Wakatsuki Laboratory

Publications

  1. Currie, M. J., Davies, J. S., Scalise, M., Gulati, A., Wright, J. D., Newton-Vesty, M. C., Abeysekera, G. S., Subramanian, R., Wahlgren, W. Y., Friemann, R., Allison, J. R., Mace, P. D., Griffin, M. D., Demeler, B., Wakatsuki, S., Drew, D., Indiveri, C., Dobson, R. C., North, R. A. Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter. eLife 2024 February DOI 10.7554/eLife.92307
  2. Christou, N. E., Apostolopoulou, V., Melo, D. V., Ruppert, M., Fadini, A., Henkel, A., Sprenger, J., Oberthuer, D., Günther, S., Pateras, A., Rahmani Mashhour, A., Yefanov, O. M., Galchenkova, M., Reinke, P. Y., Kremling, V., Scheer, T. E., Lange, E. R., Middendorf, P., Schubert, R., De Zitter, E., Lumbao-Conradson, K., Herrmann, J., Rahighi, S., Kunavar, A., Beale, E. V., Beale, J. H., Cirelli, C., Johnson, P. J., Dworkowski, F., Ozerov, D., Bertrand, Q., Wranik, M., Bacellar, C., Bajt, S., Wakatsuki, S., Sellberg, J. A., Huse, N., Turk, D., Chapman, H. N., Lane, T. J. Time-resolved crystallography captures light-driven DNA repair. Science. 2023; 382 (6674): 1015-1020. doi: 10.1126/science.adj4270. PMID: 38033070
  3. Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun. 2023 Mar 28;14(1):1733. doi: 10.1038/s41467-023-37254-w.PMID: 36977673
  4. Davies JS, Currie MJ, North RA, Scalise M, Wright JD, Copping JM, Remus DM, Gulati A, Morado DR, Jamieson SA, Newton-Vesty MC, Abeysekera GS, Ramaswamy S, Friemann R, Wakatsuki S, Allison JR, Indiveri C, Drew D, Mace PD, Dobson RCJ. Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun. 2023 Feb 27;14(1):1120. doi: 10.1038/s41467-023-36590-1. PubMed PMID: 36849793; PubMed Central PMCID: PMC9971032.
  5. Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ. Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions. Nat Commun. 2023 Feb 1;14(1):545. doi: 10.1038/s41467-023-36235-3. PubMed PMID: 36726015; PubMed Central PMCID: PMC9892032.
  6. Hameedi MA, Prates TE, Garvin MR, Mathews II, Amos BK, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong V, Mitchell JC, Labbe A, Galanie S, Wakatsuki S, Jacobson D. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nature Communications, 2022; 13 (1): 5285, https://doi.org/10.1038/s41467-022-32922-9.
  7. DeMirci H, Rao Y, Stoffel GM, Vögeli B, Schell K, Gomez A, Batyuk A, Gati C, Sierra RG, Hunter MS, Dao EH, Ciftci HI, Hayes B, Poitevin F, Li P-N, Kaur M, Tono K, Saez DA, Deutsch S, Yoshikuni Y & Wakatsuki S. Intersubunit Coupling Enables Fast CO2 -Fixation by Reductive Carboxylases. ACS Central Science, 2022, https://doi.org/10.1021/acscentsci.2c00057. 
  8. Zhang K, Horikoshi N, Li S, Powers AS, Hameedi MA, Pintilie GD, Chae H-D, Khan YA, Suomivuori C-M, Dror RO, Sakamoto KM, Chiu W, Wakatsuki S. Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia. ACS Central Science, 2022, https://doi.org/10.1021/acscentsci.1c01090. 
  9. Garcia AA, Mathews II, Horikoshi N, Matsui T, Kaur M, Wakatsuki S, Mochly-Rosen D. Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants. J Biological Chemistry, 2022, https://doi.org/10.1016/j.jbc.2022.101610.
