著者

飯野 亮太 鈴木 健一 中村 彰彦

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.60, no.2, pp.133-134, 2020 (Released:2020-03-27)

著者

児玉 孝雄

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.50, no.2, pp.094-095, 2010 (Released:2010-03-30)

参考文献数

7

著者

中村 彰彦 岡崎 圭一 古田 忠臣 櫻井 実 飯野 亮太

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.59, no.6, pp.330-333, 2019 (Released:2019-11-25)

参考文献数

7

著者

水谷 泰久

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.59, no.6, pp.291, 2019 (Released:2019-11-25)

著者

新海 暁男

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.54, no.5, pp.247-252, 2014 (Released:2014-09-30)

参考文献数

34

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Adaptive immunity is acquired when foreign substances enter the body. Interestingly, this immune system exists not only higher organisms but also many bacteria. The CRISPR-Cas systems are the bacterial adaptive immune systems against foreign DNA and RNA derived from phages or plasmids. Many bacteria can memorize the sequences of foreign DNA and RNA, and remove them by means of these systems. Structural and functional studies of these systems have dramatically progressed over the past few years. In particular, one of the CRISPR-Cas systems, Cas9, has received considerable attention as a highly efficient tool for genome editing.

著者

新土 優樹

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.59, no.3, pp.171-172, 2019 (Released:2019-05-25)

著者

岸本 泰司

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.50, no.4, pp.195-198, 2010 (Released:2010-07-25)

参考文献数

10

著者

上田 哲男 小畠 陽之助

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.25, no.3, pp.91-99, 1985-05-25 (Released:2009-05-25)

参考文献数

17

被引用文献数

1

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Biological cell is the smallest system in which energy is transformed and information is processed autonomously. This complex and fascinating system is in the far from equilibrium state, and hence can manifest self-excited oscillations. Here we will describe rhythmic locomotion in amoeboid cells, oscillatory responses to chemical stimuli and rhythmic morphogenesis. Their biological and biophysical implications are discussed.

著者

宮下 治 タマ フロハンス

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.57, no.2, pp.090-094, 2017 (Released:2017-03-30)

参考文献数

20

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Hybrid approaches combine computational modeling techniques with low-resolution structural data. Such approaches have proven to be powerful tools to obtain new 3D structural and dynamical information on biological systems. Currently, major applications focus on cryo-EM data. Methods and some applications to construct atomic structural models of new functional states will be reviewed. In addition, possible extension to data from X-ray free electron laser, which currently provides low-resolution data, will be discussed.

著者

河村 悟

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.48, no.5, pp.269-269, 2008 (Released:2008-09-25)

著者

Junko Taguchi Akio Kitao

出版者

一般社団法人 日本生物物理学会

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

vol.13, pp.117-126, 2016 (Released:2016-07-14)

参考文献数

37

被引用文献数

7

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We examine the dynamic features of non-trivial allosteric binding sites to elucidate potential drug binding sites. These allosteric sites were previously found to be allosteric after determination of the protein-drug co-crystal structure. After comprehensive search in the Protein Data Bank, we identify 10 complex structures with allosteric ligands whose structures are very similar to their functional forms. Then, possible pockets on the protein surface are searched as potential ligand binding sites. To mimic ligand binding to the pocket, complex models are generated to fill out each pocket with pseudo ligand blocks consisting of spheres. Normal mode analysis of the elastic network model is performed for the complex models and unbound structures to assess the change of protein dynamics induced by ligand binding. We examine nine profiles to describe the dynamic and positional characteristics of the pockets, and identify the change of fluctuation around the ligand, ΔMSFbs, as the best profile for distinguishing the allosteric sites from the other sites in 8 structures. These cases should be considered as examples of dynamics-driven allostery, which accompanies significant changes in protein dynamics. ΔMSFbs is suggested to be used for the search of potential dynamics-driven allosteric sites in proteins for drug discovery.

