2025年度

4/14 相場

Giessen, et al., “Large protein organelles form a new iron seqestration system with high storage capacity” eLife, 2019,

https://elifesciences.org/articles/46070

4/21 一宮

Wagschal, et al., “Chromohalobacter salixigens uronate dehydrogenase: directed evolution for improved thermal stability and mutant CsUDH-inc X-ray crystal structure” Process Biochem. 2022.

https://www.sciencedirect.com/science/article/pii/S1359511319310992?via%3Dihub

4/28 杉崎

Ohara, et al., “Reversible assembly of an artificial protein nanocage using alkaline earth metal ions” J. Am. Chem. Soc. (2023).

https://pubs.acs.org/doi/10.1021/jacs.2c09537


6/2 相場

Zheng, et al, “Observation of the Protein-Inorganic Interface of Ferritin by Cryo-Electron Microscopy” J. Am. Chem. Soc. (2025)
https://pubs.acs.org/doi/10.1021/jacs.4c13873

6/9 一宮

Sun, et al, “Regulation of acetyl-coa biosynthesis via an intertwined acetyl-coa synthetase/acetyltransferase complex” Nat. Commun. (2025)

https://www.nature.com/articles/s41467-025-57842-2

7/14 吉田
Mori et al., “Molecular basis for the diversification of lincosamide biosynthesis by pyridoxal phosphte-dependent enzymes” Nat. Chem. (2024).

https://www.nature.com/articles/s41557-024-01687-7

8/11 杉崎

Murakawa, et al, “Neutoron crystallography of a semiquinone radical intermediate of copper amine oxidase reveals a substrate-assisted conformational change of the peptidyl quinone cofactor” ACS Catal. (2023)

https://pubs.acs.org/doi/10.1021/acscatal.3c02629

10/27 一宮
Pak, et al. , “Using AlphaFold to predict the impact of single mutations on protein stability and function” PLoS One (2023)
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0282689

11/17 杉崎

Steinhilper et al., “Two-stage binding of mitochondrial ferredoxin-2 to the core iron-sulfur cluster assembly complex” Nat. Commun. (2025)

https://www.nature.com/articles/s41467-024-54585-4


11/10 相場

Wagner, et al., “Visualizing chaperonin function in situ by cryo-electron tomography” Nature (2024)

https://www.nature.com/articles/s41586-024-07843-w


12/15 一宮　

Kshirsagar, et al., “Rapid accurate prediction of protein homo-oligomer symmetry using Seq2Symm” Nat. Commun (2025).


https://www.nature.com/articles/s41467-025-57148-3


12/15 杉崎

Yang, et al., “Crystal structure of the iron-sulfur cluster transfer protein ApbC from Escherichia coli” Biochem. Biophys. Res. Commun. (2024).

https://www.sciencedirect.com/science/article/pii/S0006291X24007034

Lab_seminar

原則、対面で実施＠セミナー室１、２、9:30開始

論文紹介（journal club）

(1) 発表の１週間前に全員に紹介する予定の原著論文のpdfとsupporting information(word、excel,   

      or pdf)を、全員にメール添付で送る。

(2)   また、発表前日までに、発表のpowerpointスライドを全員にメール添付で送る。

(3)   紹介する論文は最新のもの（２年以内をめど）を、１報選ぶ。

(4)   過去に紹介された論文は不可（下記の以前の論文リストも参考に）である。

(5)   紹介する論文を選ぶ際には、なぜ選んだか、その理由も考えておくこと。

(6)   内容理解、発表のために、選んだ論文が引用した重要な論文も、調べておくこと。

(7)   発表は２０-３０分程度を目安に、

       研究の背景、目的、意義、方法、結果、考察、展望などを、筋道を立てて話すこと。

(8)   必要に応じ、発表のスライドには引用文献を適宜入れること。


研究報告 (progress report)

