- Insights into the low-temperature adaptation of an enzyme as studied through ancestral sequence reconstruction
Cui S, Dasgupta S, Yagi S, Kimura M, Furukawa R, Tagami S, Akanuma S.
- Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat
Fujikawa T, Sasamoto T, Zhao F, Yamagishi A, Akanuma S.
Sci Rep 14, 398, https://doi.org/10.1038/s41598-023-50828-4 (2024)
Springer Nature
- Ancestral sequence reconstruction of the ribosomal protein uS8 and reduction of amino acid usage to a smaller alphabet
Zhao F, Akanuma S.
J Mol Evol, https://doi.org/10.1007/s00239-022-10078-w (2022)
Springer Nature
- Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins
Akanuma S, Yamaguchi M, Yamagishi A.
PLoS ONE 16(10):e0258821, https://doi.org/10.1371/journal.pone.0258821 (2021)
PLOS
- 原始タンパク質における少数種アミノ酸組成の実験的検証
赤沼哲史
- Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties
Furukawa R, Toma W, Yamazaki K, Akanuma S.
Sci. Rep. 10, 15493, https://doi.org/10.1038/s41598-020-72418-4 (2020)
Springer Nature
- Reconstruction and characterization of thermally stable and catalytically active proteins comprising an alphabet of ∼13 amino acids
Kimura M, Akanuma S.
J. Mol. Evol. 88, 372–381, doi:10.1007/s00239-020-09938-0 (2020)
Springer
- Establishment of mesophilic-like catalytic properties in a thermophilic enzyme without affecting its thermal stability
Akanuma S, Bessho M, Kimura H, Furukawa R, Yokobori S, Yamagishi A.
- The Common Ancestor of All Modern Life
Akanuma S.
In: Astrobiology：From the Origins of Life to the Search for Extraterrestrial Intelligence (eds. eds. Yamagishi A, Kakegawa T, Usui T) Springer, 91-103 (2019)
Springer
- 祖先型再構成タンパク質を用いた原始アミノ酸組成の探索
赤沼哲史
- 人類への進化のはじまり：生命の起源と全生物の最後の共通祖先
赤沼哲史、渋江怜
人間科学研究 31(2)、139-145 (2018)
国立国会図書館
- Reduced amino acid set proteins suggest a role of prebiotic amino acids in primitive protein synthesis
Shibue R, ,Akanuma S.
- Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins
Shibue R, Sasamoto T, Shimada M, Zhang B, Yamagishi A, Akanuma S.
- Creation of artificial protein-protein interactions using α-helices as interfaces
Yagi S, Akanuma S, Yamagishi A.
Biophys Rev. doi: 10.1007/s12551-017-0352-9 (2018)
Springer
- Activation of macrophages by a laccase-polymerized polyphenol is dependent on phosphorylation of Rac1
Tajima K, Akanuma S, Matsumoto-Akanuma A, Yamanaka D, Ishibashi KI, Adachi Y, Ohno N.
Biochem. Biophys. Res. Commun. 495(3), 2209–2213. doi: 10.1016/j.bbrc.2017.12.095 (2018)
ScienceDirect
- Selection of a platinum-binding sequence in a loop of a four-helix bundle protein
Yagi S, Akanuma S, Kaji A, Niiro H, Akiyama H, Uchida T, Yamagishi A.
J. Biosci. Bioeng. 125(2), 192-198, doi: 10.1016/j.jbiosc.2017.09.006 (2018)
ScienceDirect
- Characterization of a thermostable mutant of Agaricus brasiliensis laccase created by phylogeny-based design
Hamuro Y, Tajima K, Matsumoto-Akanuma A, Sakamoto S, Furukawa R, Yamagishi A, Ohno N, Akanuma S.
J. Biosci. Bioeng. 124(6), 623-629, doi: 10.1016/j.jbiosc.2017.07.004 (2017)
ScienceDirect
- Characterization of reconstructed ancestral proteins suggests a change in temperature of the ancient biosphere
Akanuma S.
Life 7(3), 33; doi:10.3390/life7030033 (2017)
MDPI
- Reconstructed ancestral enzymes suggest long-term cooling of Earth's photic zone since the Archean
Garcia AK, Schopf JW, Yokobori SI, Akanuma S, Yamagishi A.
