Stable and Minimum Size Solubilization of Membrane Proteins with Cocktails of Phospholipid Analogues

Mai Takagi, Ayana Nagatani, Kenichi Kawano, Ayami Hata, Azusa Yokoyama, Koichi Hayashida, Haruka Hoshi, Mao Sakurai, Tsuyoshi Oyama, Yusuke Kuroda, Yousuke Yamaoka, Takahiro Fujiwara, Yohei Miyanoiri, Masaru Hoshino, Yoshiaki Yano, Kiyosei Takasu, Katsumi Matsuzaki

ACS Applied Materials & Interfaces　2024/11/07　Research paper (scientific journal)

Enhancing solution structural analysis of large molecular proteins through optimal stereo array isotope labeling of aromatic amino acids

Yohei Miyanoiri, Mitsuhiro Takeda, Kosuke Okuma, Tsutomu Terauchi, Masatsune Kainosho

Biophysical Chemistry　p. 107328-107328　2024/09　Research paper (scientific journal)

Direct evidence for a deprotonated lysine serving as a H-bond “acceptor” in a photoreceptor protein

Takayuki Nagae, Mitsuhiro Takeda, Tomoyasu Noji, Keisuke Saito, Hiroshi Aoyama, Yohei Miyanoiri, Yutaka Ito, Masatsune Kainosho, Yuu Hirose, Hiroshi Ishikita, Masaki Mishima

Proceedings of the National Academy of Sciences　Vol. 121　No. 36　2024/08/27　Research paper (scientific journal)

Iron-sulphur protein catalysed [4+2] cycloadditions in natural product biosynthesis

Yu Zheng, Katsuyuki Sakai, Kohei Watanabe, Hiroshi Takagi, Yumi Sato-Shiozaki, Yuko Misumi, Yohei Miyanoiri, Genji Kurisu, Toshihiko Nogawa, Ryo Takita, Shunji Takahashi

Nature Communications　Vol. 15　No. 1　2024/07/10　Research paper (scientific journal)

Green/red light-sensing mechanism in the chromatic acclimation photosensor

Takayuki Nagae, Yuya Fujita, Tatsuya Tsuchida, Takanari Kamo, Ryoka Seto, Masako Hamada, Hiroshi Aoyama, Ayana Sato-Tomita, Tomotsumi Fujisawa, Toshihiko Eki, Yohei Miyanoiri, Yutaka Ito, Takahiro Soeta, Yutaka Ukaji, Masashi Unno, Masaki Mishima, Yuu Hirose

Science Advances　Vol. 10　No. 24　2024/06/14　Research paper (scientific journal)

Identification of potential C1-binding sites in the immunoglobulin CL domains

Saeko Yanaka, Atsuji Kodama, Shigetaka Nishiguchi, Rina Fujita, Jiana Shen, Pornthip Boonsri, Duckyong Sung, Yukiko Isono, Hirokazu Yagi, Yohei Miyanoiri, Takayuki Uchihashi, Koichi Kato

International Immunology　Vol. 36　No. 8　p. 405-412　2024/04/02　Research paper (scientific journal)

Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy

Kayo Imamura, Ken-Ichi Akagi, Yohei Miyanoiri, Hirokazu Tsujimoto, Takatsugu Hirokawa, Hideo Ashida, Kaori Murakami, Asuka Inoue, Ryoji Suno, Takahisa Ikegami, Naotaka Sekiyama, So Iwata, Takuya Kobayashi, Hidehito Tochio

Structure　2024/01　Research paper (scientific journal)

Changes in the hydrophobic network of the FliGMC domain induce rotational switching of the flagellar motor.

Tatsuro Nishikino, Atsushi Hijikata, Seiji Kojima, Tsuyoshi Shirai, Masatsune Kainosho, Michio Homma, Yohei Miyanoiri

iScience　Vol. 26　No. 8　p. 107320-107320　2023/08/18　Research paper (scientific journal)

Elucidation of the molecular mechanism determining the direction of rotation of bacterial flagellar motor protein through high-pressure NMR measurements

Tatsuro NISHIKINO, Yohei MIYANOIRI

The Review of High Pressure Science and Technology　Vol. 33　No. 2　p. 83-90　2023/06/01　Research paper (scientific journal)

Highly Dispersed 3C Silicon Carbide Nanoparticles with a Polydopamine/Polyglycerol Shell for Versatile Functionalization

Shingo Sotoma, Hiroshi Abe, Yohei Miyanoiri, Takeshi Ohshima, Yoshie Harada

ACS Applied Materials & Interfaces　2023/04/18　Research paper (scientific journal)

