Papers - OTA Motonori
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Dual-wield NTPases: a novel protein family mined from AlphaFold protein structure database Reviewed International journal
K. Sakuma, R, Koike, M. Ota
Prot. Sci. Vol. in press 2024
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Elastic network model reveals distinct flexibilities of capping proteins bound to CARMIL and twinfilin-tail Reviewed International journal
Koike, R; Ota, M
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 92 ( 1 ) page: 37 - 43 2024.1
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Prediction of chaperonin GroE substrates using small structural patterns of proteins Reviewed International journal
Minami Shintaro, Niwa Tatsuya, Uemura Eri, Koike Ryotaro, Taguchi Hideki, Ota Motonori
FEBS OPEN BIO Vol. 13 ( 4 ) page: 779 - 794 2023.4
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How AlphaFold2 predicts conditionally folding regions annotated in an intrinsically disordered protein database Reviewed International journal
H. Anbo, K. Sakuma, S. Fukuchi, M. Ota
Biology Vol. 12 page: 182 2023.1
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Classification of proteins inducing liquid-liquid phase separation: sequential, structural and functional characterization Invited Reviewed International journal
Ozawa Yuhei, Anbo Hiroto, Ota Motonori, Fukuchi Satoshi
JOURNAL OF BIOCHEMISTRY 2022.12
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Structures and mechanisms of actin ATP hydrolysis Reviewed International journal
Kanematsu Y., Narita A., Oda T., Koike R., Ota M., Takano Y., Moritsugu K., Fujiwara I., Tanaka K., Komatsu H., Nagae T., Watanabe N., Iwasa M., Maéda Y., Takeda S.
Proceedings of the National Academy of Sciences of the United States of America Vol. 119 ( 43 ) page: e2122641119 2022.10
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Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2 Reviewed
FEBS OPEN BIO Vol. 12 ( 1 ) page: 285 - 294 2021.11
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Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins Invited Reviewed
Hijikata Atsushi, Shionyu Clara, Nakae Setsu, Shionyu Masafumi, Ota Motonori, Kanaya Shigehiko, Shirai Tsuyoshi
Biophys. Physicobiol. Vol. 18 ( 0 ) page: 226 - 240 2021.10
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Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail Reviewed
Takeda Shuichi, Koike Ryotaro, Fujiwara Ikuko, Narita Akihiro, Miyata Makoto, Ota Motonori, Maeda Yuichiro
J. Mol. Biol. Vol. 433 ( 9 ) page: 166891 2021.4
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Crystal structure of human V-1 in the apo form Reviewed
S. Takeda, R. Koike, T. Nagae, I. Fujiwara, A. Narita, Y. Maéda, M. Ota
Acta. Cryst. F Vol. 77 ( Pt 1 ) page: 13 - 21 2021.1
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Knowledge-based Modeling of SARS-CoV-2 Proteins and Predicting its Potential Drugs Invited Reviewed
HIJIKATA Atsushi, SHIONYU-MITSUYAMA Clara, NAKAE Setsu, SHIONYU Masafumi, OTA Motonori, KANAYA Shigehiko, SHIRAI Tsuyoshi
Seibutsu Butsuri Vol. 61 ( 2 ) page: 102 - 106 2021
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Knowledge-based strutural models of SARS-CoV-2 proteins and their complexes with potential drugs Reviewed
A. Hijikata, C. Shionyu-Mitsuyama, S. Nakae, M. Shionyu, M. Ota, S. Kanaya, T. Shirai
FEBS Lett. Vol. 594 page: 1960 - 1973 2020.5
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All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins Reviewed
R. Koike, M. Ota
Biophys. Physicobiol. ( 16 ) page: 280-286 2019.11
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Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins Reviewed
R. Koike, M. Amano, K. Kaibuchi, M. Ota
Protein Sci. Vol. 29 page: 564-571 2019.11
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MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers Reviewed
S. Minami, K. Sawada, M. Ota, G. Chikenji
Bioinformatics Vol. 34 page: 3324-3331 2018.10
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Using 1HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method Reviewed
H. Okazaki, N. Matsuo, T. Tenno, N. Goda, Y. Shigemitsu, M. Ota, H. Hiroaki
Protein Sci. Vol. 27 page: 1821-1830 2018.8
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Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins Reviewed
N. Matsuo, N. Goda, K. Shimizu, S. Fukuchi, M. Ota, H. Hiroaki
Int. J. Mol. Sci. Vol. 19 page: 401 2018.1
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Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding Reviewed
E. Uemura, T. Niwa, S. Minami, K. Takemoto, S. Fukuchi, K. Machida, H. Imataka, T. Ueda, M. Ota, H. Taguchi
Sci. Rep. Vol. 8 page: 678 2018.1
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Structural changes of homodimers in the PDB Reviewed
R. Koike, T. Amemiya, T. Horii, M. Ota
J. Str. Biol. page: in press 2018
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Rules for connectivity of secondary structure elements of proteins: Two-layer αβ sandwiches Reviewed
S. Minami, G. Chikenji, M. Ota