Proc. Natl. Acad. Sci. USA 114(18), 4619–4624 (2017)
PNAS
- 耐熱性酵素の創成と好熱菌酵素の低温高活性化
赤沼哲史
- When Archaea appeared—Molecular phylogenetic analyses of G1P dehydrogenase, G3P dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having G1P-polar lipids
Yokobori S, Nakajima Y, Akanuma S, Yamagishi A.
Archaea 2016, Article ID 1802675, 16 pages (2016)
Hindawi
- A strategy for designing thermostable enzymes by reconstructing ancestral sequences possessed by ancient life
Akanuma S, Yamagishi A.
In: Biotechnology of Extremophiles: Advances and Challenges (ed. Rampelotto PH) Springer, 581-596 (2016)
Springer
- Ancestral reconstruction of enzymes
Akanuma S, Yamagishi A.
In: Understanding enzymes; Function, Design, Engineering and Analysis (ed. Svendsen A), Pan Stanford, 683–706 (2016)
PanStanford
- De novo design of protein–protein interactions through modification of inter-molecular helix–helix interface residues
Yagi S, Akanuma S, Yamagishi M, Uchida T, Yamagishi A.
BBA-Proteins and Proteomics 1864(5), 479-487 (2016)
ScienceDirect
- Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060
Fukuda Y, Abe A, Tamura T, Kishimoto T, Sogabe A, Akanuma S, Yokobori SI, Yamagishi A, Imada K, Inagaki K.
- ゲノム配列の比較から明らかになった初期生命の好熱性
赤沼哲史
- 全生物の最後の共通祖先コモノート
赤沼哲史
細胞工学 35(2), 124-128 (2016)
細胞工学
- Robustness of predictions of extremely thermally stable proteins in ancient organisms
Akanuma S, Yokobori S, Nakajima Y, Bessho M, Yamagishi A.
Evolution 69(11), 2954-2962 (2015)
Wiley
- Characterization of the low-temperature activity of Sulfolobus tokodaii glucose-1-dehydrogenase mutants
Sugii T, Akanuma S, Yagi S, Yagyu K, Shimoda Y, Yamagishi A.
- Addition of negatively charged residues can reverse the decrease in the solubility of an acidic protein caused by an artificially introduced non-polar surface patch
Yagi S, Akanuma S, Yamagishi A.
- Cloning and characterization of laccase DNA from the Royal Sun Medicinal Mushroom, Agaricus brasiliensis (Higher Basidiomycetes)
Matsumoto-Akanuma A, Akanuma S, Motoi M, Yamagishi A, Ohno N.
Int. J. Med. Mush. 16(4), 375-393 (2014)
- N-terminal hydrophobic amino acids of ATF5 confer IL-1β-induced stabilization
Abe T, Kojima M, Akanuma S, Iwashita H, Yamazaki T, Okuyama R, Ichikawa K, Umemura M, Nakano H, Takahashi S, Takahashi Y.
J. Biol. Chem. 289(7), 3888-3900 (2014)
- Preparation of Phi29 DNA polymerase free of amplifiable DNA using ethidium monoazide, an ultraviolet-free light-emitting diode lamp and trehalose
Takahashi H, Yamazaki H, Akanuma S, Kanahara H, Saito T, Chimuro Kobayashi T, Ohtani T, Yamamoto K, Sugiyama S, Kobori T.
- Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation
Fukuda M, Komatsu Y, Yamada H, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
Molecular Simulation 40(6), 498-503 (2014)
T＆Fonline
- Coarse-Grained Molecular Dynamics Simulation of IPMDH
Hirata Y, Komatsu Y, Fukuda M, Yamada H, Miyakawa T, Morikawa R, Akanuma S, Yamagishi A, Takasu M.
JPS Conf. Proc. 1, 016010 (2014) doi:10.1016/j.jbiosc.2014.03.002
JPS
- Computer Simulation Analysis of the Protein Binding Interfaces that Form a 4-Helix Bundle Motif
Fukuda M, Yamada H, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
JPS Conf. Proc. 1, 016020 (2014) doi:10.1016/j.jbiosc.2014.03.002
JPS
- 全生物の共通祖先遺伝子の復元
赤沼哲史、山岸明彦
バイオサイエンスとインダストリー 72(1), 19-23 (2014)
B&I
- Experimental evidence for the thermophilicity of ancestral life
Akanuma S, Nakajima Y, Yokobori S, Kimura M, Nemoto N, Mase T, Miyazono K, Tanokura M, Yamagishi A.