著者

Akihiro Okamoto Yoshihide Tokunou Junki Saito

出版者

一般社団法人 日本生物物理学会

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

vol.13, pp.71-76, 2016 (Released:2016-05-27)

参考文献数

32

被引用文献数

11

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Outer-membrane c-type cytochrome (OM c-Cyt) complexes in several genera of iron-reducing bacteria, such as Shewanella and Geobacter, are capable of transporting electrons from the cell interior to extracellular solids as a terminal step of anaerobic respiration. The kinetics of this electron transport has implications for controlling the rate of microbial electron transport during bioenergy or biochemical production, iron corrosion, and natural mineral cycling. Herein, we review the findings from in-vivo and in-vitro studies examining electron transport kinetics through single OM c-Cyt complexes in Shewanella oneidensis MR-1. In-vitro electron flux via a purified OM c-Cyt complex, comprised of MtrA, B, and C proteins from S. oneidensis MR-1, embedded in a proteoliposome system is reported to be 10- to 100-fold faster compared with in-vivo estimates based on measurements of electron flux per cell and OM c-Cyts density. As the proteoliposome system is estimated to have 10-fold higher cation flux via potassium channels than electrons, we speculate that the slower rate of electron-coupled cation transport across the OM is responsible for the significantly lower electron transport rate that is observed in-vivo. As most studies to date have primarily focused on the energetics or kinetics of interheme electron hopping in OM c-Cyts in this microbial electron transport mechanism, the proposed model involving cation transport provides new insight into the rate detemining step of EET, as well as the role of self-secreted flavin molecules bound to OM c-Cyt and proton management for energy conservation and production in S. oneidensis MR-1.

著者

武森 信曉

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.56, no.2, pp.116-119, 2016 (Released:2016-03-31)

参考文献数

10

著者

小林 徹也 上村 淳

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.53, no.2, pp.086-089, 2013 (Released:2013-03-28)

参考文献数

20

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Biological systems can operate robustly even with substantial stochasticity in their components. One possible but not yet proven mechanism to implement robust operation with noisy components is that relevant information for robust control is embedded in apparently stochastic signals. In this work, by employing Bayesian theory, we theoretically show that intracellular reactions with specific structures can implement statistically optimal dynamics to decode (extract) the relevant information embedded (encoded) within the apparently noisy signal. We also demonstrate that the decoding dynamics is related to a noise-induced transition, implying that optimal dynamics to suppress noise behaves as if exploiting noise for signal amplification.

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.54, no.2, pp.120-121, 2014 (Released:2014-03-28)

著者

野地 博行

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.53, no.5, pp.233-233, 2013 (Released:2013-09-25)

著者

近藤 宗平

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.14, no.3, pp.118-126, 1974-05-25 (Released:2009-05-25)

参考文献数

45

被引用文献数

1 1

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Recent knowledge of DNA repair is reviewed in perspective with emphasis on Escherichia coli. Enzymatic phtoreactivation is the simplest and the most general among the three major DNA repair systems. Excision repair is also common from microorganisms to human and yet its molecular mechanism is not universal. Tolerance repair, i.e., post-replication repair, is effective for the widest variety of DNA damage and rather different between lower and higher forms. From these characteristics, it is proposed that DNA repair mechanisms evolved in the order of photoreactivation, excision repair and tolerance repair after the primary living systems were created by solar ultraviolet.

著者

井上 圭一 今野 雅恵 川﨑 佑真 María del Carmen MARÍN

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.63, no.5, pp.257-260, 2023 (Released:2023-11-25)

参考文献数

16

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シゾロドプシンは真核生物の最終共通祖先に最も近縁な現生種のアスガルドアーキアから見付かった光駆動型内向きH+ポンプロドプシンであり,アスガルドアーキアが光を使って生きている可能性を示唆するものである.H+輸送機構など多くの点でシゾロドプシンは他のロドプシンと異なる.その最新の研究を解説する.

著者

今村(滝川) 寿子 望月 敦史

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.48, no.4, pp.221-227, 2008 (Released:2008-07-25)

参考文献数

29

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A cyanobacterial clock protein KaiC shows circadian cycling of the phosphorylation level in vitro. We first developed an observation-based model. The KaiC-KaiA complex formation consequently reduces free KaiA molecules, thereby may exert a negative feedback effect toward KaiC phosphorylation. However, this model was shown not to be adequate to generate the KaiC phosphorylation cycle. Then, we analyzed generalized models and determined necessary conditions to generate the cycle. Based on the result, we realized the observed pattern of the KaiC phosphorylation cycle and predicted an unknown state that lies between KaiC phosphorylation and the formation of the KaiC/KaiA complex.

著者

清水 浩 戸谷 吉博

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.62, no.2, pp.104-109, 2022 (Released:2022-05-25)

参考文献数

24

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地球規模のCO2問題が叫ばれる中,光合成微生物による化学物質や燃料の環境調和型生産の重要性が注目されている.シミュレーション,代謝フラックス解析,進化工学といったシステムバイオロジーの手法による多様な光環境における藍藻(シアノバクテリア)の光合成システムに関する最近の研究成果を解説する.