Publications

T. Mori, M. Kulik, O. Miyashita, J. Jung, F. Tama and Y. Sugita. Acceleration of cryo-EM flexible fitting by efficient space partitioning for large biomolecular systems. Structure 2018

 M. Nakano,  O. Miyashita,  S. Jonic, A. Tokuhisa, F. Tama. Single-particle XFEL 3D Reconstruction of Ribosome-size Particles based on Fourier Slice Matching: Requirements to Reach Subnanometer ResolutionJ. Synchrotron Rad. 2018

A. Srivastava, T. Hirota, S. Irle and F. Tama. Conformational dynamics of human Protein Kinase CK2α and its effect on function and inhibition. Proteins. 2018

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. 2017

T. Shimizu and F. Tama. Editorial overview: Macromolecular assemblies. Curr. Opin. Struc. Biol. 2017

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. 2017

O. Miyashita and F. Tama. Hybrid approach for biological structure modeling: cryo-electron microscopy and X-ray free electron laser data. Seibutsu Butsuri 2017

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. 2016 

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. 2016

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. 2015 43(21): 10114-25

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 2014 20:1218-19

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

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. 2014 188:134-41

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 10:2644-55

J. Lega, S. Buxner, B. Blonder and F. Tama Exploration in integrated sciences J. Coll. Sci. Teach. 2014

JR Lopez-Blanco, O.  Miyashita, F. Tama and P. Chacon Normal Mode Analysis Techniques in Structural Biology. In: eLS. John Wiley & Sons, Ltd: Chichester. 2014

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

Q Jin, CO Sorzano, JM de la Rosa-Trevín, JR Bilbao-Castro, R. Núñez-Ramírez, O. Llorca , F. Tama, S. Jonić. Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes. Structure 2014 22:496-506

L. Ashtrom, 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. 2013 46:140-9

Lyumkis, H. Talley, A. Stewart, S. Shah, CK. Park, F. Tama, CS Potter, B. Carragher, NC. Horton. Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization. Structure 2013 8:21:1848-58

Nogales-Cadenas, S. Jonic, F. Tama, A. Arteni, D. Tabas-Madrid, M. Vazquez, A. Pascual-Montano, CO. Sorzano. 3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy. Nucl. Acid. Res., 2013 41:W363-W367

J. Baker, N. Biais and F. Tama. In silico studies of Pilus IV, Plos Computational Biology 2013 9(4):e1003032

B. Fritz, SA. Roberts, A. Ahmed, L. Breci, W. Li, A. Weichsel, JL. Brailey, VH. Wysocki, F. Tama, WR. Montfort. Molecular Model of a Soluble Guanylyl Cyclase Fragment Determined by Small-Angle X-ray Scattering and Chemical Cross-Linking. Biochemistry 2013 52:1568-82

A. Ahmed and F. Tama. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data. J. Struct. Biol. 2013 182: 67-7

B.A.J. Baumann, D.W. Taylor, Z. Huang, F. Tama, P.M. Fagnant, K.M. Trybus and K. Taylor. Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation, J Mol Biol. 2012 415:274-87

A. Ahmed, P.C. Whitford, K.Y. Sanbonmatsu and F. Tama. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data, J. Struc. Biol 2012 177:561-70

J. Baker, SH Wright and F.Tama. Simulations of substrate transport in the multidrug transporter EmrD, Proteins 2012 80:1620-32

Zhang, X. He, J. Baker, F. Tama, G. Chang and S.H. Wright Twelve Transmembrane Helices form the functional core of Mammalian Mate1, J. Biol. Chem. 2012 287:27971-82

O. Miyashita, C. Gorba and F. Tama. Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis. J. Struc. Biol., 2011 173:451-60

P.C. Whitford, A. Ahmed, Y. Yu, S.P. Hennelly, F. Tama, C.M.T. Spahn, J.N. Onuchic and K.Y. Sanbonmatsu. Atomic Details of Ribosomal Translocation Revealed Through Simulation Based Modeling, Proc. Natl. Acad. Sci. USA 2011 108:18943-8

I. Grubisic, M.N. Shokhirev, M. Orzechowski, O. Miyashita and F. Tama. Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps J. Struc. Biol., 2010 169:95-105

