Faculty Profiles - TAMA Florence

Xphase3d: Memory-Distributed Phase Retrieval for Reconstructing Large-Scale 3D Density Maps of Biological Macromolecules Reviewed International journal

Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama

2024 IEEE International Conference on Cluster Computing (CLUSTER) page： 394 - 402 2024.9

Structure determination using high-order spatial correlations in single-particle X-ray scattering. Reviewed International journal

Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama

IUCrJ Vol. 11 ( Pt 1 ) page： 92 - 108 2024.1

Language：English Publishing type：Research paper (scientific journal)

Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns. Here, a method is proposed to determine the 3D structure of a sample by analyzing the double, triple and quadruple spatial correlations in diffraction patterns. This ab initio method can reconstruct the basic shape of an irregular unsymmetric 3D sample without requiring any prior knowledge of the sample. The impact of background and noise on correlations is investigated and corrected to ensure the success of reconstruction under simulated experimental conditions. Additionally, the feasibility of using the correlation-based approach to process incomplete partial diffraction patterns is demonstrated. The proposed method is a variable addition to existing algorithms for 3D reconstruction and will further promote the development and adoption of XFEL single-particle imaging techniques.

DOI： 10.1107/S2052252523009831

Controlling the Circadian Clock with High Temporal Resolution through Photodosing. Reviewed International journal Open Access

Kolarski D, Sugiyama A, Breton G, Rakers C, Ono D, Schulte A, Tama F, Itami K, Szymanski W, Hirota T, Feringa BL

Journal of the American Chemical Society Vol. 141 ( 40 ) page： 15784 - 15791 2019.10

Language：Japanese Publishing type：Research paper (scientific journal)

Circadian clocks, biological timekeepers that are present in almost every cell of our body, are complex systems whose disruption is connected to various diseases. Controlling cellular clock function with high temporal resolution in an inducible manner would yield an innovative approach for the circadian rhythm regulation. In the present study, we present structure-guided incorporation of photoremovable protecting groups into a circadian clock modifier, longdaysin, which inhibits casein kinase I (CKI). Using photodeprotection by UV or visible light (400 nm) as the external stimulus, we have achieved quantitative and light-inducible control over the CKI activity accompanied by an accurate regulation of circadian period in cultured human cells and mouse tissues, as well as in living zebrafish. This research paves the way for the application of photodosing in achieving precise temporal control over the biological timing and opens the door for chronophotopharmacology to deeper understand the circadian clock system.

DOI： 10.1021/jacs.9b05445

Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS. Reviewed Open Access

Putarjunan A, Ruble J, Srivastava A, Zhao C, Rychel AL, Hofstetter AK, Tang X, Zhu JK, Tama F, Zheng N, Torii KU

Nature plants Vol. 5 ( 7 ) page： 742 - 754 2019.7

Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations. Reviewed Open Access

Nagai T, Tama F, Miyashita O

Biophysical journal Vol. 116 ( 3 ) page： 395 - 405 2019.2

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning Reviewed Open Access

Mori Takaharu, Kulik Marta, Miyashita Osamu, Jung Jaewoon, Tama Florence, Sugita Yuji

STRUCTURE Vol. 27 ( 1 ) page： 161 - + 2019.1

Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth. Reviewed International journal Open Access

Oshima T, Niwa Y, Kuwata K, Srivastava A, Hyoda T, Tsuchiya Y, Kumagai M, Tsuyuguchi M, Tamaru T, Sugiyama A, Ono N, Zolboot N, Aikawa Y, Oishi S, Nonami A, Arai F, Hagihara S, Yamaguchi J, Tama F, Kunisaki Y, Yagita K, Ikeda M, Kinoshita T, Kay SA, Itami K, Hirota T

Science advances Vol. 5 ( 1 ) page： eaau9060 2019.1

Language：Japanese Publishing type：Research paper (scientific journal)

Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type-dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.

DOI： 10.1126/sciadv.aau9060

Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes Reviewed

Srivastava Arpita, Tama Florence, Kohda Daisuke, Miyashita Osamu

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 87 ( 1 ) page： 81 - 90 2019.1

Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching. Reviewed Open Access

Miki Nakano, Osamu Miyashita, Florence Tama

Biophysics and physicobiology Vol. 16 page： 367 - 376 2019

Language：Japanese Publishing type：Research paper (scientific journal)

Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL.

DOI： 10.2142/biophysico.16.0_367

Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging Reviewed Open Access

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

IET IMAGE PROCESSING Vol. 12 ( 12 ) page： 2264 - 2274 2018.12

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Reviewed Open Access

Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F

International journal of molecular sciences Vol. 19 ( 11 ) 2018.11

Gaussian mixture model for coarse-grained modeling from XFEL. Reviewed Open Access

