著者

豊島 有 飯野 雄一

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.57, no.1, pp.020-022, 2017 (Released:2017-01-26)

参考文献数

9

著者

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.13, pp.245-247, 2016 (Released:2016-11-18)

参考文献数

13

被引用文献数

1 2

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.5, pp.256-256, 2012 (Released:2012-09-26)

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.3, pp.174-174, 2014 (Released:2014-05-27)

著者

田中 幸吉

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.20, no.2, pp.84-93, 1980-03-25 (Released:2009-05-25)

参考文献数

9

---

This article is an introductory overview on artificial intelligence and its applications.The first section explains artificial intelligence and presents a bibliographical survey of related research and development works.The following section contains a brief review on some research topics together with perspectives obtained from a methodological view point.Lastly, some interesting and practical applications of artificial intelligence are illustrated along with the works of the present author.

著者

Oanh T. P. Kim Manh D. Le Hoang X. Trinh Hai V. Nong

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.173-180, 2016 (Released:2016-07-14)

参考文献数

42

被引用文献数

20

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Tumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development. Recent studies demonstrate that triterpene saponins from Vietnamese ginseng are efficient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simulations of TNF-α with three different triterpene saponins (majonoside R2, vina-ginsenoside R1 and vina-ginsenoside R2) were performed to evaluate their binding ability. Our results showed that the triterpene saponins have a good binding affinity with protein TNF-α. The saponins were docked to the pore at the top of the “bell” or “cone” shaped TNF-α trimer and the complexes were structurally stable during 100 ns molecular dynamics simulation. The predicted binding sites would help to subsequently investigate the inhibitory mechanism of triterpene saponins.

著者

Hiroo Imai Nami Suzuki-Hashido Yoshiro Ishimaru Takanobu Sakurai Lijie Yin Wenshi Pan Masaji Ishiguro Katsuyoshi Masuda Keiko Abe Takumi Misaka Hirohisa Hirai

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.165-171, 2016 (Released:2016-07-14)

参考文献数

14

被引用文献数

1 5

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In mammals, bitter taste is mediated by TAS2Rs, which belong to the family of seven transmembrane G protein-coupled receptors. Since TAS2Rs are directly involved in the interaction between mammals and their dietary sources, it is likely that these genes evolved to reflect species-specific diets during mammalian evolution. Here, we analyzed the amino acids responsible for the difference in sensitivities of TAS2R16s of various primates using a cultured cell expression system. We found that the sensitivity of TAS2R16 varied due to several amino acid residues. Mutation of amino acid residues at E86T, L247M, and V260F in human and langur TAS2R16 for mimicking the macaque TAS2R16 decreased the sensitivity of the receptor in an additive manner, which suggests its contribution to the potency of salicin, possibly via direct interaction. However, mutation of amino acid residues 125 and 133 in human TAS2R16, which are situated in helix 4, to the macaque sequence increased the sensitivity of the receptor. These results suggest the possibility that bitter taste sensitivities evolved independently by replacing specific amino acid residues of TAS2Rs in different primate species to adapt to species-specific food.

著者

Masayuki Oda Takeshi Tsumuraya Ikuo Fujii

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.135-138, 2016 (Released:2016-07-14)

参考文献数

14

被引用文献数

2

---

We analyzed the correlation between the conformational strain and the binding kinetics in antigen-antibody interactions. The catalytic antibodies 6D9, 9C10, and 7C8 catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. The crystal structure of 6D9 complexed with a transition-state analog (TSA) suggests that 6D9 binds the substrate to change the conformation of the ester moiety to a thermodynamically unstable twisted conformation, enabling the substrate to reach the transition state during catalysis. The present binding kinetic analysis showed that the association rate for 6D9 binding to the substrate was much lower than that to TSA, whereas those for 9C10 and 7C8 binding were similar to those to TSA. Considering that 7C8 binds to the substrate with little conformational change in the substrate, the slow association rate observed in 6D9 could be attributed to the conformational strain in the substrate.

著者

Yuka Suzuki 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.13, pp.127-134, 2016 (Released:2016-07-14)

参考文献数

26

被引用文献数

4

---

We investigated the effect of ATP binding to GroEL and elucidated a role of ATP in the conformational change of GroEL. GroEL is a tetradecamer chaperonin that helps protein folding by undergoing a conformational change from a closed state to an open state. This conformational change requires ATP, but does not require the hydrolysis of the ATP. The following three types of conformations are crystalized and the atomic coordinates are available; closed state without ATP, closed state with ATP and open state with ADP. We conducted simulations of the conformational change using Elastic Network Model from the closed state without ATP targeting at the open state, and from the closed state with ATP targeting at the open state. The simulations emphasizing the lowest normal mode showed that the one started with the closed state with ATP, rather than the one without ATP, reached a conformation closer to the open state. This difference was mainly caused by the changes in the positions of residues in the initial structure rather than the changes in “connectivity” of residues within the subunit. Our results suggest that ATP should behave as an insulator to induce conformation population shift in the closed state to the conformation that has a pathway leading to the open state.