Soluble domains of cytochrome c-556 and Rieske iron–sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis

Hiraku Kishimoto, Chihiro Azai, Tomoya Yamamoto, Risa Mutoh, Tetsuko Nakaniwa, Hideaki Tanaka, Yohei Miyanoiri, Genji Kurisu, Hirozo Oh-oka

Current Research in Structural Biology　p. 100101-100101　2023/04　Research paper (scientific journal)

Phosphatidylinositol-3,4,5-trisphosphate interacts with alpha-synuclein and initiates its aggregation and formation of Parkinson’s disease-related fibril polymorphism

Chi Jing Choong, César Aguirre, Keita Kakuda, Goichi Beck, Hiroki Nakanishi, Yasuyoshi Kimura, Shuichi Shimma, Kei Nabekura, Makoto Hideshima, Junko Doi, Keiichi Yamaguchi, Kichitaro Nakajima, Tomoya Wadayama, Hideki Hayakawa, Kousuke Baba, Kotaro Ogawa, Toshihide Takeuchi, Shaymaa Mohamed, Mohamed Badawy, Shigeo Murayama, Seiichi Nagano, Yuji Goto, Yohei Miyanoiri, Yoshitaka Nagai, Hideki Mochizuki, Kensuke Ikenaka

ACTA NEUROPATHOLOGICA　Vol. 145　No. 5　p. 573-595　2023/03　Research paper (scientific journal)

Biological Magnetic Resonance Data Bank

Jeffrey C Hoch, Kumaran Baskaran, Harrison Burr, John Chin, Hamid R Eghbalnia, Toshimichi Fujiwara, Michael R Gryk, Takeshi Iwata, Chojiro Kojima, Genji Kurisu, Dmitri Maziuk, Yohei Miyanoiri, Jonathan R Wedell, Colin Wilburn, Hongyang Yao, Masashi Yokochi

Nucleic Acids Research　Vol. 51　No. D1　p. D368-D376　2022/12/07　Research paper (scientific journal)

The residual structure of acid‐denatured β2‐microglobulin is relevant to an ordered fibril morphology

Ryosuke Tomiyama, Masatomo So, Keiichi Yamaguchi, Yohei Miyanoiri, Kazumasa Sakurai

Protein Science　Vol. 32　No. 1　2022/11/02　Research paper (scientific journal)

Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states

Yuhi Hosoe, Yohei Miyanoiri, Suyong Re, Saki Ochi, Yuya Asahina, Toru Kawakami, Masataka Kuroda, Kenji Mizuguchi, Masayuki Oda

The FEBS Journal　Vol. 290　No. 9　p. 2366-2378　2022/10/25　Research paper (scientific journal)

Conformational change in the monomeric alpha-synuclein imparts fibril polymorphs

Cesar Aguirre, Kensuke Ikenaka, Masatomo So, Takahiro Maruno, Keiichi Yamaguchi, Kichitaro Nakajima, Chi-Jing Choong, Kei Nabekura, Goichi Beck, Kentaro Tomii, Yu Yamamori, Junko Doi, Tomoyasu Matsubara, Maho Morishima, Keita Kakuda, Makoto Hideshima, Yasuyoshi Kimura, Seiichi Nagano, Kousuke Baba, Shigeo Murayama, Hirotsugu Ogi, Yoshitaka Nagai, Yasushi Kawata, Susumu Uchiyama, Yohei Miyanoiri, Yuji Goto, Hideki Mochizuki

bioRxiv　2022/02/10　Research paper (scientific journal)

Relative configuration of Cys-Pro ester peptides in thioester formation.

Toru Kawakami, Eri Sasakura, Yohei Miyanoiri, Hironobu Hojo

Journal of peptide science : an official publication of the European Peptide Society　Vol. 28　No. 8　2022/01/18　Research paper (scientific journal)

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Takayuki Nagae, Masashi Unno, Taiki Koizumi, Yohei Miyanoiri, Tomotsumi Fujisawa, Kento Masui, Takanari Kamo, Kei Wada, Toshihiko Eki, Yutaka Ito, Yuu Hirose, Masaki Mishima

Proceedings of the National Academy of Sciences　Vol. 118　No. 20　p. e2024583118-e2024583118　2021/05/18　Research paper (scientific journal)

Conformational space sampled by domain reorientation of linear diubiquitin reflected in its binding mode for target proteins

Xue-ni Hou, Naotaka Sekiyama, Yasuko Ohtani, Feng Yang, Yohei Miyanoiri, Kenn-ichi Akagi, Xun-Cheng Su, Hidehito Tochio

ChemPhysChem　Vol. 22　No. 14　p. 1505-1517　2021/04/29　Research paper (scientific journal)

