way forward to the nation wide structural genomics projects. Journal of the Crystallographic Society of Japan. 2001; 43(3):280-282.
  147. Binda C, Bossi RT, Wakatsuki S, Arzt S, Coda A, et al. Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase. Structure. 2000 Dec 15;8(12):1299-308. PubMed PMID: 11188694.
  148. Yao M, Ose T, Sugimoto H, Horiuchi A, Nakagawa A, et al. Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus. J Biol Chem. 2000 Nov 3;275(44):34557-65. PubMed PMID: 10938279.
  149. Wakatsuki S, Earnest T. The Impact of Synchrotron Radiation in Protein Crystallography. Synchrotron radiation news. 2000; 13(5):4-8.
  150. Yamashita A, Kato H, Wakatsuki S, Tomizaki T, Nakatsu T, et al. Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 19 A resolution: implication for stereospecific substrate binding and catalysis. Biochemistry. 1999 Jun 15;38(24):7630-7. PubMed PMID: 10387002.
  151. Tanaka I, Nakagawa A, Hosaka H, Wakatsuki S, Mueller F, et al. Matching the crystallographic structure of ribosomal protein S7 to a three-dimensional model of the 16S ribosomal RNA. RNA. 1998 May;4(5):542-50. PubMed PMID: 9582096; PubMed Central PMCID: PMC1369638.
  152. Wakatsuki S, Belrhali H, Mitchell EP, Burmeister WP, McSweeney SM, et al. ID14 'Quadriga', a Beamline for Protein Crystallography at the ESRF. J Synchrotron Radiat. 1998 May 1;5(Pt 3):215-21. PubMed PMID: 15263481.
  153. Vassylyev DG, Takeda S, Wakatsuki S, Maeda K, Maéda Y. Crystal structure of troponin C in complex with troponin I fragment at 23-A resolution. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4847-52. PubMed PMID: 9560191; PubMed Central PMCID: PMC20176.
  154. Vassylyev DG, Takeda S, Wakatsuki S, Maeda K, Maeda Y. Drastic rearrangement of Troponin C domains induced by the binding of Troponin I fragment. Proceedings of the National Academy of Sciences of the United States of America. 1998; 95:4847-4852.
  155. Wakatsuki S, Belrhali H, Mitchell EP, Burmeister WP, McSweeney SM, et al. ID14 Quadriga, a beamline for protein crystallography at the ESRF. Synchrotron radiation. 1998; 2(2):97-106.
  156. Burmeister WP, Bourgeois D, Kahn R, Belrhali H, Mitchell EP, et al. Diamonds, a multilayer and a sagitally focusing crystal as optical dlements on the ID14/Quadriga-3 beamline at ESRF. Proceedings of SPIE. 1998; 3448:188-196.
  157. Vassylyev DG, Takeda S, Wakatsuki S, Maeda K, Maéda Y. The crystal structure of troponin C in complex with N- terminal fragment of troponin I The mechanism of how the inhibitory action of troponin I is released by Ca(2+)-binding to troponin C. Adv Exp Med Biol. 1998;453:157-67. PubMed PMID: 9889826.
  158. Hosaka H, Nakagawa A, Tanaka I, Harada N, Sano K, et al. Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor. Structure. 1997 Sep 15;5(9):1199-208. PubMed PMID: 9331423.
  159. Saijo Y, Takeda S, Scherer A, Kobayashi T, Maéda Y, et al. Production, crystallization, and preliminary X-ray analysis of rabit skeletal muscle troponin complex consisting of troponin C and fragment (1-47) of troponin I. Protein Sci. 1997 Apr;6(4):916-8. PubMed PMID: 9098903; PubMed Central PMCID: PMC2144766.
  160. Clifton IJ, Duke EM, Wakatsuki S, Ren Z. [Evaluation of Laue diffraction patterns. Methods Enzymol. 1997;277:448-67. PubMed PMID: 18488319.