  10. Sanders B, Pohkrel S, Labbe A, Mathews I, Cooper C, Davidson R, Phillips G, Weiss K, Zhang Q, O'Neill H, Kaur M, Ferrins L, Jurgen Schmidt J, Reichard W, Surendranathan S, Kumaran D, Andi B, Babnigg G, Moriarty N, Adams P, Joachimiak A, Jonsson C, Wakatsuki S, Galanie S, Head M, Parks J. Potent and Selective Covalent Inhibitors of the Papain-like Protease from SARS-CoV-2. Research Square. 2021 Oct 8;rs.3.rs-906621. doi: 10.21203/rs.3.rs-906621/v1.
  11. Destan E, Yuksel B, Tolar BB, Ayan E, Deutsch S, Yoshikuni Y, Wakatsuki S, Francis CA, DeMirci H.  Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Scientific reports. 2021; 11 (1): 22849.
  12. Horikoshi N, Hwang S, Gati C, Matsui T, Castillo-Orellana C, Raub AG, Garcia AA, Jabbarpour F, Batyuk A, Broweleit J, Xiang X, Chiang A, Broweleit R, Vöhringer-Martinez E, Mochly-Rosen D, Wakatsuki S.Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency. Proc Natl Acad Sci U S A. 2021 Jan 26;118(4). doi: 10.1073/pnas.2022790118. PubMed PMID: 33468660.
  13. Li P, Wakatsuki S, Pianetta PA, Liu Y. Hybrid real- and reciprocal-space full-field imaging with coherent illumination. Journal of Optics. 2020 October; 22(11):115611. doi: 10.1088/2040-8986/abbeca.
  14. Piton J, Pojer F, Wakatsuki S, Gati C, Cole ST. High resolution CryoEM structure of the ring-shaped virulence factor EspB from Mycobacterium tuberculosis. J Struct Biol X. 2020;4:100029. doi: 10.1016/j.yjsbx.2020.100029. eCollection 2020. PubMed PMID: 32875288; PubMed Central PMCID: PMC7451430.
  15. Lourenço RF, Saurabh S, Herrmann J, Wakatsuki S, Shapiro L. The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA. mBio. 2020 Jun 9;11(3). doi: 10.1128/mBio.00448-20. PubMed PMID: 32518183; PubMed Central PMCID: PMC7373187.
  16. Santoso MR, Ikeda G, Tada Y, Jung JH, Vaskova E, Sierra RG, Gati C, Goldstone AB, von Bornstaedt D, Shukla P, Wu JC, Wakatsuki S, Woo YJ, Yang PC. Exosomes From Induced Pluripotent Stem Cell-Derived Cardiomyocytes Promote Autophagy for Myocardial Repair.J Am Heart Assoc. 2020 Mar 17;9(6):e014345. doi: 10.1161/JAHA.119.014345. Epub 2020 Mar 5. PubMed PMID: 32131688.
  17. Velez G, Sun YJ, Khan S, Yang J, Herrmann J, Chemudupati T, MacLaren RE, Gakhar L, Wakatsuki S, Bassuk AG, Mahajan VB. Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. Cell Rep. 2020 Jan 21;30(3):881-892.e5. doi: 10.1016/j.celrep.2019.12.077. PubMed PMID: 31968260; PubMed Central PMCID: PMC7001764.
  18. Herrmann J, Li PN, Jabbarpour F, Chan ACK, Rajkovic I, Matsui T, Shapiro L, Smit J, Weiss TM, Murphy MEP, Wakatsuki S. A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly. Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):388-394. doi: 10.1073/pnas.1909798116. Epub 2019 Dec 17. PubMed PMID: 31848245; PubMed Central PMCID: PMC6955313.