Conformational features and ionization states of Lys side chains in a protein studied using the stereo-array isotope labeling (SAIL) method

Mitsuhiro Takeda, Yohei Miyanoiri, Tsutomu Terauchi, Masatsune Kainosho

Magnetic Resonance　Vol. 2　No. 1　p. 223-237　2021/04/26　Research paper (scientific journal)

高度な安定同位体標識による高分子量蛋白質の溶液NMR解析法

宮ノ入洋平, 武田光広, 寺内 勉, 甲斐荘正恒

酵素工学ニュース　Vol. 85　p. 6-10　2021/04　Research paper (scientific journal)

NMR assignments of the N-glycans of the Fc fragment of mouse immunoglobulin G2b glycoprotein

Saeko Yanaka, Yoshiki Yamaguchi, Takeshi Takizawa, Yohei Miyanoiri, Rina Yogo, Ichio Shimada, Koichi Kato

Biomolecular NMR Assignments　Vol. 15　No. 1　p. 187-192　2021/04　Research paper (scientific journal)

Carbonyl 13C-detect solution-state protein NMR experiments to circumvent amide-solvent exchange broadening: Application to β2-microglobulin

Yuichi Yoshimura, Masatomo So, Yohei Miyanoiri

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics　Vol. 1869　No. 3　p. 140593-140593　2021/03　Research paper (scientific journal)

Isoelectric point-amyloid formation of α-synuclein extends the generality of the solubility and supersaturation-limited mechanism

Koki Furukawa, Cesar Aguirre, Masatomo So, Kenji Sasahara, Yohei Miyanoiri, Kazumasa Sakurai, Keiichi Yamaguchi, Kensuke Ikenaka, Hideki Mochizuki, Jozsef Kardos, Yasushi Kawata, Yuji Goto

Current Research in Structural Biology　Vol. 2　p. 35-44　2020/04/05　Research paper (scientific journal)

Recent developments in isotope-aided NMR methods for supramolecular protein complexes -SAIL aromatic TROSY.

Yohei Miyanoiri, Mitsuhiro Takeda, Tsutomu Terauchi, Masatsune Kainosho

Biochimica et biophysica acta. General subjects　Vol. 1864　No. 2　p. 129439-129439　2019/10　Research paper (scientific journal)

Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations.

Saeko Yanaka, Rina Yogo, Rintaro Inoue, Masaaki Sugiyama, Satoru G Itoh, Hisashi Okumura, Yohei Miyanoiri, Hirokazu Yagi, Tadashi Satoh, Takumi Yamaguchi, Koichi Kato

Antibodies (Basel, Switzerland)　Vol. 8　No. 3　2019/07/01　Research paper (scientific journal)

Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H-13C Labeling and Fast Magic-Angle Spinning NMR.

Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P

Journal of the American Chemical Society　Vol. 141　No. 28　p. 11183-11195　2019/06　Research paper (scientific journal)

Rotational direction of flagellar motor from the conformation of FliG middle domain in marine Vibrio.

Tatsuro Nishikino, Atsushi Hijikata, Yohei Miyanoiri, Yasuhiro Onoue, Seiji Kojima, Tsuyoshi Shirai, Michio Homma

Scientific reports　Vol. 8　No. 1　p. 17793-17793　2018/12/12　Research paper (scientific journal)

分子動力学シミュレーションとNMR法で迫るべん毛モーターの回転制御機構

宮ノ入洋平, 土方敦司, 本間道夫

生物物理　Vol. 58　No. 5　p. 251-254　2018/10　Research paper (scientific journal)

Evolution and diversification of the plant gibberellin receptor GID1.

Yoshida H, Tanimoto E, Hirai T, Miyanoiri Y, Mitani R, Kawamura M, Takeda M, Takehara S, Hirano K, Kainosho M, Akagi T, Matsuoka M, Ueguchi-Tanaka M

Proceedings of the National Academy of Sciences of the United States of America　Vol. 115　No. 33　p. E7844-E7853　2018/08　Research paper (scientific journal)

Perspective: next generation isotope-aided methods for protein NMR spectroscopy

Masatsune Kainosho, Yohei Miyanoiri, Tsutomu Terauchi, Mitsuhiro Takeda

Journal of Biomolecular NMR　Vol. 71　No. 3　p. 1-9　2018/06/22　Research paper (scientific journal)

Stable-isotope-aided NMR spectroscopy

Yohei Miyanoiri, Mitsuhiro Takeda, Masatsune Kainosho

Modern Magnetic Resonance　p. 469-486　2018/06/13　Part of collection (book)

