Faculty Profiles - TAMA Florence

Papers - TAMA Florence

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Applications of coarse-grained and multiscale modeling. Reviewed International journal

Yennamalli RM, Tama F

Biophysical journal Vol. 125 ( 2 ) page： E1 - E4 2026.1

Visualizing the Functional Dynamics of P-Glycoprotein and Its Modulation by Elacridar via High-Speed Atomic Force Microscopy. Reviewed International journal Open Access

Kanaoka Y, Hamaguchi-Suzuki N, Nonaka Y, Yamashita S, Miyashita O, Ito A, Ogasawara S, Tama F, Murata T, Uchihashi T

International journal of molecular sciences Vol. 27 ( 1 ) 2025.12

Local peptide signalling induces stomatal closure under drought stress. Reviewed International journal Open Access

Shimotohno A, Matsubayashi Y, Du Y, Senthilvadivel V, Suzuki T, Kato H, Kesherwani M, Kono M, Mishiro-Sato E, Kano K, Kojima M, Takebayashi Y, Sakakibara H, Soma F, Tama F, Hirota T, Torii KU, Yamaguchi-Shinozaki K, Fukuda H

Nature communications Vol. 17 ( 1 ) page： 177 2025.12

Single-Cell Fluorescence Analysis of Lipid Droplet Compositional Dynamics during Triacylglycerol Catabolism Reviewed International journal

Junwei Wang, Keiji Kajiwara, Manish Kesherwani, Florence Tama, Yuki Ohsaki, Shigehiro Yamaguchi, Masayasu Taki

Journal of the American Chemical Society Vol. 147 page： 41514 2025.10

Flexible Fitting to Infer Atomistic-Precision Models of Large-Amplitude Conformational Dynamics in Biomolecules from High-Speed Atomic Force Microscopy Imaging Reviewed International journal Open Access

Romain Amyot, Osamu Miyashita, Xuan Wu, Kazusa Takeda, Noriyuki Kodera, Hiroki Konno, Florence Tama, Holger Flechsig

ACS Nano Vol. 19 page： 34065 - 34079 2025.9

Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations Reviewed International journal Open Access

Raghavan, SS; Shinoda, K; Nango, E; Tama, F; Miyashita, O

STRUCTURAL DYNAMICS-US Vol. 12 ( 5 ) 2025.9

Energy-Efficient Neural Network Training for Scientific Datasets with Advanced Similarity Analytics and Orchestration Reviewed International coauthorship International journal

NG KW.; Yildiz O.; Peterka T.; , Tama F.; Osamu Miyashita O.; Schuman C.; Taufer M.

International Conference on Computational Science page： 756 - 765 2025.6

Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis. Reviewed International journal

Xuan Wu, Osamu Miyashita, Florence Tama

The journal of physical chemistry. B 2024.9

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

Observing a single biomolecule performing its function is fundamental in biophysics as it provides important information for elucidating the mechanism. High-speed atomic force microscopy (HS-AFM) is a unique and powerful technique that allows the observation of biomolecular motion in a near-native environment. However, the spatial resolution of HS-AFM is limited by the physical size of the cantilever tip, which restricts the ability to obtain atomic details of molecules. In this study, we propose a novel computational algorithm designed to derive atomistic models of conformational dynamics from AFM images. Our method uses normal-mode analysis to describe the expected motions of the molecule, allowing these motions to be represented with a limited number of coordinates. This approach mitigates the problem of overinterpretation inherent in the analysis of AFM images with limited resolution. We demonstrate the effectiveness of our algorithm, NMFF-AFM, using synthetic data sets for three proteins that undergo significant conformational changes. NMFF-AFM is a fast and user-friendly program that requires minimal setup and has the potential to be a valuable tool for biophysical studies using HS-AFM.

DOI： 10.1021/acs.jpcb.4c04189

PubMed

Data Science for Integrated Dynamic Structural Biology-the 21st IUPAB Congress session summary commentary Invited Reviewed International coauthorship International journal

BIOPHYSICAL REVIEWS 2024.9

Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging. Reviewed International journal Open Access

Wu Q, Taki M, Tanaka Y, Kesherwani M, Phung QM, Enoki S, Okada Y, Tama F, Yamaguchi S

Angewandte Chemie (International ed. in English) page： e202400711 2024.2

Structure determination using high-order spatial correlations in single-particle X-ray scattering Reviewed Open Access

Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama

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

Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches. Invited Reviewed International journal Open Access

Miyashita O, Tama F

Current opinion in structural biology Vol. 82 page： 102653 2023.7

MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation. Reviewed International coauthorship International journal Open Access

Vuillemot R, Mirzaei A, Harastani M, Hamitouche I, Fréchin L, Klaholz BP, Miyashita O, Tama F, Rouiller I, Jonic S

