著者

Daichi Yamada Tatsuya Iwata Junpei Yamamoto Kenichi Hitomi Takeshi Todo Shigenori Iwai Elizabeth D. Getzoff Hideki Kandori

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.12, pp.139-144, 2015 (Released:2015-12-22)

参考文献数

34

被引用文献数

1 8

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Photolyases (PHRs) are DNA repair enzymes that revert UV-induced photoproducts, either cyclobutane pyrimidine dimers (CPD) or (6-4) photoproducts (PPs), into normal bases to maintain genetic integrity. (6-4) PHR must catalyze not only covalent bond cleavage, but also hydroxyl or amino group transfer, yielding a more complex mechanism than that postulated for CPD PHR. Previous mutation analysis revealed the importance of two histidines in the active center, H354 and H358 for Xenopus (6-4) PHR, whose mutations significantly lowered the enzymatic activity. Based upon highly sensitive FTIR analysis of the repair function, here we report that both H354A and H358A mutants of Xenopus (6-4) PHR still maintain their repair activity, although the efficiency is much lower than that of the wild type. Similar difference FTIR spectra between the wild type and mutant proteins suggest a common mechanism of repair in which (6-4) PP binds to the active center of each mutant, and is released after repair, as occurs in the wild type. Similar FTIR spectra also suggest that a decrease in volume by the H-to-A mutation is possibly compensated by the addition of water molecule(s). Such a modified environment is sufficient for the repair function that is probably controlled by proton-coupled electron transfer between the enzyme and substrate. On the other hand, two histidines must work in a concerted manner in the active center of the wild-type enzyme, which significantly raises the repair efficiency.

著者

Saki Aoto Kei Yura

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.12, pp.103-116, 2015 (Released:2015-12-02)

参考文献数

69

被引用文献数

2

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We addressed the evolutionary trace of hetero-oligomer interfaces by comparing the structures of paralogous proteins; one of them is a monomer or homo-oligomer and the other is a hetero-oligomer. We found different trends in amino acid conservation pattern and hydrophobicity between homo-oligomer and hetero-oligomer. The degree of amino acid conservation in the interface of homo-oligomer has no obvious difference from that in the surface, whereas the degree of conservation is much higher in the interface of hetero-oligomer. The interface of homo-oligomer has a few very conserved residue positions, whereas the residue conservation in the interface of hetero-oligomer tends to be higher. In addition, the interface of hetero-oligomer has a tendency of being more hydrophobic compared with the one in homo-oligomer. We conjecture that these differences are related to the inherent symmetry in homo-oligomers that cannot exist in hetero-oligomers. Paucity of the structural data precludes statistical tests of these tendencies, yet the trend can be applied to the prediction of the interface of hetero-oligomer. We obtained putative interfaces of the subunits in CPSF (cleavage and polyadenylation specificity factor), one of the human pre-mRNA 3’-processing complexes. The locations of predicted interface residues were consistent with the known experimental data.

著者

Tetsuichi Wazawa Nobuyuki Morimoto Takeharu Nagai Makoto Suzuki

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.12, pp.87-102, 2015 (Released:2015-12-02)

参考文献数

57

被引用文献数

1

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Investigation of the rotational motion of a fluorescent probe tethered to a protein helps to elucidate the local properties of the solvent and protein near the conjugation site of the probe. In this study, we have developed an instrument for frequency-domain fluorescence (FDF) anisotropy measurements, and studied how the local properties around a protein, actin, can be elucidated from the rotational motion of a dye tethered to actin. Rhodamine 6G (R6G) was attached to Cys-374 using newly-synthesized R6G-maleimide with three different oligo(ethylene glycol) (OEG) linker lengths. The time-resolved anisotropy decay of R6G tethered to G-actin was revealed to be a combination of the two modes of the wobbling motion of R6G and the tumbling motion of G-actin. The rotational diffusion coefficient (RDC) of R6G wobbling was ~0.1 ns–1 at 20°C and increased with OEG linker length. The use of the three R6G-actin conjugates of different linker lengths was useful to not only figure out the linker length dependence of the rotational motion of R6G but also validate the analyses. In the presence of a cosolvent of glycerol, although the tumbling motion of G-actin was retarded in response to the bulk viscosity, the wobbling motion of R6G tethered to actin exhibited an increase of RDC as glycerol concentration increased. This finding suggests an intricate relationship between the fluid properties of the bulk solvent and the local environment around actin.

