メンバー構成員

上級研究員　宮下 治

学歴

研究・教育歴

研究テーマ

1. 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
2. タンパク質の結晶

出版物

1. Ahlstrom, L. S. & Miyashita, O. Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer. Proteins, in press.
2. 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).
3. 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).
4. 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).
5. 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).
6. 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).
7. 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)
8. 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).
9. 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).
10. 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).
11. 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).
12. 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).
13. 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).
14. 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).
15. 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).
16. 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).
17. 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).
18. 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).
19. 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).
20. 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).
21. 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).
22. 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).
23. 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).
24. Moritsugu, K., Miyashita, O. & Kidera, A. Temperature dependence of vibrational energy transfer in a protein molecule. J Phys Chem B 107, 3309-3317 (2003).
25. 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).
26. Tama, F., Miyashita, O., Kitao, A. & Go, N. Molecular dynamics simulation shows large volume fluctuations of proteins. Eur Biophys J 29, 472-480 (2000).
27. Moritsugu, K., Miyashita, O. & Kidera, A. Vibrational energy transfer in a protein molecule. Phys Rev Lett 85, 3970-3973 (2000).
28. 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).
29. Miyashita, O. & Go, N. Pressure dependence of protein electron transfer reactions: Theory and simulation. J Phys Chem B 103, 562-571 (1999).