Postdoctoral Scientist, University of California at San Diego
2006年
Research Assistant Professor, University of Arizona
2007年
Assistant Professor, University of Arizona
2013年
理化学研究所計算化学研究機構 研究員
2013年
理化学研究所計算化学研究機構 上級研究員（現在に至る）
研究テーマ
計算構造生物学による生体超分子構造解析と創薬応用研究
タンパク質の結晶
出版物
Ahlstrom, L. S. & Miyashita, O. Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer. Proteins, in press.
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 Model46 140–149 (2013).
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. Biochemistry52, 3332-3345 (2013).
Ahlstrom, L. S. & Miyashita, O. Comparison of a Simulated λ Cro Dimer Conformational Ensemble to Its NMR Models. Int J Quantum Chem113, 518–524 (2013).
Ahlstrom, L. S. & Miyashita, O. Molecular Simulation Uncovers the Conformational Space and Dominant Forms of the λ Cro Dimer in Solution. Biophys J101, 2516-24 (2011).
Miyashita, O., Gorba, C. & Tama, F. Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis. J Struct Biol173, 451-460 (2011).
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 Chem32, 1043-1053 (2011)
Campbell, Z. T., Baldwin, T. O. & Miyashita, O. Analysis of the Bacterial Luciferase Mobile Loop by Replica-Exchange Molecular Dynamics. Biophys J99, 4012-4019 (2010).
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 Biol169, 95-105 (2010).
Vorontsov, I. I. & Miyashita, O. Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose. Biophys J97, 2532-2540 (2009).
Gorba, C., Miyashita, O. & Tama, F. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data. Biophys J94, 1589-1599 (2008).
Whitford, P. C., Miyashita, O., Levy, Y. & Onuchic, J. N. Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol366, 1661-1671 (2007).
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 Sci361, 1439-1443 (2006).
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 USA102, 3558-3563 (2005).
Miyashita, O., Wolynes, P. G. & Onuchic, J. N. Simple energy landscape model for the kinetics of functional transitions in proteins. J Phys Chem B109, 1959-1969 (2005).
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 Biol351, 131-143 (2005).
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 Biol337, 985-999 (2004).
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 Biol147, 315-326 (2004).
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 USA101, 16174-16179 (2004).
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 Biol341, 93-106 (2004).
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. Biochemistry42, 11651-11660 (2003).
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 B107, 1230-1241 (2003).
Miyashita, O., Onuchic, J. N. & Wolynes, P. G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci USA100, 12570-12575 (2003).
Moritsugu, K., Miyashita, O. & Kidera, A. Temperature dependence of vibrational energy transfer in a protein molecule. J Phys Chem B107, 3309-3317 (2003).
Miyashita, O., Axelrod, H. L. & Onuchic, J. N. Different scenarios for inter-protein electron tunneling: The effect of water-mediated pathways. J Biol Phys28, 383-394 (2002).
Tama, F., Miyashita, O., Kitao, A. & Go, N. Molecular dynamics simulation shows large volume fluctuations of proteins. Eur Biophys J29, 472-480 (2000).
Moritsugu, K., Miyashita, O. & Kidera, A. Vibrational energy transfer in a protein molecule. Phys Rev Lett85, 3970-3973 (2000).
Miyashita, O. & Go, N. Reorganization energy of protein electron transfer reaction: Study with structural and frequency signature. J Phys Chem B104, 7516-7521 (2000).
Miyashita, O. & Go, N. Pressure dependence of protein electron transfer reactions: Theory and simulation. J Phys Chem B103, 562-571 (1999).
