Osamu Miyashita
Assistant Professor of Biochemistry and Molecular Biophysics
Ph.D. 2000, Kyoto University
Theoretical and Computational Biophysics, Molecular Dynamics Simulations, Protein Electron Transfer, Protein Allostery
Research Interests
My research interests have been centered on the role of conformational dynamics of biological molecules on their functions. Main information for understanding the mechanism of biological molecules is the atomic structures obtained from X-ray crystallography. From the structure, we can learn what elements are necessary for the functions. However, the structure is a static picture and it cannot explain how the biological molecules perform their functions. If we could see and observe how the molecules are moving, how it would be very helpful to understand its mechanism. This is why we use computer simulations. Using computers, we can simulate how the molecules are actually moving. However, even with the most powerful computer, it is difficult to simulate the entire event of the functions. Moreover, the biological molecules are not working in deterministic way as our macro machines do. Since the biological molecules are so small, they are working in the thermal fluctuations, i.e. under (or using) the noise from solvent or other biological molecules, we need to describe the biological event in statistical manner. In my researches, I aim to develop theoretical frameworks to describe the biological functions in terms of statistical physics, and use computational approach to simulate the real biological systems.
Selected Publications
Gorba, C., Miyashita, O. & Tama, F. 2008. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data. Biophys J 94, 1589-1599.
Whitford, P. C., Miyashita, O., Levy, Y. & Onuchic, J. N. 2007. Conformational transitions of adenylate kinase: switching by cracking.
J Mol Biol 366, 1661-1671.
Onuchic, J. N., Kobayashi, C., Miyashita, O., Jennings, P. & Baldridge, K. K. 2006. Exploring biomolecular machines: energy landscape control of biological reactions. Philos Trans R Soc Lond B Biol Sci 361, 1439-1443.
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.
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.
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.
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.
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.
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.
Tama, F; Miyashita, O; Brooks, CL. 2004. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337 (4): 985-999.
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.
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.Biochemistry 42 (40): 11651-11660.
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.
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.
Miyashita, O; Axelrod, HL; Onuchic, JN. 2002. Different scenarios for inter-protein electron tunneling: The effect of water-mediated pathways.J. Biol. Physics 28 (3): 383-394.
Tama, F; Miyashita, O; Kitao, A; Go, N. 2000. Molecular dynamics simulation shows large volume fluctuations of proteins. European Biophysics Journal with Biophysics Letters 29 (7): 472-480.
Moritsugu, K; Miyashita, O; Kidera, A. 2000. Vibrational energy transfer in a protein molecule.Physical Review Letters85 (18): 3970-3973.
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.
Miyashita, O; Go, N. 1999. Pressure dependence of protein electron transfer reactions: Theory and simulation. J. Phys. Chem. B 103 (3): 562-571.