研究者詳細 - 小池　亮太郎

論文 - 小池　亮太郎

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Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins. 査読有り Open Access

Koike R, Amano M, Kaibuchi K, Ota M.

Protein Sci. 2020年2月

Structural changes of homodimers in the PDB. 査読有り

Koike R, Amemiya T, Horii T, Ota M.

J Struct Biol. 2017年12月

Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes. 査読有り

Koike R, Takeda S, Maeda Y, Ota M.

Proteins 頁： - 2016年7月

Hierarchical description and extensive classification of protein structural changes by Motion Tree. 査読有り Open Access

Koike R, Ota M, Kidera A.

J Mol Biol 426 巻頁： 756-762 2014年2月

SCPC: A method to structurally compare protein complexes. 査読有り Open Access

Koike R, Ota M

Bioinformatics 28 巻頁： 324-330 2012年2月

Nucleotide-dependent actin conformations revealed by multiscale enhanced sampling. 査読有り

Kenta Omoto, Ryoaro Koike, Motonori Ota

Biophys J. 125 巻 ( 1 ) 頁： 317 - 325 2026年1月

Dual-wield NTPases: A novel protein family mined from AlphaFold DB. 査読有り

Sakuma Koya, Koike Ryotaro, Ota Motonori

Protein Science 2024年4月

Elastic network model reveals distinct flexibilities of capping proteins bound to CARMIL and twinfilin-tail 査読有り

Koike Ryotaro, Ota Motonori

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2023年7月

記述言語：英語出版者・発行元：Proteins: Structure, Function and Bioinformatics

Capping protein (CP) binds to the barbed end of an actin-filament and inhibits its elongation. CARMIL binds CP and dissociates it from the barbed end of the actin-filament. The binding of CARMIL peptide alters the flexibility of CP, which is considered to facilitate the dissociation. Twinfilin also binds to CP through its C-terminal tail. The complex structures of the CP/twinfilin-tail (TW-tail) peptide indicate that the binding sites of CARMIL and TW-tail overlap. However, TW-tail binding does not facilitate the dissociation of CP from the barbed end. We extensively investigated the flexibilities of CP in the CP/TW-tail or CP/CARMIL complexes using an elastic network model and concluded that TW-tail binding does not alter the flexibility of CP. Our extensive analysis also highlighted that the strong contacts of peptides with the two domains of CP, that is, the CP-L and CP-S domains, are key to changing the flexibilities of CP. CARMIL peptides can interact strongly with both of the domains, while TW-tail peptides exclusively interact with the CP-S domain because the binding site of TW-tail on CP relatively shifts to the CP-S domain compared with that of CP/CARMIL. This result supports our hypothesis that the dissociation of CP from the barbed end is regulated by the flexibility of CP.

DOI： 10.1002/prot.26560

Web of Science

Scopus

PubMed

Rational design of phase separating peptides based on phase separating protein sequence of p53 査読有り Open Access

Kamagata Kiyoto, Hando Atsumi, Ariefai Maulana, Iwaki Nanako, Kanbayashi Saori, Koike Ryotaro, Ikeda Keisuke

SCIENTIFIC REPORTS 13 巻 ( 1 ) 頁： 5648 2023年4月

記述言語：英語出版者・発行元：Scientific Reports

Artificial phase-separating (PS) peptides can be used in various applications such as microreactors and drug delivery; however, the design of artificial PS peptides remains a challenge. This can be attributed to the limitation of PS-relevant residues that drive phase separation by interactions of their pairs in short peptides and the difficulty in the design involving interaction with target PS proteins. In this study, we propose a rational method to design artificial PS peptides that satisfy the requirements of liquid droplet formation and co-phase separation with target PS proteins based on the target PS protein sequence. As a proof of concept, we designed five artificial peptides from the model PS protein p53 using this method and confirmed their PS properties using differential interference contrast and fluorescence microscopy. Single-molecule fluorescent tracking demonstrated rapid diffusion of the designed peptides in their droplets compared to that of p53 in p53 droplets. In addition, size-dependent uptake of p53 oligomers was observed in the designed peptide droplets. Large oligomers were excluded from the droplet voids and localized on the droplet surface. The uptake of high-order p53 oligomers into the droplets was enhanced by the elongated linker of the designed peptides. Furthermore, we found that the designed peptide droplets recruited p53 to suppress gel-like aggregate formation. Finally, we discuss aspects that were crucial in the successful design of the artificial PS peptides.

