論文メモ
随時更新します。各項目内はおおよそ時系列に並んでいます。
META body
・三浦先生、META body命名 (Condensate Formation by Metabolic Enzymes in Saccharomyces cerevisiae, 2022, https://doi.org/10.3390/microorganisms10020232)
G body
・試験管内での解糖系の最適化(Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis, 2011, https://doi.org/10.1038/nchembio.541)
・赤血球膜内面に集合 (Identification of the Components of a Glycolytic Enzyme Metabolon on the Human Red Blood Cell Membrane, 2013, https://doi.org/10.1074/jbc.M112.428573)
・低酸素条件下でenolaseが集合 (Spatial reorganization of Saccharomyces cerevisiae enolase to alter carbon metabolism under hypoxia,2013 https://doi.org/10.1128/ec.00093-13)
・筋肉細胞 (The Structural and Functional Coordination of Glycolytic Enzymes in Muscle: Evidence of a Metabolon?, 2014, https://doi.org/10.3390/biology3030623)
・アクチンによって安定化 (A glycolytic metabolon in Saccharomyces cerevisiae is stabilized by F-actin, 2013, https://doi.org/10.1111/febs.12387)
・シナプスに局在化 (Glycolytic Enzymes Localize to Synapses under Energy Stress to Support Synaptic Function, 2016, https://doi.org/10.1016/j.neuron.2016.03.011)
・がん細胞、G bodyのサイズによって活性化する経路が変化(Identification of a multienzyme complex for glucose metabolism in living cells, 2017, https://doi.org/10.1074/jbc.m117.783050)
・ホスホフルクトキナーゼ2の天然変性領域のリン酸化 (Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress, 2017, https://doi.org/10.1016/j.celrep.2017.06.082)
・三浦先生、日本語総説 (解糖系酵素の局在制御とリンクした代謝制御, 2020, https://doi.org/10.1271/kagakutoseibutsu.58.10)
・RNAが必要 (RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia, 2020, https://doi.org/10.7554/eLife.48480)
・小スケール低酸素培養 (Small-scale hypoxic cultures for monitoring the spatial reorganization of glycolytic enzymes in Saccharomyces cerevisiae,2021 https://doi.org/10.1002/cbin.11617)
・Noncoding RNA (The long noncoding RNA glycoLINC assembles a lower glycolytic metabolon to promote glycolysis, 2022, https://doi.org/10.1016/j.molcel.2021.11.017)
Purinosome
・発見 (Reversible compartmentalization of de novo purine biosynthetic complexes in living cells, 2008,https://doi.org/10.1126/science.1152241)
・どの酵素が近傍にいるか (Mapping protein-protein proximity in the purinosome, 2012, https://doi.org/10.1074/jbc.M112.407056)
・シャペロンの共局在(Hsp70/Hsp90 chaperone machinery is involved in the assembly of the purinosome, 2013, https://doi.org/10.1073/pnas.1300173110)
・細胞周期に依存する (Purinosome formation as a function of the cell cycle, 2015, https://doi.org/10.1073/pnas.1423009112)
・AMPKによる下方制御 (Sequestration-Mediated Downregulation of de Novo Purine Biosynthesis by AMPK, 2016, https://doi.org/10.1021/acschembio.6b00039)
・ミトコンドリアに局在 (Spatial colocalization and functional link of purinosomes with mitochondria, 2016, https://doi.org/10.1126/science.aac6054)
・2017年時点でのレビュー (A New View into the Regulation of Purine Metabolism: The Purinosome, 2017, https://doi.org/10.1016/j.tibs.2016.09.009)
・ミトコンドリアと微小管 (Microtubule-directed transport of purine metabolons drives their cytosolic transit to mitochondria, 2018, https://doi.org/10.1073/pnas.1814042115)
・低酸素条件下 (Hypoxia drives the assembly of the multienzyme purinosome complex, 2020, https://doi.org/10.1073/pnas.1423009112)
・メタボロミクスと質量分析イメージング (Metabolomics and mass spectrometry imaging reveal channeled de novo purine synthesis in cells, 2020, https://doi.org/10.1126/science.aaz6465)
Metabolon
・メタボロンの概念 (Complexes Of Sequential Metabolic Enzymes, 1987, https://doi.org/10.1146/annurev.bi.56.070187.000513)
・アップデートされた細胞内区画化の概念 (On the origin of intracellular compartmentation and organized metabolic systems, 2004, https://doi.org/10.1023/b:mcbi.0000009855.14648.2c)