  19. Li PN, Herrmann J, Wakatsuki S, van den Bedem H. Transport Properties of Nanoporous, Chemically Forced Biological Lattices. J Phys Chem B. 2019 Dec 12;123(49):10331-10342. doi: 10.1021/acs.jpcb.9b05882. Epub 2019 Nov 27. PubMed PMID: 31721579.
  20. Chae HD, Cox N, Capolicchio S, Lee JW, Horikoshi N, Kam S, Ng AA, Edwards J, Butler TL, Chan J, Lee Y, Potter G, Capece MC, Liu CW, Wakatsuki S, Smith M, Sakamoto KM. SAR optimization studies on modified salicylamides as a potential treatment for acute myeloid leukemia through inhibition of the CREB pathway. Bioorg Med Chem Lett. 2019 Aug 15;29(16):2307-2315. doi: 10.1016/j.bmcl.2019.06.023. Epub 2019 Jun 19. PubMed PMID: 31253529.
  21. Herhaus L, van den Bedem H, Tang S, Maslennikov I, Wakatsuki S, Dikic I, Rahighi S.Molecular Recognition of M1-Linked Ubiquitin Chains by Native and Phosphorylated UBAN Domains. J Mol Biol. 2019 Aug 9;431(17):3146-3156. doi: 10.1016/j.jmb.2019.06.012. Epub 2019 Jun 24. PubMed PMID: 31247202.
  22. 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 Jul 17;14(14):1321-1324. doi: 10.1002/cmdc.201900341. Epub 2019 Jun 27. PubMed PMID: 31183991; PubMed Central PMCID: PMC6701841.
  23. Stoffel GMM, Saez DA, DeMirci H, Vögeli B, Rao Y, Zarzycki J, Yoshikuni Y, Wakatsuki S, Vöhringer-Martinez E, Erb TJ. Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13964-13969. doi: 10.1073/pnas.1901471116. Epub 2019 Jun 26. PubMed PMID: 31243147; PubMed Central PMCID: PMC6628652.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
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  151. 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.
  152. 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.
  153. 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.
  154. 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.
  155. 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.
  156. 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.
  157. 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.
  158. 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.
  159. 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.
  160. Wakatsuki S. Structural Biology of Protein Transport. Journal of the Crystallographic Society of Japan. 2003 March; 45:26-31.
  161. Wakatsuki S. Impact of insertion devices on macromolecular crystallography. Undulators, Wigglers and Their Applications by Taylor & Francis Inc.. 2003; :293-321.
  162. Wakatsuki S. Structural Genomics of intracellular transport and post-translational transport. Science & Technology Journal. 2002 August; 11(8):26-27.
  163. 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.
  164. 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.
  165. 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.
  166. 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.
  167. 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.
  168. 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.
  169. 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.
  170. Wakatsuki S, Earnest T. The Impact of Synchrotron Radiation in Protein Crystallography. Synchrotron radiation news. 2000; 13(5):4-8.
  171. 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.
  172. 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.
  173. 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.
  174. 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.
  175. 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.
  176. 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.
  177. 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.
  178. 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.
  179. 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.
  180. 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.
  181. Clifton IJ, Duke EM, Wakatsuki S, Ren Z. [Evaluation of Laue diffraction patterns. Methods Enzymol. 1997;277:448-67. PubMed PMID: 18488319.
  182. 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.
  183. 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.
  184. 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.
  185. 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.
  186. 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.
  187. 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.
  188. 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.
  189. Wakatsuki S. LEAP for time-resolved protein crystallography. CCP4 study weekend, Data Collection and Analysis. 1993;
  190. 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.
  191. 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.
  192. 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.
  193. 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.
  194. 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.
  195. 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. 

Manuscripts in Archives

  1. Deconstructing the structural conservation of distantly related bacterial nucleoid-associated proteins using functional chimeras, Rogério F. Lourenço, Saumya Saurabh, Jonathan Herrmann, Soichi Wakatsuki, Lucy Shapiro, bioRxiv 804138; doi: https://doi.org/10.1101/804138