Isotope-aided methods for biological NMR spectroscopy: Past, Present, and Future

Masatsune Kainosho, Yohei Miyanoiri, Mitsuhiro Takeda

Experimental Approaches of NMR Spectroscopy: Methodology and Application to Life Science and Materials Science　p. 37-61　2017/11/23　Part of collection (book)

Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na+-Driven Flagella

Yohei Miyanoiri, Atsushi Hijikata, Yuuki Nishino, Mizuki Gohara, Yasuhiro Onoue, Seiji Kojima, Chojiro Kojima, Tsuyoshi Shirai, Masatsune Kainosho, Michio Homma

STRUCTURE　Vol. 25　No. 10　p. 1540-+　2017/10　Research paper (scientific journal)

Biochemical characterization of the flagellar stator-associated inner membrane protein FliL from Vibrio alginolyticus

Ananthanarayanan Kumar, Miyu Isumi, Mayuko Sakuma, Shiwei Zhu, Yuuki Nishino, Yasuhiro Onoue, Seiji Kojima, Yohei Miyanoiri, Katsumi Imada, Michio Homma

JOURNAL OF BIOCHEMISTRY　Vol. 161　No. 4　p. 331-337　2017/04　Research paper (scientific journal)

C-13-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)

Mitsuhiro Takeda, Yohei Miyanoiri, Tsutomu Terauchi, Masatsune Kainosho

JOURNAL OF BIOMOLECULAR NMR　Vol. 66　No. 1　p. 37-53　2016/09　Research paper (scientific journal)

Highly efficient residue-selective labeling with isotope-labeled Ile, Leu, and Val using a new auxotrophic E-coli strain

Yohei Miyanoiri, Yojiro Ishida, Mitsuhiro Takeda, Tsutomu Terauchi, Masayori Inouye, Masatsune Kainosho

JOURNAL OF BIOMOLECULAR NMR　Vol. 65　No. 2　p. 109-119　2016/06　Research paper (scientific journal)

New methyl specific isotope labeling methods on structural analysis for large molecular protein

Miyanoiri Y, Takeda M, Kainosho M

Journal of the Spectroscopical Society of Japan　Vol. 65　No. 1　p. 46-49　2016/02

Recent advances in NMR methods for determining the structures and dynamics of larger proteins

Youhei Miyanoiri, Mitsuhiro Takeda, Masatsune Kainosho

Seikagaku　Vol. 88　No. 4　p. 452-464　2016

Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates

Mitsuhiro Takeda, Yohei Miyanoiri, Tsutomu Terauchi, Chun-Jiun Yang, Masatsune Kainosho

JOURNAL OF MAGNETIC RESONANCE　Vol. 241　p. 148-154　2014/04　Research paper (scientific journal)

Expression and purification of a GRAS domain of SLR1, the rice DELLA protein

Tomomi Sato, Yohei Miyanoiri, Mitsuhiro Takeda, Youichi Naoe, Rie Mitani, Ko Hirano, Sayaka Takehara, Masatsune Kainosho, Makoto Matsuoka, Miyako Ueguchi-Tanaka, Hiroaki Kato

PROTEIN EXPRESSION AND PURIFICATION　Vol. 95　p. 248-258　2014/03　Research paper (scientific journal)

1P174 Attempt to reconstruct the stator complex of the bacterial Na^+-driven flagellar motor into Nanodisc(12. Cell biology,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Gohara Mizuki, Takekawa Norihiro, Miyanoiri Yohei, Kainosho Masatune, Kojima Seiji, Homma Michio

Seibutsu Butsuri　Vol. 54　No. 1　2014

Differential isotope-labeling for Leu and Val residues in a protein by E. coli cellular expression using stereo-specifically methyl labeled amino acids

Yohei Miyanoiri, Mitsuhiro Takeda, Kosuke Okuma, Akira M. Ono, Tsutomu Terauchi, Masatsune Kainosho

JOURNAL OF BIOMOLECULAR NMR　Vol. 57　No. 3　p. 237-249　2013/11　Research paper (scientific journal)

Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel

Makoto Ihara, Shin Hamamoto, Yohei Miyanoiri, Mitsuhiro Takeda, Masatsune Kainosho, Isamu Yabe, Nobuyuki Uozumi, Atsuko Yamashita

Journal of Biological Chemistry　Vol. 288　No. 21　p. 15303-15317　2013/05/24　Research paper (scientific journal)

3P196 Flagellar stator protein of Vibrio PomA alone could form multimeric complex(12. Cell biology,Poster)

Gohara Mizuki, Takekawa Norihiro, Miyanoiri Yohei, Kainosho Masatune, Kojima Seiji, Homma Michio