Katayama, J. Wang, F. Tama, L. Chollet, E. Gogol, R Collier, M. Fisher. Three-Dimensional Structure of the Anthrax Toxin Pore Inserted into Lipid Nanodiscs and Lipid Vesicles. Proc. Natl. Acad. Sci. USA 2010 7:3453-7

C. Gorba and F. Tama. Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data. Bioinformatics and biology insights 2010 4:43-54

C. Gorba, O. Miyashita and F. Tama. Computational methods for flexible fitting of high-resolution structure toward low-resolution 1 dimensional data Biophys. J. 2010 94:1589-1599

Orzechowski and F. Tama. Flexible fitting of high-resolution X-ray structures into cryo-electron microscopy maps using biased Molecular Dynamics simulations Biophys. J. 2008 95: 5692-5705

R. Konecny, J. Trylska, F. Tama, D. Zhang , NA. Baker, CL. Brooks III and JA. McCammon. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 2006 82: 106-120

B. Sherman, R. H. Guenther, F. Tama, T. L. Sit, CL. Brooks III, A. M. Mikhailov, E. V. Orlova, T.S. Baker and S. A. Lommel Removal of Divalent Cations Induces Structural Transitions in Red clover necrotic mosaic virus Revealing a Potential Mechanism for RNA Release J. Virology, 2006 80: 10395-10406

F. Tama, G. Ren, CL. Brooks III and AK. Mitra Model of the toxic complex of anthrax : responsive conformational changes in both the lethal factor rand the protective antigen heptamer. Protein Science, 2006 15: 2190-200

F. Tama and CL. Brooks III. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis.
J. Mol. Biol. 2005 345: 299-314

F. Tama, M. Feig, CL. Brooks, III and KA. Taylor. The Requirement for Mechanical Coupling Between Head and S2 Domains in Smooth Muscle Myosin ATPase Regulation and its Implications for Dimeric Motor Function J. Mol. Biol. 2005 345: 837-854

J. Falke, F. Tama, CL. Brooks III, EP. Gogol and MT. Fisher. The 13 Å Structure of a Chaperonin GroEL-Protein Substrate complex by Cryo-Electron Microscopy. J. Mol. Biol. 2005 348: 219-230

Mitra, C. Scaffitzel, T. Shaikh, F. Tama, S. Jenni, CL. Brooks III, N. Ban and J. Frank. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 2005 438: 318-324

W. Wriggers, P. Chacon, J. Kovacs, F. Tama and S. Birmanns. Topology representing Neural Networks reconcile biomolecular shape structure and dynamics. Neurocomputing 2004 56: 365-379

J. Trylska, R. Konecny, F. Tama, CL. Brooks III and JA McCammon. Motions of the ribosome modulate electrostatic properties. Biopolymers 2004 74: 423-431

F. Tama, O. Miyashita and CL. Brooks III. NMFF: Flexible high-resolution annotation of low-resolution experimental data from cryo-EM maps using normal mode analysis.
 J. Struc. Biol. 2004 147: 315-326

F. Tama, O. Miyashita and CL. Brooks, III. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.
 J. Mol. Biol. 2004 337: 985-999

F. Tama, M. Valle, J. Frank and CL Brooks III. Understanding the ratchet-like inter-subunit reorganization of the ribosome. 
Proc. Natl. Acad. Sci. USA 2003 100: 9319-9323

P. Chacon, F. Tama and W. Wriggers. Mega-dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 2003 326: 485-492

F. Tama and CL. Brooks III. Exploring Large-Scale Conformational Changes in Virus Maturation.
J. Mol. Biol. 2002 318: 733-747

F. Tama, W. Wriggers and CL. Brooks III. Exploring global distortions of biological macromolecules from low-resolution structural information and elastic network theory.
 J. Mol. Biol. 2002 321: 297-305

F. Tama and Y.H. Sanejouand. Conformational change of Proteins arising from Normal Mode Analysis.
Protein. Eng. 2001 14: 1-6

F. Tama, F.X. Gadea, O. Marques and Y.H. Sanejouand. A building block approach for determining low-frequency normal modes of macromolecules. 
Proteins 2000 41: 1-7

F. Tama, O. Miyashita, A. Kitao and N. Go. Molecular dynamics simulation shows large volume fluctuation of proteins. 
Eur. Biophys. J. 2000 29: 472-480

Advertisements