研究者詳細 - TAMA Florence

論文 - TAMA Florence

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Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging 査読有り

Jin Qiyu, Miyashita Osamu, Tama Florence, Yang Jie, Jonic Slavica

IET IMAGE PROCESSING 12 巻 ( 12 ) 頁： 2264 - 2274 2018年12月

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics 査読有り

Srivastava Ashutosh, Nagai Tetsuro, Srivastava Arpita, Miyashita Osamu, Tama Florence

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 19 巻 ( 11 ) 2018年11月

Gaussian mixture model for coarse-grained modeling from XFEL 査読有り

Nagai Tetsuro, Mochizuki Yuki, Joti Yasumasa, Tama Florence, Miyashita Osamu

OPTICS EXPRESS 26 巻 ( 20 ) 頁： 26734 - 26749 2018年10月

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images 査読有り

Tiwari Sandhya P., Tama Florence, Miyashita Osamu

BMC BIOINFORMATICS 19 巻 2018年9月

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution 査読有り

Nakano Miki, Miyashita Osamu, Jonic Slavica, Tokuhisa Atsushi, Tama Florence

JOURNAL OF SYNCHROTRON RADIATION 25 巻頁： 1010 - 1021 2018年7月

Conformational dynamics of human protein kinase CK2 alpha and its effect on function and inhibition 査読有り

Srivastava Ashutosh, Hirota Tsuyoshi, Irle Stephan, Tama Florence

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 86 巻 ( 3 ) 頁： 344 - 353 2018年3月

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data 査読有り

Miyashita Osamu, Tama Florence

INTEGRATIVE STRUCTURAL BIOLOGY WITH HYBRID METHODS 1105 巻頁： 199 - 217 2018年

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL. 査読有り

Nakano M, Miyashita O, Jonic S, Song C, Nam D, Joti Y, Tama F

Journal of synchrotron radiation 24 巻 ( Pt 4 ) 頁： 727 - 737 2017年7月

Computational investigation of binding and dynamics in Tom20-mitochondrial targeting signal complex

Srivastava A., Miyashita O., Tama F.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46 巻頁： S232 - S232 2017年7月

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations 査読有り

Miyashita Osamu, Kobayashi Chigusa, Mori Takaharu, Sugita Yuji, Tama Florence

JOURNAL OF COMPUTATIONAL CHEMISTRY 38 巻 ( 16 ) 頁： 1447 - 1461 2017年6月

Editorial overview: Macromolecular assemblies 査読有り

Shimizu Toshiyuki, Tama Florence

CURRENT OPINION IN STRUCTURAL BIOLOGY 43 巻頁： VII - ix 2017年4月

構造解析へのハイブリッドアプローチ：電子顕微鏡とX線自由電子レーザーからの実験データの活用

宮下治, タマフロハンス

生物物理 57 巻 ( 2 ) 頁： 90 - 94 2017年

記述言語：日本語出版者・発行元：一般社団法人日本生物物理学会

<p>Hybrid approaches combine computational modeling techniques with low-resolution structural data. Such approaches have proven to be powerful tools to obtain new 3D structural and dynamical information on biological systems. Currently, major applications focus on cryo-EM data. Methods and some applications to construct atomic structural models of new functional states will be reviewed. In addition, possible extension to data from X-ray free electron laser, which currently provides low-resolution data, will be discussed.</p>

DOI： 10.2142/biophys.57.090

Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory 査読有り

Nakano Miki, Tateishi-Karimata Hisae, Tanaka Shigenori, Tama Florence, Miyashita Osamu, Nakano Shu-ichi, Sugimoto Naoki

CHEMICAL PHYSICS LETTERS 660 巻頁： 250 - 255 2016年9月

Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns 査読有り

Tokuhisa Atsushi, Jonic Slavica, Tama Florence, Miyashita Osamu

JOURNAL OF STRUCTURAL BIOLOGY 194 巻 ( 3 ) 頁： 325 - 336 2016年6月

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory 査読有り

Nakano Miki, Tateishi-Karimata Hisae, Tanaka Shigenori, Tama Florence, Miyashita Osamu, Nakano Shu-ichi, Sugimoto Naoki

NUCLEIC ACIDS RESEARCH 43 巻 ( 21 ) 頁： 10114-10125 2015年12月

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol 査読有り

Carlos Oscar S. Sorzano, Jose Miguel de la Rosa-Trevin, Florence Tama, Slavica Jonic

JOURNAL OF STRUCTURAL BIOLOGY 188 巻 ( 2 ) 頁： 134 - 141 2014年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ACADEMIC PRESS INC ELSEVIER SCIENCE

This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction. (C) 2014 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.jsb.2014.09.005

Web of Science

Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins 査読有り

Sunita Patel, Elizabeth Vierling, Florence Tama

BIOPHYSICAL JOURNAL 106 巻 ( 12 ) 頁： 2644 - 2655 2014年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：CELL PRESS