著者

Georgios Iakovou Stephen Laycock Steven Hayward

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.97-103, 2016 (Released:2016-07-14)

参考文献数

37

被引用文献数

5

---

Interactive haptics-assisted docking provides a virtual environment for the study of molecular complex formation. It enables the user to interact with the virtual molecules, experience the interaction forces via their sense of touch, and gain insights about the docking process itself. Here we use a recently developed haptics software tool, Haptimol_RD, for the rigid docking of protein subunits to form complexes. Dimers, both homo and hetero, are loaded into the software with their subunits separated in space for the purpose of assessing whether they can be brought back into the correct docking pose via rigid-body movements. Four dimers were classified into two types: two with an interwinding subunit interface and two with a non-interwinding subunit interface. It was found that the two with an interwinding interface could not be docked whereas the two with the non-interwinding interface could be. For the two that could be docked a “sucking” effect could be felt on the haptic device when the correct binding pose was approached which is associated with a minimum in the interaction energy. It is clear that for those that could not be docked, the conformation of one or both of the subunits must change upon docking. This leads to the steric-based concept of a locked or non-locked interface. Non-locked interfaces have shapes that allow the subunits to come together or come apart without the necessity of intra-subunit conformational change, whereas locked interfaces require a conformational change within one or both subunits for them to be able to come apart.

著者

Kentaro Ishii Masanori Noda Susumu Uchiyama

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.87-95, 2016 (Released:2016-07-14)

参考文献数

32

被引用文献数

32

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The interactions of small molecules with proteins (protein–ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein–ligand interactions. These interactions typically accompany association–dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development. Mass spectrometry (MS) has been used to determine the precise molecular masses of molecules. Recent advancements in MS enable us to determine the molecular masses of protein–ligand complexes without disrupting the non-covalent interactions through the gentle desolvation of the complexes by increasing the vacuum pressure of a chamber in a mass spectrometer. This method is called MS under non-denaturing conditions or native MS and allows the unambiguous determination of protein–ligand interactions. Under a few assumptions, MS has also been applied to determine the dissociation constants for protein–ligand interactions. The structural information of a protein–ligand interaction, such as the location of the interaction and conformational change in a protein, can also be analyzed using hydrogen/deuterium exchange MS. In this paper, we briefly describe the history, principle, and recent applications of MS for the study of protein–ligand interactions.

著者

Tsukasa Nakamura Kentaro Tomii

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.139-147, 2016 (Released:2016-07-14)

参考文献数

19

被引用文献数

5

---

Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analysis demands a fast and efficient method for comparing ligand binding pockets. Previously we proposed a fast alignment-free method based on a simple representation of a ligand binding pocket with one 11-dimensional vector, which is suitable for such analysis. Based on that method, we conducted this study to expand and revise similarity measures of binding pockets and to investigate the effects of those modifications with two datasets for improving the ability to detect similar binding pockets. The new method exhibits higher detection performance of similar binding pockets than the previous methods and another existing accurate alignment-dependent method: APoc. Results also show that the effects of the modifications depend on the difficulty of the dataset, implying some avenues for methods of improvement.

著者

武藤(細谷) 照子

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.27, no.2, pp.75-83, 1987-03-25 (Released:2009-05-25)

参考文献数

61

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The sex of an individual is determined at fertilization by the combination of sex chromosomes, e.g., XX or XY in mammals. Morphological sex differences become evident during the organization of gonadal primordia into ovaries or testes. Consequently, fetal testes produce hormones which are responsible for the development of the male phenotype. The absence of male hormones results in the development of the females phenotype. It has been proposed that a male dominant, histocompatibility-Y (H-Y) antigendetermines testicular differentiation, based on the finding that individuals with testest are H-Y antigen positive regardless of their sex karyotype. Recently, this hypothesis has been challenged bý the finding of several exceptions, e.g., development of ovaries in the presence of H-Y antigen, and testes in its absence.A testis-determining gene (Tdy or TDF) has been thought to occur on the Y chromosome. Over 100 Y-specific DNA fragments have been examined with only one possible candidate for the Tdy gene. In addition to the Tdy gene, at least two autosomal genes (tda-1 and Tas) appear to be involved in testis determination. It has been suggested that gonadal sex determination may also be influenced by environmental factors.Fetal rat and mouse ovaries develop testicular structures (ovotestes) after transplantation into various sites of adult host animals. This finding suggests that XX gonadal primordial cells can differentiate into testicular cells. Electron microscopic examinations have revealed that testicular structures of mouse ovotestes are comparable to those of the genetic male. Furthermore, it has been shown that ovotestes produce hormones and glycoproteins characteristic of normal neontal testes. These results provide strong evidence for sex reversal by transplantation. The study of the factors involved in the induction of ovotestis development should aid better understanding of the mechanism of gonadal sex determination.