著者

朴 三用

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.074-079, 2010 (Released:2010-03-30)

参考文献数

14

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Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. Influenza virus reproduces rapidly, mutates frequently, and occasionally crosses species barriers. The recent emergence of swine-origin influenza H1N1 and avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. I describe two crystal structures of complexes made by fragments of PA and PB1, and PB1 and PB2. These novel interfaces are surprisingly small, yet they play a crucial role in regulating the 250 kDa polymerase complex, and are completely conserved among swine, avian and human influenza viruses. Given their importance to viral replication and strict conservation, the PA/PB1 and PB1/PB2 interfaces appear to be promising targets for novel anti-influenza drugs of use against all strains of influenza A virus. It is hoped that the structures presented here will assist the search for such compounds.

著者

杉村 薫 石原 秀至

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.55, no.4, pp.210-211, 2015 (Released:2015-07-31)

参考文献数

7

著者

Yuki Yanagisawa Kosuke Hasegawa Naohisa Wada Masatoshi Tanaka Takao Sekiya

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.12, pp.69-78, 2015 (Released:2015-11-12)

参考文献数

19

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Chemiluminescence (CL) of firefly luciferin (Ln) consisting of red and green emission peaks can be generated by dissolving oxygen (O2) gas in deoxygenated dimethyl sulfoxide containing potassium tert-butoxide (t-BuOK) even without the enzyme luciferase. In this study, the characteristics of CL of Ln are examined by varying the concentrations of both Ln ([Ln]) and t-BuOK ([t-BuOK]). The time courses of the green and the red luminescence signals are also measured using a 32-channel photo sensor module. Interestingly, addition of 18-crown-6 ether (18-crown-6), a good clathrate for K+, to the reaction solution before exposure to O2 changes the luminescence from green to red when [t-BuOK] = 20 mM and [18-crown-6] = 80 mM. Based on our experimental results, we propose a two-pathway model where K+ plays an important role in the regulation of Ln CL to explain the two-color luminescence observed from electronically excited oxyluciferin via dioxetanone.

著者

吉川 雅英 八木 俊樹

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.48, no.6, pp.325-329, 2008 (Released:2008-12-02)

参考文献数

21

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Eukaryotic cilia and flagella are highly specialized organelles that play important roles in generating motions and sensing flows. Here, we review recent progresses in cilia / flagella studies, focusing on their structural studies by cryo-electron microscopy.

著者

末次 志郎 高橋 重成 伊藤 弓弦 竹村 和浩 嶋田 睦 北尾 彰朗 森 泰生

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.55, no.5, pp.262-265, 2015 (Released:2015-09-29)

参考文献数

10

著者

Eiji Kanamori Shin-ichi Kawaguchi Seiki Kuramitsu Tsutomu Kouyama Midori Murakami

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.12, pp.47-56, 2015 (Released:2015-10-10)

参考文献数

23

被引用文献数

1 6

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The crystal structures of citrate synthase from the thermophilic eubacteria Thermus thermophilus HB8 (TtCS) were determined for an open form at 1.5 Å resolution and for closed form at 2.3 Å resolution, respectively. In the absence of ligands TtCS in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. TtCS was also co-crystallized with citrate and coenzyme-A to form an orthorhombic crystal with two homodimers in the asymmetric unit. Citrate and CoA are found in the active site situated between the large domain and the small domain in all subunit whereas the complex shows two distinct closed conformations, the fully closed form and partially closed form.Structural comparisons are performed to describe conformational changes associated with binding of products of TtCS. Upon binding of citrate, basic residues in the active site move toward citrate and make a hydrogen bond network in the active site, inducing a large-scale rotation of the small domain relative to the large domain. CoA is sandwiched between the small and large domains and then the cysteamine tail is inserted into the active site with a cooperative rotation around mainchain dihedrals in the hinge region connecting helices M and N. According to this rotation these helices are extended to close the active site completely. The considerable flexibility and structural rearrangements in the hinge region are crucial for an ordered bibi reaction in catalysis for microbial CSs.

著者

藤本 和宏

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.51, no.3, pp.140-143, 2011 (Released:2011-05-25)

参考文献数

10

著者

Takumi Koshiba

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.12, pp.31-35, 2015 (Released:2015-09-09)

参考文献数

27

被引用文献数

1

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Protein-protein interactions are essential biological reactions occurring at inter- and intra-cellular levels. The analysis of their mechanism is generally required in order link to understand their various cellular functions. Bioluminescence resonance energy transfer (BRET), which is based on an enzymatic activity of luciferase, is a useful tool for investigating protein-protein interactions in live cells. The combination of the BRET system and biomolecular fluorescence complementation (BiFC) would provide us a better understanding of the hetero-oligomeric structural states of protein complexes. In this review, we discuss the application of BRET to the protein-protein interactions of mitochondrial-associated proteins and discuss its physiological relevance.

