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

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

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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

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

---

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

---

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

---

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

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

西川 和男 八木 久晴 馬場 藍 Digel I. Demirci T. Artmann G.M.

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理

巻号頁・発行日

vol.44, 2004

著者

井上 豪 裏出 良博

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.47, no.1, pp.036-043, 2007 (Released:2007-02-21)

参考文献数

22

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The structural based drug-design (SBDD) is one of the useful methods for producing a novel medicine. We recently succeeded in X-ray crystallographic determination of two target molecules. One is human hematopoietic prostaglandin (PG) D synthase (H-PGDS) that produces PGD2 as an allergic mediator in mast cells and Th2 cells. The other is Trypanosoma brucei PGF2α synthase (TbPGFS), a member of the aldo-ketoreductase superfamily, catalyzes the NADPH-dependent reduction of PGH2 to PGF2α, whose overproduction during trypanosomiasis causes miscarriage in infected female subjects. In this report, we introduce the recent progress in the research of the high resolution structures of human H-PGDS and TbPGFS useful for SBDD.

著者

田口 英樹

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.46, no.3, pp.130-136, 2006 (Released:2006-05-25)

参考文献数

27

被引用文献数

1 1

---

The chaperonin GroEL is an essential molecular chaperone that assists protein folding in the cell. ATP-dependent conformational change of GroEL leads to the stable binding of cochaperonin GroES, forming a cage-shaped complex that accommodates a substrate protein to complete the folding. After the elucidation of the outline of the molecular mechanism over the last decade, now we are ready to answer the important questions; how GroEL encapsulate the substrate protein? How the substrate protein influences the functional cycle of GroEL? What is the role of ATP hydrolysis in the GroEL-assisted folding? Is the folding in the GroEL-ES cavity is same as that in the bulk solution? Here I review the recent progress on the GroEL study and discuss the essential role of chaperonin GroEL.

著者

矢野 雅文 三浦 治己

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.5, pp.306-311, 1999-09-25 (Released:2000-04-12)

参考文献数

9

被引用文献数

1

---

It is assumed that positional information within a developing organism is represented by a morphogen gradient. However, it is not yet understood how positional information is organized in a size invariant manner. To achieve such size invariance, it is necessary for an organism to organize the polarity of positional information in advance. We focus on tactic behavior of the Physarum plasmodium and propose a model that describes the organization of size invariant positional information, in which the direction of the phase wave represents the polarity. We would like to point out that self-referential dynamics exist in our model, and their implementation is discussed. Our mode may be applied to other developmental systems.

著者

浜田 大三 Dobson Christopher.M.

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.40, 2000

著者

龍野 正実

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.6, pp.368-377, 2007 (Released:2007-11-30)

参考文献数

50

被引用文献数

1 1

---

The replay of behaviorally induced multi-neuronal activity patterns during subsequent sleep or quiet waking is conjectured to play an important role in the consolidation process of certain types of memory. During the early stages of memory consolidation, the hippocampus appears to be critical; however, over time the involvement of the hippocampus decreases as the memories become gradually consolidated in the neocortex. In this article, we review how temporal spike patterns are replayed during sleep and the possible interactions of the hippocampus and neocortex through these patterns.

著者

田中 正太郎 小橋川 敬博 三浦 和紀 西宮 佳志 三浦 愛 津田 栄

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.130-135, 2003 (Released:2003-05-23)

被引用文献数

3 1

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In 1969, the first antifreeze protein (AFP) was discovered from the blood plasma of Antarctic Nototheniids. In the past thirty years, different types of AFP have been found in many life forms that exhibit freezing tolerance, such as bacteria, fungi, plants, insects, and vertebrates. These discoveries have evoked us many questions regarding to the antifreeze mechanism and its biological significance for preventing their tissues from freezing damage. At present, ice physicist, biologist, chemist, biochemist, molecular biologist, physiologist, and NMR and X-ray structural biologists are subjecting AFP, which greatly improves our understandings about AFP and accelerates its applicability to various cryo-industries. In the present review we will describe an updated biophysical aspects of AFP to highlight the interests of this research field.

著者

河野 敬一 相沢 智康

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.2, pp.109-112, 1999-03-25 (Released:2000-04-12)

参考文献数

8

著者

岡田 公太郎 神崎 亮平

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.43, no.2, pp.101-104, 2003 (Released:2003-03-25)

著者

中野 修一 杉本 直己

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.46, no.5, pp.251-256, 2006 (Released:2006-09-25)

参考文献数

29

被引用文献数

1

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The medium of biomolecules in a living cell differs remarkably from a dilute solution, and many properties of biomolecules that are not observed in vitro are emerged as a result of such intracellular environments. Molecular crowding which is one of the important intracellular environments changes equilibria and rates of biomolecular interactions. Studies with solutions containing high concentration of water-soluble inert cosolutes reveal influences of the molecular crowding on the structures and interactions of proteins and nucleic acids, providing significant insights not only into traditional biology but also bionanotechnology.