DOI： 10.1038/s41598-023-32632-2

Prediction of chaperonin GroE substrates using small structural patterns of proteins 査読有り Open Access

Minami Shintaro, Niwa Tatsuya, Uemura Eri, Koike Ryotaro, Taguchi Hideki, Ota Motonori

FEBS OPEN BIO 13 巻 ( 4 ) 頁： 779 - 794 2023年4月

記述言語：英語出版者・発行元：FEBS Open Bio

Molecular chaperones are indispensable proteins that assist the folding of aggregation-prone proteins into their functional native states, thereby maintaining organized cellular systems. Two of the best-characterized chaperones are the Escherichia coli chaperonins GroEL and GroES (GroE), for which in vivo obligate substrates have been identified by proteome-wide experiments. These substrates comprise various proteins but exhibit remarkable structural features. They include a number of α/β proteins, particularly those adopting the TIM β/α barrel fold. This observation led us to speculate that GroE obligate substrates share a structural motif. Based on this hypothesis, we exhaustively compared substrate structures with the MICAN alignment tool, which detects common structural patterns while ignoring the connectivity or orientation of secondary structural elements. We selected four (or five) substructures with hydrophobic indices that were mostly included in substrates and excluded in others, and developed a GroE obligate substrate discriminator. The substructures are structurally similar and superimposable on the 2-layer 2α4β sandwich, the most popular protein substructure, implying that targeting this structural pattern is a useful strategy for GroE to assist numerous proteins. Seventeen false positives predicted by our methods were experimentally examined using GroE-depleted cells, and 9 proteins were confirmed to be novel GroE obligate substrates. Together, these results demonstrate the utility of our common substructure hypothesis and prediction method.

DOI： 10.1002/2211-5463.13590

Structures and mechanisms of actin ATP hydrolysis 査読有り Open Access

Kanematsu Yusuke, Narita Akihiro, Oda Toshiro, Koike Ryotaro, Ota Motonori, Takano Yu, Moritsugu Kei, Fujiwara Ikuko, Tanaka Kotaro, Komatsu Hideyuki, Nagae Takayuki, Watanabe Nobuhisa, Iwasa Mitsusada, Maeda Yuichiro, Takeda Shuichi

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 119 巻 ( 43 ) 頁： e2122641119 2022年10月

記述言語：英語出版者・発行元：Proceedings of the National Academy of Sciences of the United States of America

The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) PG–O3B bond cleavage; 3) four concomitant events: W1–PO32 formation, OH2 and proton cleavage, nucleophilic attack by the OH2 against PG, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.

DOI： 10.1073/pnas.2122641119

Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail 査読有り Open Access

Takeda Shuichi, Koike Ryotaro, Fujiwara Ikuko, Narita Akihiro, Miyata Makoto, Ota Motonori, Maeda Yuichiro

JOURNAL OF MOLECULAR BIOLOGY 433 巻 ( 9 ) 頁： 166891 2021年4月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Journal of Molecular Biology

Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.

DOI： 10.1016/j.jmb.2021.166891

Crystal structure of human V-1 in the apo form 査読有り Open Access

Takeda Shuichi, Koike Ryotaro, Nagae Takayuki, Fujiwara Ikuko, Narita Akihiro, Maeda Yuichiro, Ota Motonori

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 77 巻 ( Pt 1 ) 頁： 13 - 21 2021年1月

記述言語：日本語掲載種別：研究論文（学術雑誌）出版者・発行元：Acta Crystallographica Section F: Structural Biology Communications

V-1, also known as myotrophin, is a 13 kDa ankyrin-repeat protein that binds and inhibits the heterodimeric actin capping protein (CP), which is a key regulator of cytoskeletal actin dynamics. The crystal structure of V-1 in complex with CP revealed that V-1 recognizes CP via residues spanning several ankyrin repeats. Here, the crystal structure of human V-1 is reported in the absence of the specific ligand at 2.3 Å resolution. In the asymmetric unit, the crystal contains two V-1 monomers that exhibit nearly identical structures (Cαr.m.s.d. of 0.47 Å). The overall structures of the two apo V-1 chains are also highly similar to that of CP-bound V-1 (Cαr.m.s.d.s of <0.50 Å), indicating that CP does not induce a large conformational change in V-1. Detailed structural comparisons using the computational program All Atom Motion Tree revealed that CP binding can be accomplished by minor side-chain rearrangements of several residues. These findings are consistent with the known biological role of V-1, in which it globally inhibits CP in the cytoplasm.

