BMCB-Faculty Research, Osamu Miyashita

Assistant Professor of Biochemistry & Molecular Biophysics
Ph.D., 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.

Select Publications

Any link on the below references will take you off of the BMCB site and to an abstract of that particular paper.

Miyashita, O., M.Y. Okamura, and J.N. Onuchic. 2005. Interprotein electron transfer from cytochrome c(2) to photosynthetic reaction center: Tunneling across an aqueous interface. Proceedings of the National Academy of Sciences U.S.A. 102: 3558-3563.

Wong, L., S.A. Lieser, O. Miyashita, M. Miller, K. Tasken, J.N. Onuchic, J.A. Adams, V.L. Woods, and P.A. Jennings. 2005. Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation. Journal of Molecular Biology 351: 131-143.

Miyashita, O., P.G. Wolynes, and J.N. Onuchic. 2005. Simple energy landscape model for the kinetics of functional transitions in proteins. Journal of Physical Chemistry B 109: 1959-1969.

Miyashita, O., J.N. Onuchic, and M.Y. Okamura. 2004. Transition state and encounter complex for fast association of cytochrome c(2) with bacterial reaction center. Proceedings of the National Academy of Sciences U.S.A. 101: 16174-16179.

Tama, F., O. Miyashita, and C.L. Brooks. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. Journal of Structural Biology 147: 315-326.

Wong, L., S. Lieser, B. Chie-Leon, O. Miyashita, B. Aubol, J. Shaffer, J.N. Onuchic, P.A. Jennings, V.L. Woods, and J.A. Adams. 2004. Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk. Journal of Molecular Biology 341: 93-106.

Tama, F., O. Miyashita, and C.L. Brooks. 2004. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. Journal of Molecular Biology 337: 985-999.

Miyashita, O., J.N. Onuchic, and P.G. Wolynes. 2003. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proceedings of the National Academy of Sciences U.S.A. 100: 12570-12575.

Miyashita, O., J.N. Onuchic, and M.Y. Okamura. 2003. Continuum electrostatic model for the binding of cytochrome c(2) to the photosynthetic reaction center from Rhodobacter sphaeroides. Biochemistry 42: 11651-11660.

Moritsugu, K, O. Miyashita, and A. Kidera. 2003. Temperature dependence of vibrational energy transfer in a protein molecule. Journal of Physical Chemistry B 107: 3309-3317.

Miyashita, O., M.Y. Okamura, and J.N. Onuchic. 2003. Theoretical understanding of the interprotein electron transfer between cytochrome c(2) and the photosynthetic reaction center. Journal of Physical Chemistry B 107: 1230-1241.

Miyashita, O., H.L. Axelrod, and J.N. Onuchic. 2002. Different scenarios for inter-protein electron tunneling: The effect of water-mediated pathways. Journal of Biological Physics 28: 383-394.

Tama, F., O. Miyashita, A. Kitao, and N. Go. 2000. Molecular dynamics simulation shows large volume fluctuations of proteins. European Biophysics Journal with Biophysics Letters 29: 472-480.

Moritsugu, K., O. Miyashita, and A. Kidera. 2000. Vibrational energy transfer in a protein molecule. Physical Review Letters 85: 3970-3973.

Miyashita, O., and N. Go. 2000. Reorganization energy of protein electron transfer reaction: Study with structural and frequency signature. Journal of Physical Chemistry B 104: 7516-7521.

Miyashita, O., and N. Go. 1999. Pressure dependence of protein electron transfer reactions: Theory and simulation. Journal of Physical Chemistry B 103: 562-571.

Contact Information

Mailing:
Dr. Osamu Miyashita, Assistant Professor
Department of Biochemistry & Molecular Biophysics
University of Arizona
Biological Sciences West 446
P. O. Box 210088
Tucson, AZ 85721-0088

Telephone:
520-626-9701

Fax:
520-626-9204

Email:
mystosm@email.arizona.edu

Please e-mail any comments to:
bmcb@email.arizona.edu