Prot. Sci. Vol. 26 page: 2257-2267 2017.11
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Itinerary profiling to analyze a large number of protein-folding trajectories Reviewed
M. Ota, M. Ikeguchi, A. Kidera
Biophys. Physicobiol. Vol. 13 page: 295-304 2016.11
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Interface property responsible for effective interactions of protean segments: Intrinsically disordered regions that undergo disorder-to-order transitions upon binding Reviewed
D. Shaji, T. Amemiya, R. Koike R, M. Ota
BBRC Vol. 478 page: 123-127 2016.9
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Profile comparison revealed deviation from structural constraint at the positively selected sites Reviewed
H. Oda , M. Ota, H. Toh
Biosystems Vol. 147 page: 67-77 2016.7
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Multiple-localization and hub proteins Reviewed
M. Ota, H. Gonja, R. Koike, S. Fukuchi
PLoS ONE Vol. 11 page: e0156455 2016.6
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Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes Reviewed
R. Koike, S. Takeda, Y. Maéda, M. Ota
Proteins Vol. 84 page: 948-956 2016.4
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Investigation of the fatty acid transporter-encoding genes SLC27A3 and SLC27A4 in autism Reviewed
M. Maekawa, Y. Iwayama, T. Ohnishi, M. Toyoshima, C. Shimamoto, Y. Hisano, T. Toyota, S. Balan, H. Matsuzaki, Y. Iwata, S. Takagai, K. Yamada, M. Ota, S. Fukuchi, Y. Okada, W. Akamatsu, M. Tsujii, N. Kojima, Y. Owada, H. Okano, N. Mori, T. Yoshikawa
Sci. Rep. Vol. 5 page: 16239 2015.11
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Domain-motion enhanced (DoME) model for efficient conformational sampling of multi-domain proteins Reviewed
C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, Y. Sugita
J. Phys. Chem. B Vol. 119 page: 14584-14593 2015.11
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A method for systematic assessment of intrinsically disordered protein regions by NMR Reviewed
N. Goda, K. Shimizu, Y. Kuwahara, T. Noguchi, T. Ikegami, M. Ota, H. Hiroaki
Int. J. Mol. Sci. Vol. 16 page: 15743-15760 2015.7
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Hierarchical domain-motion analysis of conformational changes in Sarcoplasmic Reticulum Ca2+-ATPase Reviewed
C. Kobayashi, R. Koike, M. Ota, Y. Sugita
Proteins Vol. 83 page: 746-756 2015.4
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An optimized Npro-based method for the expression and purification of intrinsically disordered proteins for an NMR study Reviewed
N. Goda, N. Matsuo, T. Tenno, S. Ishino, Y. Ishino, S. Fukuchi, M. Ota, H. Hiroaki
IDP Vol. 3 page: 1-6 2015.2
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Hierarchical description and extensive classification of protein structural changes by Motion Tree Reviewed
R. Koike, M. Ota, A. Kidera
J. Mol. Biol. Vol. 426 page: 752-762 2014.2
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IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners Reviewed
S. Fukuchi, T. Amemiya, S. Sakamoto, Y. Nobe, K. Hosoda, Y. Kado, SD. Murakami, R. Koike, H. Hiroaki, M. Ota
Nucleic Acids Res. Vol. 42 page: D320-D325 2014.1
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Exon resequencing of H3K9 methyltransferase complex genes, EHMT1, EHMT2 and WIZ, in Japanese autism subjects Reviewed
S. Balan, Y. Iwayama, M. Maekawa, T. Toyota, T. Ohnishi, M. Toyoshima, C. Shimamoto, K. Esaki, K. Yamada, Y. Iwata, K. Suzuki, M. Ide, M. Ota, S. Fukuchi, M. Tsujii, N. Mori, Y. Shinkai, T. Yoshikawa
Molecular Autism page: in the press 2014
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Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening Reviewed
T. Tenno, N. Goda, Y. Umetsu, M. Ota, K. Kinoshita, H. Hiroaki
Molecules Vol. 18 page: 9567-9581 2013.8
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Substrate-shielding and hydrolytic reaction in hydrolases Reviewed
Y. Kanematsu, R. Koike, T. Amemiya, M. Ota
Vol. 81 page: 926-932 2013.2
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An assignment of intrinsically disordered regions of proteins based on NMR structures Reviewed
M. Ota, R. Koike, T. Amemiya, T. Tenno, P. R. Romero, H. Hiroaki, A. K. Dunker, S. Fukuchi
J. Str. Biol. Vol. 181 page: 29-36 2013.1
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Influence of structural symmetry on protein dynamics Reviewed
Y. Matsunaga, R. Koike, M. Ota, J. Tame, A. Kidera
PLos One Vol. 7 page: e50011 2012.11
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A nobel biclustering approach with iterative optimization to analyze gene expression data Reviewed
S. Sutheworapong, M. Ota, H. Ohta, K. Kinoshita
Adv. Appl. Bioinform. Chem. Vol. 5 page: 23-59 2012.9
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SCPC: A method to structurally compare protein complexes
R. Koike, M. Ota
Bioinformatics page: in press 2012.2
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PSCDB: a database for protein structural change upon ligand binding
T. Amemiya, R. Koike, A. Kidera, M. Ota
Nucleic Acids Res. page: in press 2012
