Centers & Labs

RIKEN Advanced Institute for Computational Science

Computational Structural Biology Research Unit

Research Unit Leader: Florence Tama (Ph.D.)
Florence  Tama(Ph.D.)

Biological complexes, structured ensembles of proteins or proteins/nucleic acids, perform many vital cellular functions, such as gene transcription, protein synthesis or regulation of cellular transport, and dysfunctions of those result in severe diseases. In order to understand diseases and develop treatments, the functional mechanisms of these biological complexes need to be elucidated. A crucial step in this process is the characterization of the structure and dynamics of these complexes. As large complexes are difficult to study by X-ray crystallography, alternative low-resolution experimental techniques such as cryo-electron microscopy, small angle X-ray scattering and fluorescence resonance energy transfer are often used to characterize their conformational states. Additionally, new experimental developments of X-ray Free Electron Lasers (XFEL, such as in SPring 8, RIKEN) should provide structural information close to atomic resolution. Our goal is to develop computational methods to obtain atomic level description of the functional states of biological complexes. Such methods will rely on the integration of various experimental data such as high resolution X-ray crystallography, lower resolution cryo-EM and emerging near atomic resolution XFEL with computational modeling through high performance computing such as with the K-computer. In addition, we aim to collaborate with experimental groups and the pharmaceutical industry to elucidate functional mechanism of biological systems.

Main Research Field

Complex systems

Related Research Fields

Biological Sciences

Research Subjects

  • Integration of computational tools with experimental data to build structural models of biological complexes
  • Development of computational approaches to elucidate dynamics from experimental data
  • Collaborative studies of biological systems with experimental groups and the pharmaceutical industry

Selected Publications

  1. A. Logan, J. Baker, K. Ehrlich, Z. Campbell, S. Patel, I. Vorontsov, F. Tama, O. Miyashita:
    "Network Visualization of Conformational Sampling during Molecular Dynamics Simulation"
    J. Mol. Graph. Mod. 46:140-9 (2013)
  2. Q Jin, CO Sorzano, JM de la Rosa-Trevín, JR Bilbao-Castro, R. Núñez-Ramírez, O. Llorca , F. Tama, S. Jonič:
    "Iterative elastic 3D-to-2D alignment method using normal modes for studying structural
    dynamics of large macromolecular complexes"
    Structure 22(3):496-506 (2014)
  3. M. Gallagher-Jones, Y. Bessho, S. Kim, J. Park, S. Kim, D. Nam, C. Kim, Y. Kim, Y. Noh do, O.
    Miyashita, F. Tama, Y. Joti, T. Kameshima, T. Hatsui, K. Tono, Y. Kohmura, M. Yabashi, SS. Hasnain, T. Ishikawa, C. Song:
    "Macromolecular structures probed by combining single-shot free-electron laser
    diffraction with synchrotron coherent X-ray imaging"
    Nat Commun. (2014) 2:5:3798
  4. S. Patel, E. Vierling and F. Tama:
    "Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins"
    Biophys J. (2014) 106:2644-55
  5. CO Sorzano, JM de la Rosa-Trevín, F. Tama, S. Jonić.:
    "Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol"
    J Struct Biol. (2014) 188:134-41
  6. Jin Q, Sorzano CO, de la Rosa-Trevín JM, Bilbao-Castro JR, Núñez-Ramírez R, Llorca O, Tama F, Jonić S.:
    "Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes"
    Structure, in press (2014)
  7. Baker, J., Wright, S. H., and Tama, F.:
    "Simulations of substrate transport in the multidrug transporter EmrD"
    Proteins, 80, 1620-1632 (2012)
  8. Ahmed, A., Whitford, P.C., Sanbonmatsu K.Y., and Tama, F.:
    "Consensus among flexible fitting approaches improves the interpretation of cryo-EM data"
    J. Struct. Biol., 177, 561-570 (2012)
  9. Baumann, B.A.J., Taylor, D.W., Huang, Z., Tama, F., Fagnant, P.M., Trybus, K.M., and Taylor, K.:
    "Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation"
    J. Mol. Biol., 415, 274-287 (2012)
  10. Miyashita, O., Gorba, C., and Tama, F.:
    "Structure Modeling from Small Angle X-ray Scattering Data with Elastic Network Normal Mode Analysis"
    J. Struct. Biol., 173, 451-460 (2011)

Lab Members

Principal Investigator

Florence Tama
Research Unit Leader

Core Members

Atsushi Tokuhisa
Research Scientist
Miki Nakano
Postdoctoral Researcher
Sandhya Tiwari
Postdoctoral Researcher

Contact information

7-1-26,Minatojima-minami-machi,
Chuo-ku,Kobe,Hyogo
650-0047,Japan

Email: florence.tama [at] riken.jp

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