(1) 発表前日までに、発表のpowerpointスライドを全員にメール添付で送る。

(2)  発表は２０-３０分程度を目安に、

       研究の背景、目的、意義、方法、結果、考察、展望などを、筋道を立てて話すこと。

(3)  必要に応じ、発表のスライドには引用文献を適宜入れること。

2024年度
4/22 吉田
Purcell, et al., “Iron-sulfur cluster assembly scaffold protein IscU is required for activation of ferric updtake regulator (Fur) in Escherichia coli” J. Biol. Chem. 2024, 300, 107142.
https://www.sciencedirect.com/science/article/pii/S0021925824016375?via%3Dihub

6/3 相塲 
Wang, et al., “One-pot de novo synthesis of [4Fe-4S] protein using a recombinant SUF system under aerobic conditioins.” ACS Synth. Biol. 2023.
https://pubs.acs.org/doi/full/10.1021/acssynbio.3c00155

6/10 吉田

Schulz, et al. “Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2”. Nat. Commun. 2024. 15 3299.
https://www.nature.com/articles/s41467-024-47310-8

7/1 宍戸

Taraska, et al., “Short-distance probes for protein backbone structure based on energy transfer between bimane and transition metal ions”. PNAS. 2009, 106, 16227-16232.
https://www.pnas.org/doi/full/10.1073/pnas.0905207106

7/29 相塲
Clarkson, et al. “The hyperthermophilic archaeon Pyrococcus furiosus utilizes environmental iron sulfide cluster complexes as an iron source” Extremophiles (2021) 25:249-256
https://link.springer.com/article/10.1007/s00792-021-01224-1

8/6 田尻
Zivanovic, et al., “Selective persulfide detection reveals evolutionarily conserved anti-aging effects of S-sulfhydration” Cell Metab. (2019) 30(6) 1152-1170.
https://www.sciencedirect.com/science/article/pii/S1550413119305625?via%3Dihub

9/2 田尻
Ida, et al. “Reactive cysteine persulfides and S-polythiolation regulate oxidative stress and redox signaling” PNAS (2014) 111(21) , 7606-7611.
https://www.pnas.org/doi/full/10.1073/pnas.1321232111

9/9 宍戸
Siepi, et al., “Fluorescent peptide dH3w: A sensor for environmental monitoring of mercury (II)” PLos One (2018) 13(10) e0204164.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204164

10/7  相塲
Saini, J., et al., “The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans”. Sci. Rep. (2023), 13, 15120.
https://www.nature.com/articles/s41598-023-42400-x

10/28 宍戸
Fatima, S., et al. “Engineering a Conformationally Switchable Artifficial Metalloprotein”

J. Am. Chem. Soc. (2022), 144, 21606-21616.
https://pubs.acs.org/doi/10.1021/jacs.2c08885

10/28 田尻
Shaposhnikov, M. V., et al., “Simultaneous activation off the hydrogen sulfide biosynthesis ggenes (CBS and CSE) induces sex-specific geroprotective efffects in Drosophila melanogaster.” Biogeromtology, (2023), 24, 275-292.
https://link.springer.com/article/10.1007/s10522-023-10017-2

11/25 宍戸
Wang, L., et al. “Exploring the interaction between Cry1Ac protein and Zn2+, Cd2+ metal ions by fluorescence quenching and molecular docking approaches” Chemosphere (2022), 297 134105.
https://www.sciencedirect.com/science/article/pii/S0045653522005987

11/25 田尻
Araki, S., et al., Cystathionine γ-lyase self-inactivates by polysulfidation during cystine metabolism”, Int. J. Mol. Sci. (2023), 24, 9982.
https://www.mdpi.com/1422-0067/24/12/9982

12/23 吉田
Bu, et al., “Structural Basisi of the Inhibition of L-methionine γ-lyase from Fusobacterium nucleatum” Int. J. Mol. Sci. (2023) 24, 1651.
https://www.mdpi.com/1422-0067/24/2/1651

12/23  相塲
Wu, et al. “Characterization of membrane-bound sulfane reductase: A missing link in the evolution of modern day respiratory complexes” J. Biol. Chem. (2018) 293 ,16687-16696
https://www.jbc.org/article/S0021-9258(20)33233-6/fulltext