著者

冨永 貴志 冨永 洋子

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.51, no.2, pp.092-095, 2011 (Released:2011-03-30)

参考文献数

10

著者

Ryo Iizuka Takashi Funatsu

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.63-69, 2016 (Released:2016-04-22)

参考文献数

63

被引用文献数

1 9

---

The Escherichia coli chaperonin GroEL is an essential molecular chaperone that mediates protein folding in association with its cofactor, GroES. It is widely accepted that GroEL alternates the GroES-sealed folding-active rings during the reaction cycle. In other words, an asymmetric GroEL–GroES complex is formed during the cycle, whereas a symmetric GroEL–(GroES)2 complex is not formed. However, this conventional view has been challenged by the recent reports indicating that such symmetric complexes can be formed in the GroEL–GroES reaction cycle. In this review, we discuss the studies of the symmetric GroEL–(GroES)2 complex, focusing on the molecular mechanism underlying its formation. We also suggest that GroEL can be involved in two types of reaction cycles (asymmetric or symmetric) and the type of cycle used depends on the concentration of non-native substrate proteins.

著者

Akira R. Kinjo

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.45-62, 2016 (Released:2016-04-22)

参考文献数

33

被引用文献数

8

---

The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences. The model parameters for short-range and long-range interactions were determined by a self-consistent condition and by a Gaussian approximation, respectively. Using this model with and without long-range interactions, I analyzed the globin and V-set domains by increasing the “temperature” and by “mutating” a site. The correlations between residue conservation and various measures of the system’s stability indicate that the long-range interactions make the conservation pattern more specific to the structure, and increasingly stabilize better conserved residues.

著者

櫻井 芳雄

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.084-087, 2010 (Released:2010-03-30)

参考文献数

19

被引用文献数

1

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We introduce the original and present concepts of cell assembly in the working brain and discuss the problem of dynamic size of it. A local cell assembly consisting of closely neighboring neurons was especially difficult to be detected because of spike overlapping of neighboring neurons. We developed a unique technique of spike-sorting that employed independent component analysis and showed that most of closely neighboring neurons in the monkey prefrontal cortex had dynamic and sharp synchrony of firing reflecting local cell assemblies. We propose that real features of cell assemblies could contribute to development of brain-machine interfaces and neuro-rehabilitation.

著者

青島 均

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.28, no.6, pp.296-299, 1988-11-25 (Released:2009-05-25)

参考文献数

18

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Xenopus oocytes were injected with exogenous mRNA prepared from rat small intestine and kidney and their electrical responses to glucose and amino acids were measured electrophysiologically. Na+/glucose, amino acid cotransporters were expressed in the oocytes by injection of small intestine mRNA, while facilitated diffusion carrier protein(s) (uniporter) were mainly expressed by injection of kindney mRNA.

著者

今井 隆志

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.6, pp.298-299, 2010 (Released:2010-11-25)

参考文献数

8

被引用文献数

1

著者

Tatsuhito Matsuo Soichi Takeda Toshiro Oda Satoru Fujiwara

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.145-158, 2015 (Released:2015-12-22)

参考文献数

59

被引用文献数

10

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Troponin (Tn), consisting of three subunits, TnC, TnI, and TnT, is a protein in the thin filaments in muscle, and, together with another thin-filament protein tropomyosin (Tm), plays a major role in regulation of muscle contraction. Various mutations of Tn cause familial hypertrophic cardiomyopathy. These mutations are directly related to aberrations in this regulatory mechanism. Here we focus on the mutations E244D and K247R of TnT, which reside in the middle of the pathway of the Ca2+-binding signal from TnC to Tm. These mutations induce an increase in the maximum tension of cardiac muscle without changes in Ca2+-sensitivity. As a first step toward elucidating the molecular mechanism underlying this functional aberration, we carried out small-angle X-ray scattering experiments on the Tn core domain containing the wild type subunits and those containing the mutant TnT in the absence and presence of Ca2+. Changes in the overall shape induced by the mutations were detected for the first time by the changes in the radius of gyration and the maximum dimension between the wild type and the mutants. Analysis of the scattering curves by model calculations shows that TnC adopts a dumbbell structure regardless of the mutations, and that the mutations change the distributions of the conformational ensembles so that the flexible N- and C-terminal regions of TnT become close to the center of the whole moelcule. This suggests, since these regions are related to the Tn-Tm interactions, that alteration of the Tn-Tm interactions induced by the mutations causes the functional aberration.