Seibutsu Butsuri　Vol. 53　No. 1　2013

1B1424 Solution NMR analysis of FUG C-terminal domain derived from Na^+-driven motor of Vibrio(Proteins: Structure & Function I,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Gohara Mizuki, Abe-Yoshizumi Rei, Kobayashi Shiori, Miyanoiri Yohei, Hattori Yoshikazu, Kojima Chojiro, Kainosho Masatsune, Homma Michio

Seibutsu Butsuri　Vol. 52　2012

Stereo-Array Isotope Labeling Method for Studying Protein Structure and Dynamics

Yohei Miyanoiri, Mitsuhiro Takeda, Masatsune Kainosho

ISOTOPE LABELING IN BIOMOLECULAR NMR　Vol. 992　p. 83-93　2012　Research paper (scientific journal)

Alternative SAIL-Trp for robust aromatic signal assignment and determination of the chi(2) conformation by intra-residue NOEs

Yohei Miyanoiri, Mitsuhiro Takeda, JunGoo Jee, Akira M. Ono, Kosuke Okuma, Tsutomu Terauchi, Masatsune Kainosho

JOURNAL OF BIOMOLECULAR NMR　Vol. 51　No. 4　p. 425-435　2011/12　Research paper (scientific journal)

Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: Mechanism for an increase in DNA-binding affinity through phosphorylation

Takashi Nagata, Emi Niyada, Natsuki Fujimoto, Yuuya Nagasaki, Kazuaki Noto, Youhei Miyanoiri, Jun Murata, Kazuyuki Hiratsuka, Masato Katahira

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 78　No. 14　p. 3033-3047　2010/11　Research paper (scientific journal)

Myosin VI Undergoes Cargo-Mediated Dimerization

Cong Yu, Wei Feng, Zhiyi Wei, Yohei Miyanoiri, Wenyu Wen, Yanxiang Zhao, Mingjie Zhang

CELL　Vol. 138　No. 3　p. 537-548　2009/08　Research paper (scientific journal)

Structural analysis of the fundamental polymer of the sheath constructed by Sphaerotilus natans

Minoru Takeda, Yohei Miyanoiri, Takeshi Nogami, Kanae Oda, Tatsuya Saito, Katsuya Kato, Jun-ichi Koizumi, Masato Katahira

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 71　No. 12　p. 2992-2998　2007/12　Research paper (scientific journal)

1P015 Structural analysis of Musashi protein complexed with the target RNA with long-range structural information(Proteins-structure and structure-function relationship,Oral Presentations)

Ohyama Takako, Ogara Shota, Miyanoiri Youhei, Furukawa Ayako, Imai Takao, Okano Hideyuki, Nagata Takashi, Katahira Masato

Seibutsu Butsuri　Vol. 47　2007

Identification of 2-(cysteinyl)amido-2-deoxy-D-galacturonic acid residue from the sheath of Leptothrix cholodnii

Hiroko Makita, Yuichi Nakahara, Hiroyuki Fukui, Yohei Miyanoiri, Masato Katahira, Hiroko Seki, Minoru Takeda, Jun-ichi Koizumi

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 70　No. 5　p. 1265-1268　2006/05　Research paper (scientific journal)

Structural analysis for mouse Musashi1 protein

Miyanoiri Y, Katahira M

Enzyme Engineering　Vol. 55　p. 452-464　2006/04

Unichrom, a novel nuclear matrix protein, binds to the Ars insulator and canonical MARs

H Tagashira, T Shimotori, N Sakamoto, M Katahira, Y Miyanoiri, T Yamamoto, K Mitsunaga-Nakatsubo, H Shimada, S Kusunoki, K Akasaka

ZOOLOGICAL SCIENCE　Vol. 23　No. 1　p. 9-21　2006/01　Research paper (scientific journal)

Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, Musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics

Y Miyanoiri, H Kobayashi, T Imai, M Watanabe, T Nagata, S Uesugi, H Okano, M Katahira

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 278　No. 42　p. 41309-41315　2003/10　Research paper (scientific journal)

Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA

M Katahira, Y Miyanoiri, Y Enokizono, G Matsuda, T Nagata, F Ishikawa, S Uesugi

JOURNAL OF MOLECULAR BIOLOGY　Vol. 311　No. 5　p. 973-988　2001/08　Research paper (scientific journal)

Correlation between dynamics and RNA-binding of Musashi1 protein

Miyanoiri Y., Watanabe M., Miyashita H., Ikeda T., Okano H., Uesugi S., Katahira M.

Seibutsu Butsuri　Vol. 41　2001