2023年度
5/1 大塚
Hsiao, et al., “Crystal structure of the α-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer” Frontier.Chem. 2022
https://www.frontiersin.org/articles/10.3389/fchem.2022.1001311/full

5/15 吉田
Vaccaro, et al., “Biological iron-sulfur storage in a thioferrate-protein nanoparticle” Nat. Commun. 2017
https://www.nature.com/articles/ncomms16110

5/29 小川
Jespersen, et al. “Structures of the sulfite detoxifying F420-dependent enzyme from Methanococcales” Nat. Chem. Biol. 2022
https://www.nature.com/articles/s41589-022-01232-y

6/19 宍戸
Biester, et al. “Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase” J. Inorg. Biochem. 2022
https://www.sciencedirect.com/science/article/pii/S0162013422000630

6/26 林
Pang, Y. et al., “Roles of conserved active site residues in the IscS Cysteine desulfurase reaction” Front. Microbiol. (2023)
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1084205/full

7/6 大塚
Matoba, Y., et al. “Cyclization mechanisms catalyzed by an ATP-grasp enzyme essential for D-cycloserine biosynthesis”  FEBS J. (2020), 287, 2763-2778.
https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.15163

7/31 吉田
Vali, SW, et al., “The Pyrococcus furiosus ironome is dominated by [Fe4S4]2+ clusters or thioferrate-like iron depndening on the availability of elemental sulfur” J. Biol. Chem. (2021) 296, 100710
https://www.jbc.org/article/S0021-9258(21)00499-3/fulltext

8/28 小川
Nim, et al., “Delivering a toxic metal to the active site of urease” Sci. Adv. (2023) 9 eadf7790

https://www.science.org/doi/10.1126/sciadv.adf7790

10/2 宍戸
Kim, et al., “Metal-induced fluorescence quenching of photoconvertible fluorescent protein DendFP”

https://www.mdpi.com/1420-3049/27/9/2922

10/23 林

Bennett, et al., “Native mass spectrosmetric studies of IscSU reveal a cncerted, sulfur-initiated mechanism of iron-sulfur cluster assembly”
https://pubs.rsc.org/en/content/articlelanding/2023/sc/d2sc04169c

10/23 大塚

Shatalin, et al. “Inhibitors of bacterial H2S biogenesis targeting antibiotic resistance and tolerance”

https://www.science.org/doi/full/10.1126/science.abd8377


11/6 林
Karunakaran, et al. “ Structurall analysis of Atopobium parvulum SufS cystgeine desulfurase linked to Crohn’s disease” FEBS Lett. 2022

https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14295

11/13 小川
Gabler, et al., “Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species” Protein Sci. (2023)
https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4788

11/13 吉田
Martic, et al., “Heterometallic [AgFe3S4] ferredoxin variants: synthesis, characterization , and the first crystal structure of an engineered heterometallic iron-sulfur protein”  J. Biol. Inorg. Chem. (2013)
https://link.springer.com/article/10.1007/s00775-012-0971-3

11/20 宍戸
Zou, et al, “Mutant Flavin-based fluorescent protein sensors for detedting intracellular zinc and copper in Escherichia coli”  (2022)
https://pubs.acs.org/doi/10.1021/acssensors.2c01376

12/11 大塚
Matoba, et al., “Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for D-cycloserine biosynthesis” (2020) FEBS J.

https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.15163

12/18 林
Silva, et al., “Structural basis of RICs iron donation for iron-sulfur cluster biogenesis” Front. Microbiol. (2021)
https://www.frontiersin.org/articles/10.3389/fmicb.2021.670681/full

12/15 大塚
Pederick, et al., “D-alanine-D-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalet cations” J. Biol. Chem. (2023)
https://www.jbc.org/article/S0021-9258(17)49431-2/fulltext

12/25 吉田
Basak, et al,, “Stepwise O2-induced rearrangement and disassembly of the [NiFe4(OH)(u3-S)4] Active site cluster of CO dehydrogenase” (2023)
https://onlinelibrary.wiley.com/doi/10.1002/anie.202305341

 

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