・中山先生、日本語総説、フラボノイド合成 (メタボロン…植物二次代謝工学におけるインパクト, 2012, https://www.sbj.or.jp/wp-content/uploads/file/sbj/9009/9009_tokushu-2_4.pdf)
・Krebs Cycle (Krebs Cycle Metabolon: Structural Evidence of Substrate Channeling Revealed by Cross-Linking and Mass Spectrometry, 2015, https://doi.org/10.1002/anie.201409336)
・Krebs Cycle, 代謝物濃度勾配 (Krebs cycle metabolon formation: metabolite concentration gradient enhanced compartmentation of sequential enzymes,2015, https://doi.org/10.1039/C4CC08702J )
・リポソーム上で再構成 (Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum, 2016, https://doi.org/10.1126/science.aag2347)
・TCA Cycle (Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling, 2018, https://doi.org/10.1002/pro.3338)
・蛍光ベースの方法で迫れるか (How to prove the existence of metabolons?, 2018, https://doi.org/10.1007/s11101-017-9509-1 )
・フラボノイド、中間体が不安定な場合(Formation of Flavonoid Metabolons: Functional Significance of Protein-Protein Interactions and Impact on Flavonoid Chemodiversity, 2019, https://doi.org/10.3389/fpls.2019.00821)
・植物細胞におけるメタボロン(Metabolons, Enzyme–Enzyme Assemblies that Mediate Substrate Channeling, and Their Roles in Plant Metabolism, 2020, https://doi.org/10.1016/j.xplc.2020.100081)
・がん細胞 (Metabolon: a novel cellular structure that regulates specific metabolic pathways, 2021, https://doi.org/10.1002/cac2.12154)
Moonlighting Role
・解糖系酵素によってミトコンドリアと葉緑体が共局在する (A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts, 2020, https://doi.org/10.1038/s41467-020-18234-w)
Mathematical Model
・反応拡散系における酵素の最適なクラスタリング (Clustering and Optimal Arrangement of Enzymes in Reaction-Diffusion Systems, 2013, https://doi.org/10.1103/PhysRevLett.110.208104)
・反応中間体を迅速にプロセッシング、実験結果もあり (Enzyme clustering accelerates processing of intermediates through metabolic channeling, 2014, http://www.nature.com/doifinder/10.1038/nbt.3018)
・代謝物濃度、流れ、自由エネルギー (Metabolite concentrations, fluxes and free energies imply efficient enzyme usage, 2016, https://doi.org/10.1038/nchembio.2077)
・最適な区画化、バクテリアがもつカルボキシソームなどを想定 (Optimal Compartmentalization Strategies for Metabolic Microcompartments, 2017, https://doi.org/10.1016/j.bpj.2016.11.3194)
・酵素-酵素複合体の基質チャネリングへの効果 (Does metabolite channeling accelerate enzyme-catalyzed cascade reactions?, 2017, https://doi.org/10.1371/journal.pone.0172673)
・グルコース代謝の数理モデル (A Mathematical Model for Enzyme Clustering in Glucose Metabolism, 2018, https://www.nature.com/articles/s41598-018-20348-7)
・酵素の集合による分岐経路の制御 (Regulation of reaction fluxes via enzyme sequestration and co-clustering, 2019, https://doi.org/10.1098/rsif.2019.0444)
・連続反応のクラスターチャネリング、副反応を想定 (Cluster Channeling in Cascade Reactions, 2021, https://doi.org/10.1021/acs.jpcb.0c11155)
Intermolecular interaction
・タンパク質間相互作用手法まとめ (Protein-Protein Interaction Detection: Methods and Analysis, 2014, https://doi.org/10.1155/2014/147648)
・two-hybrid screens and TAP (tandem affinity purification)、メタボロンについて言及 (Protein–Protein Interactions, 2011, https://doi.org/10.1042/bst0380875)
・BiFC、近くにいたら光る (誤解しない BiFC 法のすゝめ :蛍光タンパク質を使ったタンパク質間相互作用イメー ジング, 2016, https://doi.org/10.18978/jscrp.51.1_48)
・APEX、近傍のRNAをラベリング (Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules, 2019,https://doi.org/10.1016/j.molcel.2019.07.030)
Liquid-liquid phase separation (LLPS)
・Microdroplet Chemistryとの関連 (Do Cellular Condensates Accelerate Biochemical Reactions? Lessons from Microdroplet Chemistry, 2018, https://doi.org/10.1016/j.bpj.2018.05.023
・オプトジェネティクスで酵素を集合させると代謝が変化 (Light-based control of metabolic flux through assembly of synthetic organelles, 2019, https://doi.org/10.1038/s41589-019-0284-8)
