PeopleMembers

Senior Scientist Osamu Miyashita

EDUCATION

2000 Ph.D. (Science) Kyoto University, Japan
1998 M.A. (Science) Kyoto University, Japan
1996 B.S. (Science) Kyoto University, Japan

RESEARCH AND TEACHING EXPERIENCES

2013-present RIKEN Advanced Institute for Computational Sciences, Senior Scientist
2013 RIKEN Advanced Institute for Computational Sciences, Scientist
2007 Assistant Professor, University of Arizona
2006 Research Assistant Professor, University of Arizona
2000 Postdoctoral Scientist, University of California at San Diegon
2000 JSPS postdoctoral fellowship, Kyoto University

RESEARCH PROJECTS

  1. Structure determination of biological macromolecules with XFEL and application to drug discovery
  2. Protein crystals

PUBLICATIONS

  1. Srivastava, A., Tama, F., Kohda, D., &amp Miyashita, O. Computational Investigation of the Conformational Dynamics in Tom20-Mitochondrial Presequence Tethered Complexes. Submitted.
  2. Nagai, T., Tama, F. &amp Miyashita, O. Cryo-cooling effect on DHFR crystal studied by replica-exchange molecular dynamics. Submitted.
  3. Mori, T., Kulik, M., Miyashita, O., Jung, J., Tama, F., &amp Sugita, Y. Acceleration of cryo-EM flexible fitting for large biomolecular systems by efficient space partitioning. Under revision.
  4. Tiwari, S. P., Tama, F. &amp Miyashita, O. Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. Under revision.
  5. Jin, Q., Miyashita, O., Tama, F., Yang, J. &amp Jonic, S. Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging. Under revision.
  6. Nakano, M., Miyashita, O., Jonic, S., Tokuhisa, A. &amp Tama, F. Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution. J Synchrotron Radiat 25, 1010-1021 (2018).
  7. Miyashita, O. &amp Joti, Y. X-ray free electron laser single-particle analysis for biological systems. Curr Opin Struct Biol 43, 163-169 (2017).
  8. Nakano, M. & Miyashita, O., Jonic, S., Song, C., Nam, D., Joti, Y., Tama, F. Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL. J Synchrotron Radiat. 24 727-737 (2017).
  9. Miyashita, O., Kobayashi, C., Mori, T., Sugita, Y. &amp Tama, F. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. J Comput Chem 38, 1447-1461 (2017).
  10. Ahlstrom, L. S., Vorontsov, I. I., Shi, J. &amp Miyashita, O. Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations. PLoS One 12, e0170337 (2017).
  11. 宮下治&amp タマフロハンス, 構造解析へのハイブリッドアプローチ：電子顕微鏡とX線自由電子レーザーからの実験データの活用, 生物物理会誌, 57, 90-94 (2017).
  12. Nakano, M., Tateishi-Karimata, H., Tanaka, S., Tama, F., Miyashita, O., Nakano, S. &amp Sugimoto, N. Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory. Chem Phys Lett 660, 250-255 (2016).
  13. Tokuhisa, A., Jonic, S., Tama, F. &amp Miyashita, O. Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns. J Struct Biol 194, 325-336 (2016).
  14. Nakano, M., Tateishi-Karimata, H., Tanaka, S., Tama, F., Miyashita, O., Nakano, S. &amp Sugimoto, N. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory. Nucleic Acids Res 43, 10114-10125 (2015).
  15. Ahlstrom, L. S. &amp Miyashita, O. Packing interface energetics in different crystal forms of the λ Cro dimer. Proteins 82, 1128-1141 (2014).
  16. Gallagher-Jones, M., Bessho, Y., Kim, S., Park, J., Kim, S., Nam, D., Kim, C., Kim, Y., Noh, D. Y., Miyashita, O., Tama, F., Joti, Y., Kameshima, T., Hatsui, T., Tono, K., Kohmura, Y., Yabashi, M., Hasnain, S. S., Ishikawa, T. &amp Song, C. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging. Nat Commun 5, 3798 (2014).
  17. Ahlstrom, L. S., Baker, J. L., Ehrlich, K., Campbell, Z. T., Patel, S., Vorontsov, I. I., Tama, F. & Miyashita, O. Network visualization of conformational sampling during molecular dynamics simulation. J Mol Graph Model 46 140–149 (2013).
  18. Sarkar, D. D., Edwards, S. K., Mauser, J. A., Suarez, A. M., Serowoky, M. A., Hudok, N. L., Hudok, P. L., Nuñez, M., Weber, C. S., Lynch, R. M., Miyashita, O. & Tsao, T. S. Increased Redox-Sensitive Green Fluorescent Protein Reduction Potential in the Endoplasmic Reticulum following Glutathione-Mediated Dimerization. Biochemistry 52, 3332-3345 (2013).
  19. Ahlstrom, L. S. & Miyashita, O. Comparison of a Simulated λ Cro Dimer Conformational Ensemble to Its NMR Models. Int J Quantum Chem 113, 518–524 (2013).