Journal of molecular biology Vol. 435 ( 9 ) page： 167951 2023.5

Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction Reviewed International journal Open Access

Nakano Miki, Miyashita Osamu, Tama Florence

STRUCTURAL DYNAMICS-US Vol. 10 ( 2 ) 2023.3

Composable Workflow for Accelerating Neural Architecture Search Using In Situ Analytics for Protein Classification Reviewed International coauthorship International journal

Charming, G; Patel, R; Olaya, P; Rorabaugh, AK; Miyashita, O; Caino-Lores, S; Schuman, C; Tama, F; Taufer, M

PROCEEDINGS OF THE 52ND INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, ICPP 2023 page： 756 - 765 2023

SWEET13 transport of sucrose, but not gibberellin, restores male fertility in Arabidopsis sweet13;14. Reviewed International journal Open Access

Isoda R, Palmai Z, Yoshinari A, Chen LQ, Tama F, Frommer WB, Nakamura M

Proceedings of the National Academy of Sciences of the United States of America Vol. 119 ( 42 ) page： e2207558119 2022.10

CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy. Reviewed International journal Open Access

Miller S, Kesherwani M, Chan P, Nagai Y, Yagi M, Cope J, Tama F, Kay SA, Hirota T

Proceedings of the National Academy of Sciences of the United States of America Vol. 119 ( 40 ) page： e2203936119 2022.10

Three-dimensional structure determination of gold nanotriangles in solution using X-ray free-electron laser single-particle analysis Reviewed International journal Open Access

Miki Nakano, Osamu Miyashita, Yasumasa Joti, Akihiro Suzuki, Hideyuki Mitomo, Yoshiya Niida, Ying Yang, Hirokatsu Yumoto, Takahisa Koyama, Kensuke Tono, Haruhiko Ohashi, Makina Yabashi, Tetsuya Ishikawa, YOSHITAKA BESSHO, Kuniharu Ijiro, Yoshinori Nishino, Florence Tama

Optica Vol. 9 ( 7 ) page： 776 - 784 2022.7

High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis. Reviewed International journal Open Access

Kunio Nakata, Naoyuki Miyazaki, Hiroki Yamaguchi, Mika Hirose, Tatsuki Kashiwagi, Nidamarthi H V Kutumbarao, Osamu Miyashita, Florence Tama, Hiroshi Miyano, Toshimi Mizukoshi, Kenji Iwasaki

Journal of structural biology Vol. 214 ( 2 ) page： 107842 - 107842 2022.6

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

In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called "bifid shunt." The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D4 symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546-D547-H548-N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to "closed" and "open" states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

DOI： 10.1016/j.jsb.2022.107842

Web of Science

PubMed

Light-Control over Casein Kinase 1δ Activity with Photopharmacology: A Clear Case for Arylazopyrazole-Based Inhibitors. Reviewed International journal Open Access

Albert M Schulte, Dušan Kolarski, Vidya Sundaram, Ashutosh Srivastava, Florence Tama, Ben L Feringa, Wiktor Szymanski

International journal of molecular sciences Vol. 23 ( 10 ) 2022.5

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

Protein kinases are responsible for healthy cellular processes and signalling pathways, and their dysfunction is the basis of many pathologies. There are numerous small molecule inhibitors of protein kinases that systemically regulate dysfunctional signalling processes. However, attaining selectivity in kinase inhibition within the complex human kinome is still a challenge that inspires unconventional approaches. One of those approaches is photopharmacology, which uses light-controlled bioactive molecules to selectively activate drugs only at the intended space and time, thereby avoiding side effects outside of the irradiated area. Still, in the context of kinase inhibition, photopharmacology has thus far been rather unsuccessful in providing light-controlled drugs. Here, we present the discovery and optimisation of a photoswitchable inhibitor of casein kinase 1δ (CK1δ), important for the control of cell differentiation, circadian rhythm, DNA repair, apoptosis, and numerous other signalling processes. Varying the position at which the light-responsive azobenzene moiety has been introduced into a known CK1δ inhibitor, LH846, revealed the preferred regioisomer for efficient photo-modulation of inhibitory activity, but the photoswitchable inhibitor suffered from sub-optimal (photo)chemical properties. Replacement of the bis-phenyl azobenzene group with the arylazopyrazole moiety yielded a superior photoswitch with very high photostationary state distributions, increased solubility and a 10-fold difference in activity between irradiated and thermally adapted samples. The reasons behind those findings are explored with molecular docking and molecular dynamics simulations. Results described here show how the evaluation of privileged molecular architecture, followed by the optimisation of the photoswitchable unit, is a valuable strategy for the challenging design of the photoswitchable kinase inhibitors.

DOI： 10.3390/ijms23105326

Open Access

Web of Science

PubMed

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