著者

Hitomi Nakashima Chika Okimura Yoshiaki Iwadate

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.12, pp.21-29, 2015 (Released:2015-08-21)

参考文献数

50

被引用文献数

1 6

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Cell-crawling migration plays an essential role in complex biological phenomena. It is now generally believed that many processes essential to such migration are regulated by microtubules in many cells, including fibroblasts and neurons. However, keratocytes treated with nocodazole, which is an inhibitor of microtubule polymerization – and even keratocyte fragments that contain no microtubules – migrate at the same velocity and with the same directionality as normal keratocytes. In this study, we discovered that not only these migration properties, but also the molecular dynamics that regulate such properties, such as the retrograde flow rate of actin filaments, distributions of vinculin and myosin II, and traction forces, are also the same in nocodazole-treated keratocytes as those in untreated keratocytes. These results suggest that microtubules are not in fact required for crawling migration of keratocytes, either in terms of migrating properties or of intracellular molecular dynamics.

著者

伊藤 悦朗

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.55, no.4, pp.177-177, 2015 (Released:2015-07-31)

著者

Koji Oda Masahiro Kinoshita

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.12, pp.1-12, 2015 (Released:2015-07-31)

参考文献数

47

被引用文献数

4 11

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There is an empirical rule that the thermal stability of a protein is related to the packing efficiency or core volume of the folded state and the protein tends to exhibit higher stability as the backbone and side chains are more closely packed. Previously, the wild type and its nine mutants of staphylococcal nuclease were compared by examining their folded structures. The results obtained were as follows: The stability was not correlated with the number of intramolecular hydrogen bonds, intramolecular electrostatic interaction energy, or degree of burial of the hydrophobic surface; though the empirical rule mentioned above held, it was not the proximate cause of higher stability; and the number of van der Waals contacts NvdW, or equivalently, the intramolecular van der Waals interaction energy was an important factor governing the stability. Here we revisit the wild type and its nine mutants of staphylococcal nuclease using our statistical-mechanical theory for hydration of a protein. A molecular model is employed for water. We show that the pivotal factor is the magnitude of the water-entropy gain upon folding. The gain originates from an increase in the total volume available to the translational displacement of water molecules coexisting with the protein in the system. The magnitude is highly correlated with the denaturation temperature Tm. Moreover, the apparent correlation between NvdW and Tm as well as the empirical rule is interpretable (i.e., their physicochemical meanings can be clarified) on the basis of the water-entropy effect.

著者

三宅 教尚 栗原 堅三

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.23, no.3, pp.135-145, 1983-05-25 (Released:2009-05-25)

参考文献数

58

被引用文献数

1 1

---

In the field of physiology, it has generally been Considered that changes in the phase boundary potential do not affect membrane potentials. The present review shows that the phase boundary potential directly contributes to the membrane potential of a number of cells. (1) The K+-channels of mouse neuroblastoma (N-18 cells) are open at high external K+-concentration but closed at low K+-concentration including the physiological one. Under physiological conditions, the resting membrane potentials of N-18 cells stem significantly from the phase boundary potentials. Theoretical consideration shows that changes in the phase boundary potentials directly affect the membrane potential when no selective channels are open. (2) Changes in the phase boundary potential also contribute to the receptor potentials in taste cells, olfactory cells and Tetrahymena as well as to the resting potentials of these cells: adsorption of chemical stimuli on the receptor membranes of these cells induces changes in the phase boundary potential, which leads to depolarization of the cells.

著者

藤田 克昌 袖岡 幹子

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.52, no.1, pp.034-035, 2012 (Released:2012-01-31)

参考文献数

6

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.55, no.2, pp.115-116, 2015 (Released:2015-03-31)

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.52, no.6, pp.312-312, 2012 (Released:2012-11-27)

著者

村越 秀治

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.52, no.3, pp.158-159, 2012 (Released:2012-05-30)

参考文献数

9

著者

松本 博行 黒野 定 小森 直香

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.43, no.6, pp.291-294, 2003 (Released:2003-11-23)

被引用文献数

1 1