DOI： 10.1107/S2053230X20016829

All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins. 招待有り査読有り Open Access

Koike R, Ota M.

Biophys Physicobiol. 2019年11月

Interface property responsible for effective interactions of protean segments: Intrinsically disordered regions that undergo disorder-to-order transitions upon binding. 査読有り

Shaji D, Amemiya T, Koike R, Ota M.

Biochem Biophys Res Commun. 478 巻頁： 123-127 2016年9月

Multiple-Localization and Hub Proteins. 査読有り Open Access

Ota M, Gonja H, Koike R, Fukuchi S.

PLoS One 11 巻頁： e0156455 2016年6月

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation. 査読有り Open Access

Moritsugu K, Koike R, Yamada K, Kato H, Kidera A.

PLoS One 10 巻頁： e0131583 2015年7月

Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+ -ATPase. 査読有り

Kobayashi C, Koike R, Ota M, Sugita Y.

Proteins 頁： - 2015年1月

Domain-Motion-Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. 査読有り

Kobayashi C, Matsunaga Y, Koike R, Ota M, Sugita Y.

Journal of Physical Chemistry B 頁： - 2015年

IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. 査読有り Open Access

Fukuchi S, Amemiya T, Sakamoto S, Nobe Y, Hosoda K, Kado Y, Murakami SD, Koike R, Hiroaki H, Ota M.

Nucleic Acids Res 42 巻頁： D320-D325 2014年1月

Substrate-shielding and hydrolytic reaction in hydrolases. 査読有り

Kanematsu Y, Koike R, Amemiya T, Ota M.

Proteins 頁： - 2013年6月

An assignment of intrinsically disordered regions of proteins based on NMR structures. 査読有り Open Access

Ota M, Koike R, Amemiya T, Tenno T, Romero PR, Hiroaki H, Dunker AK, Fukuchi S.

J Struct Biol. 181 巻頁： 29-36 2013年1月

Influence of structural symmetry on protein dynamics. 査読有り Open Access

Matsunaga Y, Koike R, Ota M, Tame JR, Kidera A.

PLoS One 7 巻頁： e50011 2012年11月

PSCDB: a database for protein structural change upon ligand binding. Open Access

Amemiya T, Koike R, Kidera A, Ota M.

Nucleic Acid Res. 40 巻頁： D554-D558 2012年1月

IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. Open Access

Fukuchi S, Sakamoto S, Nobe Y, Murakami SD, Amemiya T, Hosoda K, Koike R, Hiroaki H, Ota M.

Nucleic Acid Res. 40 巻頁： D507-D511 2012年1月

Cover and spacer insertions: small nonhydrophobic accessories that assist protein oligomerization.

Nishi H, Koike R, Ota M.

Proteins 79 巻頁： 2372-2379 2011年8月

Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function.

Takeda S, Koike R, Nitanai Y, Minakata S, Maéda Y, Ota M.

Phys Biol 8 巻頁： 035005 2011年6月

Classification and annotation of the relationship between protein structural change and ligand binding.

Amemiya T, Koike R, Fuchigami S, Ikeguchi M, Kidera A.

J Mol Biol 408 巻頁： 568-584 2011年5月

SAHG, a comprehensive database of predicted structures of all human proteins. Open Access

Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M.

Nucleic Acid Res. 39 巻頁： D487-D493 2011年1月

Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition. 査読有り Open Access

Takeda S., Minakata S., Koike R., Kawahata I., Narita A., Kitazawa M., Ota M., Yamakuni T., Maéda Y. and Nitanai Y.

PLoS Biol. 8 巻頁： e1000416. 2010年

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. 査読有り Open Access

Koike R., Kidera A. and Ota M.

Protein Sci. 10 巻頁： 2060-2066 2009年

Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. 査読有り

Koike R., Amemiya T., Ota M. and Kidera A.

J. Mol. Biol. 379 巻頁： 397-401 2008年

Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information. 査読有り

Koike R., Kinoshita K. and Kidera A.

Proteins 66 巻頁： 655-663 2007年

Probabilistic description of protein alignments for sequences and structures. 査読有り

Koike R., Kinoshita K. and Kidera A.

Proteins 56 巻頁： 157-166 2004年

Ring and zipper formation is the key to understanding the structural variety in all-beta proteins. 査読有り

Koike R., Kinoshita K. and Kidera A.

FEBS Lett. 533 巻頁： 9-13 2003年

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<小池 亮太郎>

論文 - 小池 亮太郎

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論文 - 小池　亮太郎