Nagai T, Mochizuki Y, Joti Y, Tama F, Miyashita O

Optics express Vol. 26 ( 20 ) page： 26734 - 26749 2018.10

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images Reviewed Open Access

Tiwari Sandhya P, Tama Florence, Miyashita Osamu

BMC BIOINFORMATICS Vol. 19 2018.9

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：BMC

Background: Advancements in biophysical experimental techniques have pushed the limits in terms of the types of phenomena that can be characterized, the amount of data that can be produced and the resolution at which we can visualize them. Single particle techniques such as Electron Microscopy (EM) and X-ray free electron laser (XFEL) scattering require a large number of 2D images collected to resolve three-dimensional (3D) structures. In this study, we propose a quick strategy to retrieve potential 3D shapes, as low-resolution models, from a few 2D experimental images by searching a library of 2D projection images generated from existing 3D structures.Results: We developed the protocol to assemble a non-redundant set of 3D shapes for generating the 2D image library, and to retrieve potential match 3D shapes for query images, using EM data as a test. In our strategy, we disregard differences in volume size, giving previously unknown structures and conformations a greater number of 3D biological shapes as possible matches. We tested the strategy using images from three EM models as query images for searches against a library of 22750 2D projection images generated from 250 random EM models. We found that our ability to identify 3D shapes that match the query images depends on how complex the outline of the 2D shapes are and whether they are represented in the search image library.Conclusions: Through our computational method, we are able to quickly retrieve a 3D shape from a few 2D projection images. Our approach has the potential for exploring other types of 2D single particle structural data such as from XFEL scattering experiments, for providing a tool to interpret low-resolution data that may be insufficient for 3D reconstruction, and for estimating the mixing of states or conformations that could exist in such experimental data.

DOI： 10.1186/s12859-018-2358-0

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution Reviewed International journal

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

JOURNAL OF SYNCHROTRON RADIATION Vol. 25 ( Pt 4 ) page： 1010 - 1021 2018.7

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：INT UNION CRYSTALLOGRAPHY

Three-dimensional (3D) structures of biomolecules provide insight into their functions. Using X-ray free-electron laser (XFEL) scattering experiments, it was possible to observe biomolecules that are difficult to crystallize, under conditions that are similar to their natural environment. However, resolving 3D structure from XFEL data is not without its challenges. For example, strong beam intensity is required to obtain sufficient diffraction signal and the beam incidence angles to the molecule need to be estimated for diffraction patterns with significant noise. Therefore, it is important to quantitatively assess how the experimental conditions such as the amount of data and their quality affect the expected resolution of the resulting 3D models. In this study, as an example, the restoration of 3D structure of ribosome from two-dimensional diffraction patterns created by simulation is shown. Tests are performed using the diffraction patterns simulated for different beam intensities and using different numbers of these patterns. Guidelines for selecting parameters for slice-matching 3D reconstruction procedures are established. Also, the minimum requirements for XFEL experimental conditions to obtain diffraction patterns for reconstructing molecular structures to a high-resolution of a few nanometers are discussed.

DOI： 10.1107/S1600577518005568

Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition Reviewed Open Access

Ashutosh Srivastava, Tsuyoshi Hirota, Stephan Irle, Florence Tama

Proteins: Structure, Function and Bioinformatics Vol. 86 ( 3 ) page： 344 - 353 2018.3

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：John Wiley and Sons Inc.

Protein kinase, casein kinase II (CK2), is ubiquitously expressed and highly conserved protein kinase that shows constitutive activity. It phosphorylates a diverse set of proteins and plays crucial role in several cellular processes. The catalytic subunit of this enzyme (CK2α) shows remarkable flexibility as evidenced in numerous crystal structures determined till now. Here, using analysis of multiple crystal structures and long timescale molecular dynamics simulations, we explore the conformational flexibility of CK2α. The enzyme shows considerably higher flexibility in the solution as compared to that observed in crystal structure ensemble. Multiple conformations of hinge region, located near the active site, were observed during the dynamics. We further observed that among these multiple conformations, the most populated conformational state was inadequately represented in the crystal structure ensemble. The catalytic spine, was found to be less dismantled in this state as compared to the “open” hinge/αD state crystal structures. The comparison of dynamics in unbound (Apo) state and inhibitor (CX4945) bound state exhibits inhibitor induced suppression in the overall dynamics of the enzyme. This is especially true for functionally important glycine-rich loop above the active site. Together, this work gives novel insights into the dynamics of CK2α in solution and relates it to the function. This work also explains the effect of inhibitor on the dynamics of CK2α and paves way for development of better inhibitors.

DOI： 10.1002/prot.25444

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data. Reviewed

Miyashita O, Tama F

Advances in experimental medicine and biology Vol. 1105 page： 199 - 217 2018

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL. Reviewed Open Access

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

Journal of synchrotron radiation Vol. 24 ( Pt 4 ) page： 727 - 737 2017.7

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：International Union of Crystallography ({IUCr})

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

DOI： 10.1107/S1600577517007767

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

Srivastava A., Miyashita O., Tama F.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Vol. 46 page： S232 - S232 2017.7

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations Reviewed

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

JOURNAL OF COMPUTATIONAL CHEMISTRY Vol. 38 ( 16 ) page： 1447 - 1461 2017.6

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：WILEY

Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low-resolution experimental data by transforming a known structure. A common application is against data from cryo-electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants. Application to simulated maps of Ca2+ ATPase and diphtheria toxin as well as experimental data of release factor 2 revealed that for these systems, multiple conformations with similar agreement with the density map exist and a large number of fitting trials are necessary to generate good models. Clustering analysis can be an effective approach to avoid over-fitting models. In addition, we show that an automatic adjustment of the biasing force constants during the fitting process, implemented as replica-exchange scheme, can improve the success rate. (c) 2017 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.24785