著者

水谷 泰久 水野 操

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.1, pp.010-013, 2011 (Released:2011-01-26)

参考文献数

18

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Time-resolved resonance Raman spectroscopy is able to provide site-selective information on protein dynamics. In this review, we will describe our apparatus of picosecond time-resolved ultraviolet resonance Raman spectroscopy and recent application to protein dynamics of bacteriorhodopsin.

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.47, no.5, pp.288-294, 2007 (Released:2007-09-28)

参考文献数

27

被引用文献数

3 1 3

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In numerous biological processes, the ensuing protein structural changes accompanying a reaction at a specific site must spatially extend to the mesoscopic dimensions of the protein to achieve a biological function. The molecular mechanism of cooperativity in oxygen binding of hemoglobin is one of the classical problems in this aspect. This review describes our recent works on protein dynamics of myoglobin and hemoglobin by using time-resolved resonance Raman spectroscopy.

著者

Ariyama Hirotaka Yamazaki Masahito

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.1, 2008-10-25

著者

太和田 勝久

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.44, no.2, pp.92-92, 2004 (Released:2004-03-23)

著者

内山 郁夫

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.42, no.6, pp.266-269, 2002 (Released:2002-11-23)

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MBGD is a database system for making use of rapidly accumulating microbial genome sequences through comparative analysis. The basic function of MBGD is to create an orthologous gene classification table, which comprises sets of "equivalent" genes among multiple genomes. In MBGD, classification tables can be created on demand with specified set of organisms and parameters. This feature becomes important to understand diversity of genomes using almost a hundred genome sequences now available.

著者

東原 和成

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.44, no.1, pp.26-31, 2004 (Released:2004-01-22)

被引用文献数

2 2

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Olfactory receptors (ORs), which comprise the largest G protein-coupled receptor family, play a pivotal role in recognizing a variety of odorants in the vertebrate olfactory system. Recent successes in functional cloning and expression of ORs facilitated construction of ligand-activity matrices of ORs. Activation of a combinatorial receptor repertoire by an odorant determines an odor quality of the odorant, while activated ORs by an odorant mixture is not simply the sum of those for its components due to OR antagonism between odorants. Mixing odorants, thereby, often results in a novel perceptual quality that is not present in each component. The recent atomic-level structure for bovine rhodopsin has provided an opportunity to elucidate a molecular basis for odorant recognition by an OR and characterize the active site of an OR.

著者

Morishima Keisuke Sakuma Yui Iwabuchi Kikuo Akiyama Yoshikatsu Yamato Masayuki Okano Teruo

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.49, no.1, 2009-09-20

著者

柳田 敏雄

出版者

The Biophysical Society of Japan General Incorporated Association

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.50, no.3, pp.116-117, 2010-05-25

被引用文献数

1 1

著者

本田 真也

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.49, no.3, pp.126-129, 2009 (Released:2009-05-25)

参考文献数

16

---

On the ideology of minimalism, we have designed a micro-protein consisting of only 10 amino acids. The molecule, CLN025, exhibits a β-hairpin structure in both crystalline state and aqueous solution. Thermal unfolding is shown to be reversible and can be fitted as a two-state transition. Molecular dynamics simulation starting from an extended conformation leads to a funnel-shaped surface and scale-free network, being the structures located at the bottom and the hub similar to the experimental ones. Considering these consequences, we proposed the concept of “ideal protein” as a way to clarify the differences between “protein” and “peptide”.

著者

難波 啓一

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.3, pp.118-123, 2003-05-25

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The bacterial flagellar filament is a helical propeller for the rapid swimming of bacteria. Its gently curved and iwisted tubular structure is made of a single protein, flagellin, by its self-assembly in a helical manner. The mechanism for the formaiion of the left-handed helical tube for swimming and its dynamic polymorphic transition into right-handed forms for tumbling in response to quick reversal of the motor rotation has been revealed in the filament and protofilament structures at atomic detail obtained by convergent application of electron cryomicroscopy, X-ray fiber diffraction and X-ray crystallography with new technological devices in each of these methods.

著者

和田 昭允

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.42, no.3, pp.140-141, 2002 (Released:2002-05-28)

著者

塚崎 智也

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.5, pp.236-237, 2011 (Released:2011-09-25)

参考文献数

10

著者

吉田 紀生 丸山 豊 PHONGPHANPHANEE Saree 清田 泰臣 平田 文男

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.51, no.5, pp.222-225, 2011 (Released:2011-09-25)

参考文献数

13

被引用文献数

2 1

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Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the 3D-RISM/RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as “recognized” by the protein. 3D-distribution functions can be obtained by means of 3D-RISM/RISM theory. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands such as water, ions, and carbon monoxide by a protein.

著者

佐藤 哲也 山西 芳裕 金久 實 藤 博幸

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.47, no.1, pp.004-011, 2007 (Released:2007-02-21)

参考文献数

6

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A distance matrix is a set of genetic distances between all possible pairs of proteins under consideration, and is used to construct a phylogenetic tree by the distance matrix method. Pazos and Valencia (2001) have developed a method to predict protein-protein interaction by evaluating the similarity of the distance matrices, under the assumption that the phylogenetic trees of interacting proteins resemble each other through co-evolution. It is known, however, that the prediction includes many false positives. We postulated that the cause of the false positives is the background similarity of the phylogenetic relationship of the source organisms. We have developed a method to exclude such information from the distance matrices with a projection operator. The number of false positives was drastically reduced from the prediction by evaluating the similarity between the residuals after the projection operation.

著者

西坂 崇之 政池 知子

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.47, no.2, pp.118-123, 2007 (Released:2007-03-31)

参考文献数

18

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F1-ATPase is a rotary molecular motor in which unidirectional rotation of the central γ-subunit is powered by ATP hydrolysis in three catalytic sites arranged 120° apart around γ. To see how hydrolysis reactions produce mechanical rotation, we observed rotation of γ under the optical microscope, while watching which of the three sites bound and released a fluorescent ATP analog. The reaction scheme, including both the number of site occupancy and reactions that trigger substeps, is now established.

著者

有本 理恵子

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.38, no.6, pp.264-266, 1998-11-01

参考文献数

8

著者

細谷 俊彦 Baccus Stephen Meister Markus

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.45, 2005

著者

田中 秀明

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.49, no.6, pp.302-303, 2009 (Released:2009-11-26)

参考文献数

9

著者

高橋 聡 石島 秋彦 大木 和夫 木下 賢吾 鈴木 誠 新村 信雄 本田 真也 若槻 壮市

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.4, pp.192-195, 2011 (Released:2011-07-25)

著者

一ノ瀬 純也 井頭 昌彦 大木 和夫

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.39, no.1, 1999-09-02