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IDEAL: intrinsically disordered proteins with extensive annotations and literature
S. Fukuchi, S. Sakamoto, Y. Nobe, SD. Murakami, T. Amemiya, K. Hosoda, R. Koike, H. Hiroaki, M. Ota
Nucleic Acids Res. page: in press 2012
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SAHG, a comprehensive database of predicted structures of all human proteins Reviewed
C. Motono, J. Nakata, R. Koike, K. Shimizu, M. Shirota, T. Amemiya, K. Tomii, N. Nagano, N. Sakaya, K. Misoo, M, Sato, A. Kidera, H. Hiroaki, T. Shirai, K. Kinoshita, T. Noguchi, M. Ota
Nucleic Acids Res. Vol. 39 page: D487 2011
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Cover and spacer insertions: small non-hydrophobic accessories that assist protein oligomerization
H. Nishi, R. Koike, M. Ota
Proteins Vol. 79 page: 2372-2379 2011
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Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function Reviewed
S. Takeda, R. Koike, Y. Nitanai, S. Minakata, Y. Maéda, M. Ota
Phys. Biol. Vol. 8 page: 035005 2011
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Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design Reviewed
Y. Matsuura, M. Ota, T. Tanaka, M. Takehira, K. Ogasahara, B. Bagautdinov, N. Kunishima, K. Yutani
J. Biochem. Vol. 148 page: 449-458 2010
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Two distinct mechanisms for actin capping proteinregulationTwo distinct mechanisms for actin capping proteinregulation- steric and allosteric inhibitionsteric and allosteric inhibition Reviewed
S. Takeda, S. Minakata, R. Koike, I. Kawahata, A. Narita, M. Kitazawa, M. Ota, T.Yamakuni, Y. Maéda, Y. Nitanai
PLos Biol. Vol. 8 page: e1000416 2010
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Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state Reviewed
H. Nishi, M. Ota
Proteins Vol. 78 page: 1563-1574 2010
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Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold Reviewed
R. Koike, A. Kidera, M. Ota
Protein Sci. Vol. 18 page: 2060-2066 2009
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An evaluation of minimal cellular functions to sustain a bacterial cell Reviewed
Y. Azuma, M. Ota
BMC Syst. Biol. Vol. 3 page: 111 2009
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An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories Reviewed
H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang
BMC Bioinformatics Vol. 9 page: 344 2008
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Protein structural change upon ligand binding correlates with enzymatic reaction mechanism Reviewed
R. Koike, T. Amemiya, M. Ota, A. Kidera
J. Mol. Biol. Vol. 379 page: 397-401 2008
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Unfolding pathways of goat α-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories Reviewed
T. Oroguchi, M. Ikeguchi, M. Ota, K. Kuwajima and A. Kidera
J. Mol. Biol. Vol. 371 page: 1354-64 2007
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Enhanced partial order curve comparison over multiple protein folding trajectories Reviewed
H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang
Comput. Syst. Bioinformatics. Conf. Vol. 6 page: 299-310 2007
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A hyperthermophilic protein acquires function at the cost of stability Reviewed
A. Mukaiyama, M. Haruki, M. Ota, Y. Koga, K. Takano and S. Kanaya
Biochemistry Vol. 24 page: 12673-12679 2006
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Stabilization of E. coli ribonuclease HI by the 'stability profile of mutant protein' (SPMP)-inspired random and non-random mutagenesis Reviewed
M. Haruki, Y. Saito, M. Ota, K. Nishikawa, S. Kanaya
J. Biotech. Vol. 25 page: 512-522 2006
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Design of λ Cro fold: solution structure of a monomeric variant of the de novo protein Reviewed
Y. Isogai, Y. Ito, T. Ikeya, Y. Shiro, M. Ota
J. Mol. Biol. Vol. 354 page: 801-814 2005
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P-cats: Prediction of catalytic residues in proteins from the tertiary structures Reviewed
K. Kinoshita and M. Ota
Bioinformatics Vol. 21 page: 3570-3571 2005
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Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry Reviewed
Y. Asada, M. Sawano, K. Ogasahara, J. Nakamura, M. Ota, C. Kuroishi, M. Sugahara, K. Yutani, N. Kunishima
J Biochem (Tokyo) Vol. 138 page: 343-353 2005
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Phylogeny of protein-folding trajectories reveals a unique pathway to native structure Reviewed
M. Ota, M. Ikeguchi and A. Kidera
Proc. Natl. Acad. Sci. USA Vol. 101 page: 17658-17663 2004
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones Reviewed
T. Imanishi et al.
PLoS. Biol. Vol. 2 page: E162 2004
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The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus Reviewed
Y. Hioki, K. Ogasahara K, S. Lee, J. Ma, M. Ishida, Y. Yamagata, Y. Matsuura, M. Ota, M. Ikeguchi, S. Kuramitsu, K. Yutani
Eur. J. Biochem. Vol. 271 page: 2624-2635 2004