  161. Miegel A, Sano KI, Yamamoto K, Maeda K, Maéda Y, et al. Production and crystallization of lobster muscle tropomyosin expressed in Sf9 cells. FEBS Lett. 1996 Sep 30;394(2):201-5. PubMed PMID: 8843164.
  162. Brown NR, Noble ME, Endicott JA, Garman EF, Wakatsuki S, et al. The crystal structure of cyclin A. Structure. 1995 Nov 15;3(11):1235-47. PubMed PMID: 8591034.
  163. Deschamps P, Engström P, Fiedler S, Riekel C, Wakatsuki S, et al. A Double Multilayer Monochromator at an ESRF Undulator for Microbeam Experiments. J Synchrotron Radiat. 1995 May 1;2(Pt 3):124-31. PubMed PMID: 16714803.
  164. Duke EM, Wakatsuki S, Hadfield A, Johnson LN. Laue and monochromatic diffraction studies on catalysis in phosphorylase b crystals. Protein Sci. 1994 Aug;3(8):1178-96. PubMed PMID: 7987213; PubMed Central PMCID: PMC2142917.
  165. Wakatsuki S, Kimura Y, Stoeckenius W, Gillis N, Eliezer D, et al. Blue form of bacteriorhodopsin and its order-disorder transition during dehydration. Biochim Biophys Acta. 1994 Apr 28;1185(2):160-6. PubMed PMID: 8167134.
  166. Clifton IJ, Wakatsuki S, Hajdu J. New sources, newer detectors, old methods— the future of protein crystallography at synchrotrons. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms. 1994 April 01; 87(1-4):76-81.
  167. Fülöp V, Phizackerley RP, Soltis SM, Clifton IJ, Wakatsuki S, et al. Laue diffraction study on the structure of cytochrome c peroxidase compound I. Structure. 1994 Mar 15;2(3):201-8. PubMed PMID: 8069633.
  168. Wakatsuki S. LEAP for time-resolved protein crystallography. CCP4 study weekend, Data Collection and Analysis. 1993;
  169. Fulop V, Phizackerley PR, Soltis MS, Clifton IJ, Wakatsuki S, et al. Dynamic Crystallographic Study on Yeast Cytochrome c peroxidase. Plant Peroxides: Biochemistry and Physiology. 1993; :21-25.
  170. Wakatsuki S, Miyake-Lye R, Hubbard S, Spann U, Gillis N, et al. Small-angle X-ray scattering/diffraction camera system at Stanford Synchrotron Radiation Laboratory. Review of Scientific. Instruments. 1992; 63(2):1736-1740.
  171. Duke EH, Hadfield A, Walters S, Wakatsuki S, Bryan RK, et al. Time-resolved diffraction studies on glycogen phosphorylase b. Philosophical Transactions of the Royal Society of London. 1992; :245-261.
  172. Andersson I, Clifton IJ, Edwards SL, Fulop V, Hadfield AT, et al. On the scope and limitations of the Laue method in kinetic crystallographic studies with macromolecules. Time-resolved Macromolecular Crystallography. 1992; :95-102.
  173. Rice M, Wakatsuki S, Bienenstock A. Composition modulation in amorphous metal-germanium alloys detected by anomalous small-angle X-ray scattering. Journal of Applied. Crystallography. 1991; 24:598-602.
  174. Hajdu J, Almo SC, Farber GK, Prater JJ, Petsko GA, et al. On the limitations of the Laue method when applied to crystals of macromolecules. Crystallographic Computing 5. 1991; :29-49.

Books and Chapters

Wakatsuki S. Synchrotron Light Sources and Free-Electron Lasers. Jaeschke E, Khan S, Schneider JR, Hastings JB, editors. Switzerland: Springer International Publishing; 2016. Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers; p.1-39. 

Gabriele M. M. StoffelDavid Adrian SaezHasan DeMirciBastian VögeliYashas RaoJan ZarzyckiYasuo YoshikuniSoichi WakatsukiEsteban Vöhringer-Martinez, and Tobias J. Erb
Gabriele M. M. StoffelDavid Adrian SaezHasan DeMirciBastian VögeliYashas RaoJan ZarzyckiYasuo YoshikuniSoichi WakatsukiEsteban Vöhringer-Martinez, and Tobias J. Erb