  20. Ahlstrom, L. S. & Miyashita, O. Molecular Simulation Uncovers the Conformational Space and Dominant Forms of the λ Cro Dimer in Solution. Biophys J 101, 2516-24 (2011).
  21. Miyashita, O., Gorba, C. & Tama, F. Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis. J Struct Biol 173, 451-460 (2011).
  22. Votontsov, I. I. & Miyashita, O. Crystal Molecular Dynamics Simulations to Speed Up MM/PB(GB)SA Evaluation of Binding Free Energies of Di-mannose Deoxy Analogs with P51G-m4-Cyanovirin-N. J Comput Chem 32, 1043-1053 (2011)
  23. Campbell, Z. T., Baldwin, T. O. & Miyashita, O. Analysis of the Bacterial Luciferase Mobile Loop by Replica-Exchange Molecular Dynamics. Biophys J 99, 4012-4019 (2010).
  24. Grubisic, I., Shokhirev, M. N., Orzechowski, M., Miyashita, O. & Tama, F. Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps. J Struct Biol 169, 95-105 (2010).
  25. Vorontsov, I. I. & Miyashita, O. Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose. Biophys J 97, 2532-2540 (2009).
  26. Gorba, C., Miyashita, O. & Tama, F. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data. Biophys J 94, 1589-1599 (2008).
  27. Whitford, P. C., Miyashita, O., Levy, Y. & Onuchic, J. N. Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol 366, 1661-1671 (2007).
  28. Onuchic, J. N., Kobayashi, C., Miyashita, O., Jennings, P. & Baldridge, K. K. Exploring biomolecular machines: energy landscape control of biological reactions. Philos Trans R Soc Lond B Biol Sci 361, 1439-1443 (2006).
  29. Miyashita, O., Okamura, M. Y. & Onuchic, J. N. Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: tunneling across an aqueous interface. Proc Natl Acad Sci USA 102, 3558-3563 (2005).
  30. Miyashita, O., Wolynes, P. G. & Onuchic, J. N. Simple energy landscape model for the kinetics of functional transitions in proteins. J Phys Chem B 109, 1959-1969 (2005).
  31. Wong, L., Lieser, S. A., Miyashita, O., Miller, M., Tasken, K., Onuchic, J. N., Adams, J. A., Woods, V. L. & Jennings, P. A. Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation. J Mol Biol 351, 131-143 (2005).
  32. Tama, F., Miyashita, O. & Brooks, C. L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol 337, 985-999 (2004).
  33. Tama, F., Miyashita, O. & Brooks, C. L. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol 147, 315-326 (2004).
  34. Miyashita, O., Onuchic, J. N. & Okamura, M. Y. Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center. Proc Natl Acad Sci USA 101, 16174-16179 (2004).
  35. Wong, L., Lieser, S., Chie-Leon, B., Miyashita, O., Aubol, B., Shaffer, J., Onuchic, J. N., Jennings, P. A., Woods, V. L. & Adams, J. A. Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk. J Mol Biol 341, 93-106 (2004).
  36. Miyashita, O., Onuchic, J. N. & Okamura, M. Y. Continuum electrostatic model for the binding of cytochrome c(2) to the photosynthetic reaction center from Rhodobacter sphaeroides. Biochemistry 42, 11651-11660 (2003).
  37. Miyashita, O., Okamura, M. Y. & Onuchic, J. N. Theoretical understanding of the interprotein electron transfer between cytochrome c(2) and the photosynthetic reaction center. J Phys Chem B 107, 1230-1241 (2003).
  38. Miyashita, O., Onuchic, J. N. & Wolynes, P. G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci USA 100, 12570-12575 (2003).
  39. Moritsugu, K., Miyashita, O. & Kidera, A. Temperature dependence of vibrational energy transfer in a protein molecule. J Phys Chem B 107, 3309-3317 (2003).
  40. Miyashita, O., Axelrod, H. L. & Onuchic, J. N. Different scenarios for inter-protein electron tunneling: The effect of water-mediated pathways. J Biol Phys 28, 383-394 (2002).
  41. Tama, F., Miyashita, O., Kitao, A. & Go, N. Molecular dynamics simulation shows large volume fluctuations of proteins. Eur Biophys J 29, 472-480 (2000).
  42. Moritsugu, K., Miyashita, O. & Kidera, A. Vibrational energy transfer in a protein molecule. Phys Rev Lett 85, 3970-3973 (2000).
  43. Miyashita, O. & Go, N. Reorganization energy of protein electron transfer reaction: Study with structural and frequency signature. J Phys Chem B 104, 7516-7521 (2000).
  44. Miyashita, O. & Go, N. Pressure dependence of protein electron transfer reactions: Theory and simulation. J Phys Chem B 103, 562-571 (1999).