研究者詳細 - 太田　元規

Prediction of chaperonin GroE substrates using small structural patterns of proteins 査読有り国際誌

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

担当区分：最終著者,　責任著者記述言語：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

How AlphaFold2 predicts conditionally folding regions annotated in an intrinsically disordered protein database 査読有り国際誌

H. Anbo, K. Sakuma, S. Fukuchi, M. Ota

Biology 12 巻頁： 182 2023年1月

Classification of proteins inducing liquid-liquid phase separation: sequential, structural and functional characterization 招待有り査読有り国際誌

Ozawa Yuhei, Anbo Hiroto, Ota Motonori, Fukuchi Satoshi

JOURNAL OF BIOCHEMISTRY 2022年12月

Structures and mechanisms of actin ATP hydrolysis 査読有り国際誌

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 119 巻 ( 43 ) 頁： e2122641119 2022年10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：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

Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2 査読有り

FEBS OPEN BIO 12 巻 ( 1 ) 頁： 285 - 294 2021年11月

Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins 招待有り査読有り

Hijikata Atsushi, Shionyu Clara, Nakae Setsu, Shionyu Masafumi, Ota Motonori, Kanaya Shigehiko, Shirai Tsuyoshi

Biophys. Physicobiol. 18 巻 ( 0 ) 頁： 226 - 240 2021年10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：一般社団法人日本生物物理学会

More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of in silico and in vitro screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity in vitro, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.

DOI： 10.2142/biophysico.bppb-v18.025

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

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

J. Mol. Biol. 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

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

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