Centers & Labs

RIKEN Center for Computational Science

Computational Structural Biology Research Team

Team 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

Keywords

  • Modeling
  • structure
  • function
  • dynamics
  • low-resolution

Selected Publications

  1. M. Nakano, O. Miyashita, S. Jonic, C. Song, D. Nam, Y. Joti and F. Tama:
    "Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL"
    J. Synchrotron Rad. 4, 727-737 (2017)
  2. T. Shimizu and F. Tama:
    "Editorial overview: Macromolecular assemblies"
    Curr. Opin. Struc. Biol. 43, vii-ix (2017)
  3. O. Miyashita, C. Kobayashi, T. Mori, Y. Sugita, F. Tama:
    "Flexible Fitting to Cryo-EM Density Map using Ensemble Molecular Dynamics Simulations"
    J. Comp. Chem. 38(16), 1447-1461 (2017)
  4. O. Miyashita and F. Tama:
    "Hybrid approach for biological structure modeling: cryo-electron microscopy and X-ray free electron laser data"
    Seibutsu Butsuri (2017)
  5. M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto:
    "Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous salvation theory"
    Chem. Phys. Lett. 660, 250-255 (2016)
  6. A. Tokuhisa, S. Jonic; F. Tama and O. Miyashita:
    "Hybrid Approach for Structural Modeling of Biological Systems from X-ray Free Electron Laser Diffraction Patterns"
    J. Struct. Biol. 194(3), 325-36 (2016)
  7. M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto:
    "Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory"
    Nucleic Acids Res. 43(21), 10114-25 (2015)
  8. Q. Jin, Q., C.O.Sanchez Soriano, J.M. de la Rosa-Trevin, F. Tama, and S. Jonic:
    "Macromolecular Dynamics by Hybrid Electron Microscopy Normal Mode Analysis"
    Microscopy and Microanalysis 20, 1218-19 (2014)
  9. Q. Jin, C.O. Sanchez Sorzano, I. Callebaut, F. Tama, S. Jonic:
    "Elastic image registration to fully explore macromolecular dynamics by electron microscopy"
    In: Image Processing (ICIP), 2014 IEEE International Conference, (2014)
  10. C.O. Sorzano, J.M. de la Rosa-Trevín, F. Tama, S. Jonić:
    "Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol"
    J. Struct. Biol. 188, 134-41 (2014)

Lab Members

Principal Investigator

Florence Tama
Team Leader

Core Members

Miki Nakano
Postdoctoral Researcher
Sandhya Tiwari
Postdoctoral Researcher