Publications
  1. Miyashita, O; Go, N. 1999. Pressure dependence of protein electron transfer reactions: Theory and simulation. J. Phys. Chem. B. 103 (3): 562-571.
  2. Miyashita, O; Go, N. 2000. Reorganization energy of protein electron transfer reaction: Study with structural and frequency signature. J. Phys. Chem. B. 104 (31): 7516-7521.
  3. Moritsugu, K; Miyashita, O; Kidera, A. 2000. Vibrational energy transfer in a protein molecule. Phys. Rev. Lett. 85 (18): 3970-3973.
  4. Tama, F; Miyashita, O; Kitao, A; Go, N. 2000. Molecular dynamics simulation shows large volume fluctuations of proteins. Eur. Biophys. J. 29 (7): 472-480.
  5. Miyashita, O; Axelrod, HL; Onuchic, JN. 2002. Different scenarios for inter-protein electron tunneling: The effect of water-mediated pathways. J. Biol. Phys. 28 (3): 383-394.
  6. Miyashita, O; Onuchic, JN; Wolynes, PG. 2003. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Natl. Acad. Sci., USA, 100 (22): 12570-12575.
  7. Miyashita, O; Onuchic, JN; Okamura, MY. 2003. Continuum electrostatic model for the binding of cytochrome c(2) to the photosynthetic reaction center from Rhodobacter sphaeroides. Biochem. 42 (40): 11651-11660.
  8. Miyashita, O; Okamura, MY; Onuchic, JN. 2003. Theoretical understanding of the interprotein electron transfer between cytochrome c(2) and the photosynthetic reaction center. J. Phys. Chem. B. 107 (5): 1230-1241.
  9. Moritsugu, K; Miyashita, O; Kidera, A. 2003. Temperature dependence of vibrational energy transfer in a protein molecule. J. Phys. Chem. B. 107 (14): 3309-3317.
  10. Miyashita, O; Onuchic, JN; Okamura, MY. 2004. Transition state and encounter complex for fast association of cytochrome c(2) with bacterial reaction center. Proc. Natl. Acad. Sci., USA,101 (46): 16174-16179.
  11. Tama, F; Miyashita, O; Brooks, CL. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147 (3): 315-326.
  12. Wong, L; Lieser, S; Chie-Leon, B; Miyashita, O; Aubol, B; Shaffer, J; Onuchic, JN; Jennings, PA; Woods, VL; Adams, JA. 2004. Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk. J. Mol. Biol. 341 (1): 93-106.
  13. Tama, F; Miyashita, O; Brooks, CL. 2004. Flexible multi-scale fitting of atomic structures into lowresolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337 (4): 985-999.
  14. Miyashita, O; Okamura, MY; Onuchic, JN. 2005. Interprotein electron transfer from cytochrome c(2) to photosynthetic reaction center: Tunneling across an aqueous interface. Proc. Natl. Acad. Sci., USA, 102 (10): 3558-3563.
  15. Miyashita, O; Wolynes, PG; Onuchic, JN. 2005. Simple energy landscape model for the kinetics of functional transitions in proteins. J. Phys. Chem. B. 109 (5): 1959-1969.
  16. Wong, L; Lieser, SA; Miyashita, O; Miller, M; Tasken, K; Onuchic, JN; Adams, JA; Woods, VL; Jennings, PA. 2005. Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation. J. Mol. Biol. 351 (1): 131-143.
  17. Onuchic, JN; Kobayashi, C; Miyashita, O; Jennings, P; Baldridge, KK 2006. Exploring biomolecular machines: energy landscape control of biological reactions. Phil. Trans. R. Soc. B 361, 1439–1443.
  18. Whitford, PC; Miyashita, O; Levy, Y; Onuchic, JN 2007. Conformational transition of adenylate kinase: switching by cracking. J. Mol. Biol. 366, 1661-1671
  19. Gorba, C; Miyashita, O; Tama, F 2008. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-simensional low-resolution data. Biophys. J. 94, 1589-1599
Last Updated ( Thursday, 17 April 2008 )