Bagautdin Bagautdinov

Material Structure Group 1

Research Scientist


 My primary research interest is in application of x-ray crystallography for structure elucidations of various condensed matters (minerals, ferroelectrics, superconductors, organic, inorganic and biological molecular crystals) to understanding and use their functions and/or rationally design new materials, drugs. For this I focus on the application and development of various advanced x-ray diffraction (single-crystal, powder, SAXS/WAXS), physical and chemical methods to determine accurate high-resolution structures at differ environments. The approach is effective to studies structural aspects of phase transformations and functional specificities in new materials with ultimate applications in different interesting fields.
 My research as a PhD student was conducted in the Institute of Solid State Physics of the Russian Academy of Sciences (Chernogolovka, Moscow district) working on the incommensurately modulated crystal structures in ferroelectrics and superconductors. The research was advanced by application of bond-valence and super-space approaches in McMaster University (Canada, Prof I.D. Brown) and in University of Bayreuth (Germany, Prof S. van Smaalen). From 1999 as JSPS postdoc I studied two-dimensionally modulated akermanite mineral structures in Hyogo University (Japan, Prof M. Ohmasa) and from 2001 was affiliated to Protein3000 project in RIKEN/SPring-8. In scope of the project I have created 67 PDB of protein, protein-ligand complex structures from various biological pathways. Mainly, I have focused on structural aspects of several pharmaceutically relevant enzymes, biotin protein ligase, circadian clock protein as well as stability and metal-binding functions of proteins. In JASRI my research is devoted to X-ray diffraction and MEM electron density studies of the polydiacetylene (PDA) crystallines. Combination of the crystalline structures with MEM electron, nuclear densities and electrostatic potentials calculations provides key insights of assembling of the PDA polymers, intermolecular hydrogen bonds, possible mechanisms of topo-chemical transformation and their unique functions. Recently, I have started to work on powder diffraction to explore the Rietveld/MEM technique potential for structure-function imaging.


  • x-ray crystallography
  • inorganic, organic and macromolecular (polymer, protein) structures
  • charge density and electrostatic potential analyses by maximum entropy method
  • hydrogen bonds
  • topo-chemical polymerization
  • phase transitions under temperature, pressure, laser irradiation
  • incommensurately modulated structures
  • powder diffraction
  • Rietveld technique

Selected research papers

  • Bagautdinov B, Matsuura Y, Yamamoto H, Sawano M, Ogasahara K, Takehira M,
    Kunishima N, Katoh E, Yutani K. (2015)
    Thermodynamic analysis of unusually thermostable CutA1 protein from human brain and its
    protease susceptibility.
    Journal of Biochemistry, 157, 169?176.
  • Bagautdinov B. (2014)
    The structures of the CutA1 proteins from Thermus thermophilus and Pyrococcus horikoshii:
    characterization of metal binding sites and metal-induced assembly.
    Acta Crystallographica F70, 404?413.
  • Bagautdinov B, Yutani K. (2011)
    Crystal structure of indole-3-glycerol phosphate synthase from Thermus thermophilus HB8:
    implications for thermal stability.
    Acta Crystallographica D67, 1054?1064.
  • Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N. (2008)
    Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate.
    Journal of Biological Chemistry, 283, 14739?14750.
  • Bagautdinov B, Kunishima N. (2007)
    The crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8
    and its cofactor and substrate complexes: insights into the enzymatic mechanism.
    Journal of Molecular Biology, 373, 424?438.
  • Tanaka T, Sawano M, Ogasahara K, Sakaguchi Y, Bagautdinov B, Katoh E,
    Kuroishi C, Shinkai A, Yokoyama S, Yutani K. (2006)
    Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 ℃.
    FEBS Letter 580, 4224-4230.
  • Bagautdinov B, Kuroishi C, Sugahara M, Kunishima N. (2005)
    Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes:
    structural basis of biotin activation.
    Journal of Molecular Biology, 353, 322?333.
  • Bagautdinov B, Hagiya K, Noguchi S, Ohmasa M, Ikeda N, Kusaka K, Iishi K. (2002)
    Low temperature study of two-dimensional modulations in akermanite crystals:
    Ca2MgSi2O7 and Ca2ZnSi2O7.
    Physics and Chemistry of Minerals, 29, 346?350.
  • Bagautdinov B, Jobst A, Ludecke J, van Smaalen S. (2001)
    Structural basis for the phase transitions of Cs2HgCl4.
    Acta Crystallographica B57, 231?236.
  • Bagautdinov B, Hagiya K, Kusaka K, Ohmasa M, Iishi K. (2000)
    Two-dimensional incommensurately modulated structure of (Sr0.13Ca0.87)2CoSi2O7 crystal.
    Acta Crystallographica B56, 811?821.
  • Bagautdinov B, Brown I.D. (2000)
    X-ray study of structural modulations in Cs2HgCl4.
    Journal of Physics: Condensed Matter 12, 8111?8125.
  • Bagautdinov B, Pilz K, Ludecke J, Van Smaalen S. (1999)
    Modulated structures of Cs2HgCl4: the 5a-superstructure at 185 K and the 3c-superstructure at 176K.
    Acta Crystallographica B55, 886-895.
  • Bagautdinov B, Luedecke J, Schneider M, Van Smaalen S. (1998)
    Disorder in the crystal structure of Cs2HgCl4 studied by the maximum entropy method.
    Acta Crystallographica B54, 626?634.

Selected oral presentations at academic conferences

  • Bagautdinov B, Sugimoto K, Sasaki S,Tanaka H, Tashiro K, Takata M.
    The roles of H-bonds in topotactic solid-state transformation of poly-DCHD
    Macro2014, 6-11 July, 2014, Chiang Mai, Thailand.
  • Bagautdinov B, Tanaka H, Shih C-H, Sugimoto K, Sasaki S, Tashiro K, Takata M.
    New insight into the polymerization and structural mechanisms of polydiacetylene DCHD:
    an X-ray/MEM study. IUCr, Madrid, Spain, 22-30 August 2011.
    Acta Cryst. (2011) A67, C27-28.
  • Bagautdinov B, Shih C-H, Sugimoto K, Sasaki S, Tanaka H, Tashiro K, Takata M.
    New insights into the monomer and polymer DCHD structures and mechanism of topochemical polymerization using MEM charge density imaging.
    58th SPSJ Symposium on Macromolecules, Japan, September 16 -18, 2009, Kumamoto, Japan Polymer Preprints, Japan (2009) Vol. 58, No. 2, 2937-2938.
  • Bagautdinov B, Kunishima N.
    X-ray visualization of protein biotinylation.
    IUCr2008 Osaka, Japan 8/2008. Acta Cryst. (2008) A64, C439.
  • Bagautdinov B, Sugahara M, Kunishima N.
    Structure of 6-Pyruvoyl Tetrahydrobiopterin Synthase from P. horikoshii OT3: Novel Oligomerisation and Substrate Binding Modes.
    Fifth East Asian Biophysics Symposium, Okinawa, 11/2006. Biophysics (2006) 46, S154.16, 2006
  • Bagautdinov B, Kuroishi C, Sugahara M, Kunishima N.
    Crystal Structure of the Biotin Protein Ligase from P. horikoshii OT3: Insights into the Mechanism of Biotin Activation.
    IUCr2005, Florence, Italy, 8/2005. Acta Cryst. (2005) A61, C188.
  • Bagautdinov B, Brown ID.
    X-Ray Study of the Incommensurately and Commensurately Modulated Phases in Cs2HgCl4.
    APERIODIC1997, Alpe d’Huez, Grenoble, France, 8/1997, p. 7.

Beam-line practical