The small heat shock proteins (sHSPs) are a virtually ubiquitous and diverse group of molecular chaperones that can bind and protect unfolding proteins from irreversible aggregation. It has been suggested that intrinsic disorder of the N-terminal arm (NTA) of sHSPs is important for substrate recognition. To investigate conformations of the NTA that could recognize substrates we performed replica exchange molecular dynamics simulations. Behavior at normal and stress temperatures of the dimeric building blocks of dodecameric HSPs from wheat (Ta16.9) and pea (Ps18.1) were compared because they display high sequence similarity, but Ps18.1 is more efficient in binding specific substrates. In our simulations, the NTAs of the dimer are flexible and dynamic; however, rather than exhibiting highly extended conformations they retain considerable alpha-helical character and contacts with the conserved alpha-crystallin domain (ACD). Network analysis and clustering methods reveal that there are two major conformational forms designated either "open" or "closed" based on the relative position of the two NTAs and their hydrophobic solvent accessible surface area. The equilibrium constant for the closed to open transition is significantly different for Ta16.9 and Ps18.1, with the latter showing more open conformations at elevated temperature correlated with its more effective chaperone activity. In addition, the Ps18.1 NTAs have more hydrophobic solvent accessible surface than those of Ta16.9. NTA hydrophobic patches are comparable in size to the area buried in many protein-protein interactions, which would enable sHSPs to bind early unfolding intermediates. Reduced interactions of the Ps18.1 NTAs with each other and with the ACD contribute to the differences in dynamics and hydrophobic surface area of the two sHSPs. These data support a major role for the conformational equilibrium of the NTA in substrate binding and indicate features of the NTA that contribute to sHSP chaperone efficiency.

DOI： 10.1016/j.bpj.2014.04.048

Web of Science

Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging 査読有り

Marcus Gallagher-Jones, Yoshitaka Bessho, Sunam Kim, Jaehyun Park, Sangsoo Kim, Daewoong Nam, Chan Kim, Yoonhee Kim, Do Young Noh, Osamu Miyashita, Florence Tama, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Kensuke Tono, Yoshiki Kohmura, Makina Yabashi, S. Samar Hasnain, Tetsuya Ishikawa, Changyong Song

NATURE COMMUNICATIONS 5 巻 2014年5月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：NATURE PUBLISHING GROUP

Nanostructures formed from biological macromolecular complexes utilizing the self-assembly properties of smaller building blocks such as DNA and RNA hold promise for many applications, including sensing and drug delivery. New tools are required for their structural characterization. Intense, femtosecond X-ray pulses from X-ray free-electron lasers enable single-shot imaging allowing for instantaneous views of nanostructures at ambient temperatures. When combined judiciously with synchrotron X-rays of a complimentary nature, suitable for observing steady-state features, it is possible to perform ab initio structural investigation. Here we demonstrate a successful combination of femtosecond X-ray single-shot diffraction with an X-ray free-electron laser and coherent diffraction imaging with synchrotron X-rays to provide an insight into the nanostructure formation of a biological macromolecular complex: RNA interference microsponges. This newly introduced multimodal analysis with coherent X-rays can be applied to unveil nano-scale structural motifs from functional nanomaterials or biological nanocomplexes, without requiring a priori knowledge.

DOI： 10.1038/ncomms4798

Web of Science

Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes 査読有り

Qiyu Jin, Carlos Oscar S. Sorzano, Jose Miguel de la Rosa-Trevin, Jose Roman Bilbao-Castro, Rafael Nunez-Ramirez, Oscar Llorca, Florence Tama, Slavica Jonic

STRUCTURE 22 巻 ( 3 ) 頁： 496 - 506 2014年3月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：CELL PRESS

This article presents a method to study large-scale conformational changes by combining electron microscopy (EM) single-particle image analysis and normal mode analysis (NMA). It is referred to as HEMNMA, which stands for hybrid electron microscopy normal mode analysis. NMA of a reference structure (atomic-resolution structure or EM volume) is used to predict possible motions that are then confronted with EM images within an automatic iterative elastic 3D-to-2D alignment procedure to identify actual motions in the imaged samples. HEMNMA can be used to extensively analyze the conformational changes and may be used in combination with classic discrete procedures. The identified conformations allow modeling of deformation pathways compatible with the experimental data. HEMNMA was tested with synthetic and experimental data sets of E. coli 70S ribosome, DNA polymerase Pol alpha and B subunit complex of the eukaryotic primosome, and tomato bushy stunt virus.

DOI： 10.1016/j.str.2014.01.004

Web of Science

ELASTIC IMAGE REGISTRATION TO FULLY EXPLORE MACROMOLECULAR DYNAMICS BY ELECTRON MICROSCOPY 査読有り

Jin Qiyu, Sanchez Sorzano Carlos Oscar, Callebaut Isabelle, Tama Florence, Jonic Slavica

2014 IEEE INTERNATIONAL CONFERENCE ON IMAGE PROCESSING (ICIP) 頁： 2075-2079 2014年

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