・液滴内では酵素と基質の親和性が増加 (Mechanistic dissection of increased enzymatic rate in a phase-separated compartment, 2021, https://doi.org/10.1038/s41589-021-00801-x)
・最新のレビュー (The role of liquid–liquid phase separation in regulating enzyme activity, 2021, https://doi.org/10.1016/j.ceb.2020.12.012)
LLPS as drug target
・ニュース記事、可能性について (Biomolecular condensates pique drug discovery curiosity, 2019, https://doi.org/10.1038/d41573-019-00069-w )
・ニュース記事 、ヘテロクロマチンとDNA損傷(Drug modulation by nuclear condensates, 2020, https://doi.org/10.1126/science.abc5318)
・レビュー、酵素の阻害や相互作用形式 (Therapeutics—how to treat phase separation- associated diseases, 2020, https://doi.org/10.1042/ETLS20190176)
・ニュース記事、Dewpoint Therapeuticsについて (Drug startups coalesce around condensates, 2021, https://doi.org/10.1038/s41587-021-00828-4 )
・IDPに結合する低分子化合物 (Intrinsically disordered proteins and biomolecular condensates as drug targets, 2021, https://doi.org/10.1016/j.cbpa.2021.02.009)
NMR
・液滴、ヒドロゲル、アミロイド形成時のIDPの構造変化 (Molecular structure in biomolecular condensates, 2020, https://doi.org/10.1016/j.sbi.2019.09.007)
・LLPSをNMRで測定するには (The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy, 2020, https://doi.org/10.1074/jbc.REV119.009847)
・FUS液滴、RNApolymeraseのC末端との相互作用、相互作用形式ごとに分類 (Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads, 2021, https://doi.org/10.1038/s41594-021-00677-4)
・FUS液滴、NMR管の壁面にくっつかないように工夫する (NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation, 2021, https://doi.org/10.1038/s41589-021-00752-3 )
Active droplets, origins of Life, Protocell
・アクティブな液滴はオストワルト成熟しない (Suppression of Ostwald ripening in active emulsions, 2015, https://doi.org/10.1103/PhysRevE.92.012317
・分裂と成長を繰り返す液滴モデル、プロトセル (Growth and division of active droplets provides a model for protocells, 2017, https://doi.org/10.1038/nphys3984 )
・アクティブな液滴内で粒子がどこに位置するか、中心体を想定 (Positioning of Particles in Active Droplets, 2018, https://doi.org/10.1103/PhysRevLett.121.158102 )
・レビュー、アクティブな液滴の物理学 (Physics of active emulsions, 2019, https://iopscience.iop.org/article/10.1088/1361-6633/ab052b)
・形成そして多様な形状変化を見せるRNA/ペプチド液滴 (Active coacervate droplets as a model for membraneless organelles and protocells, 2020, https://doi.org/10.1038/s41467-020-18815-9 )
・アクティブな液滴なオストワルト成熟しない、実験結果 (Active coacervate droplets are protocells that grow and resist Ostwald ripening, 2021, https://doi.org/10.1038/s41467-021-24111-x )
・DTT依存的に起こるペプチドの周期的な液滴形成と消失 (Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life, 2021, https://doi.org/10.1038/s41467-021-25530-6)
Other
・ミセルで閉じ込めると活性化する酵素 (Superactivity and conformational changes on α-chymotrypsin upon interfacial binding to cationic micelles, 2004, https://doi.org/10.1042/bj20031536)
・解糖系酵素はRNA結合タンパク質でもある?(The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs, 2015, https://doi.org/10.1038/ncomms10127 )
・微小空間での酵素反応、さまざまな手法のまとめ (Enzymatic reactions in confined environments, 2016, https://doi.org/10.1038/nnano.2016.54 )
・酵素にも天然変性領域を持つものが多い (Not an exception to the rule: the functional significance of intrinsically disordered protein regions in enzymes, 2017, http://dx.doi.org/10.1039/C6MB00741D)
・基質があるところへ酵素が集合 (Substrate-driven chemotactic assembly in an enzyme cascade, 2018, https://doi.org/10.1038/nchem.2905 )
・グリコーゲンの堆積と相分離 (Glycogen accumulation and phase separation drives liver tumor initiation, 2021, https://doi.org/10.1016/j.cell.2021.10.001)
・ピルビン酸キナーゼの可逆なアミロイド化、ポジティブフィードバックループ (Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly, 2021, https://doi.org/10.1038/s41556-021-00760-4)
・ストレス顆粒内で翻訳が進む (Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules, 2020, https://doi.org/10.1016/j.cell.2020.11.010)