- Simulation study of protein-protein interfaces based on the 4-helix bundle structure
Fukuda M, Komatsu Y, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
AIP Conf. Proc. 1518, 606-609 (2013)
- Chapter 12. Comparative Genomics of Thermophilic Bacteria and Archaea
Akanuma S, Yokobori S, Yamagishi A.
In "Thermophilic Microbes in Environmental and Industrial Biotechnology" (Eds. Satyanarayana, T., Litterchild J., Kawarabayasi, Y). Springer Science, pp. 331-349 (2013)
Springer
- 高機能タンパク質創製技術の現状と展望
玉腰雅忠、八木創太、赤沼哲史、山岸明彦
「技術予測レポート2023」上巻、日本能率協会総合研究所 pp. 80-91(2013)
- 進化分子工学を利用したタンパク質分子育種技術
赤沼哲史、山岸明彦
「進化分子工学 -高速分子進化によるタンパク質・核酸の開発-」、エヌ・ティー・エス、343-353 (2013)
NTS
- 祖先型設計法を用いた耐熱性タンパク質の配列探索
赤沼哲史
- 第9章 全生物の共通祖先
赤沼哲史、山岸明彦
山岸明彦編集 「アストロバイオロジー」、化学同人、118-131 (2013)
- Constructing protein nano-fiber and estimation of the electronic state around metal ions
Komatsu Y, Fukuda M, Yamada H, Kawamoto S, Miyakawa T, Morikawa R, Takasu M, Yokojima S, Akanuma S, Yamagishi A.
Int. J. Quant. Chem. 112, 3750-3755 (2012)
Wiley
- Designing the binding surface of proteins to construct nano-fibers
Komatsu Y, Yamada H, Kawamoto S, Fukuda M, Miyakawa T, Morikawa R, Takasu M, Akanuma S, Yamagishi A.
Prog. Theor. Chem. Phys. 26, 555-567 (2012)
- Substitutions of coenzyme-binding, non-polar residues improve the low-temperature activity of thermophilic dehydrogenases
Hayashi S, Akanuma S, Onuki W, Tokunaga C, Yamagishi A.
- Phylogeny-based design of a B-subunit of DNA gyrase and its ATPase domain using a small set of homologous amino acid sequences
Akanuma S, Iwami S, Yokoi T, Nakamura N, Watanabe H, Yokobori S, Yamagishi A.
- Roles for the two N-terminal (beta/alpha) modules in the folding of a (beta/alpha)8-barrel protein as studied by fragmentation analysis
Akanuma S, Yamagishi A.
- Partial purification and characterization of polyphenoloxidase from Culinary-Medicinal Royal Sun Mushroom (the Himematsutake), Agaricus brasiliensis S. Wasser et al. (Agaricomycetideae)
Matsumoto-Akanuma A, Akanuma S, Motoi M, Yamagishi A, Ohno N
- Mimicking the evolution of a thermally stable monomeric four-helix bundle by fusion of four identical single-helix peptides
Akanuma S, Matsuba T, Ueno E, Umeda N, Yamagishi A
- 酵素を創るI - 生物学的アプローチ：細胞を用いたタンパク質合成 - 大腸菌
赤沼哲史、山岸明彦
酵素利用技術体系、エヌ・ティー・エス (2010)
- 好熱菌のタンパク質はなぜ熱に強いか
赤沼哲史、山岸明彦
生化学
81 1064-1071 (2009)
PDF- Experimental evidence for the existence of a stable half-barrel subdomain in the (beta/alpha)8-barrel fold.
Akanuma S, Yamagishi A.
- Random mutagenesis improves the low-temperature activity of the tetrameric 3-isopropylmalate dehydrogenase from the hyperthermophile Sulfolobus tokodaii.
Sasaki M, Uno M, Akanuma S, Yamagishi A.
- Methods for reducing nonspecific interaction in antibody-antigen assay via atomic force microscopy.
Wakayama J, Sekiguchi H, Akanuma S, Ohtani T, Sugiyama S
Anal Biochem. 380:51-58 (2008)
PubMed