著者

Kei Fujiwara Miho Yanagisawa Shin-ichiro M. Nomura

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.10, pp.43-48, 2014 (Released:2014-08-07)

参考文献数

38

被引用文献数

1 15

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Toward reconstitution of living cells by artificial cells technology, it is critical process to understand the differences between mixtures of biomolecules and living cells. For the aim, we have developed procedures for preparation of an additive-free cell extract (AFCE) and for concentrating biomacromolecules in artificial cells. In this review, we introduce our recent progress to reconstitute intracellular environments in vitro and in artificial cells.

著者

Harshita Sharma Fumihito Ohtani Parmila Kumari Deepti Diwan Naoko Ohara Tetsuya Kobayashi Miho Suzuki Naoto Nemoto Yoshibumi Matsushima Koichi Nishigaki

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.10, pp.55-62, 2014 (Released:2014-09-06)

参考文献数

32

被引用文献数

1

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Familial clustering without any prerequisite knowledge becomes often necessary in Behavioral Science, and forensic studies in case of great disasters like Tsunami and earthquake requiring body-identification without any usable information. However, there has been no well-established method for this purpose although conventional ones such as short tandem repeats (STR) and single nucleotide polymorphism (SNP), which might be applied with toil and moil to some extent. In this situation, we could find that the universal genome distance-measuring method genome profiling (GP), which is made up of three elemental techniques; random PCR, micro-temperature gradient gel electrophoresis (μTGGE), and computer processing for normalization, can do this purpose with ease when applied to mouse families. We also confirmed that the sequencing approach based on the ccgf (commonly conserved genetic fragment appearing in the genome profile) was not completely discriminative in this case. This is the first demonstration that the familial clustering can be attained without a priori sequence information to the level of discriminating strains and sibling relationships. This method can complement the conventional approaches in preliminary familial clustering.

著者

Takeshi Kawabata Yusuke Sugihara Yoshifumi Fukunishi Haruki Nakamura

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.9, pp.113-121, 2013 (Released:2013-08-07)

参考文献数

30

被引用文献数

8 25

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A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

著者

YAMADA Naohumi IGUCHI Kakeru AGENO Yasuo 伏見 譲

出版者

日本生物物理学会

雑誌

生物物理化学 = Journal of Electrophoresis (ISSN:05824052)

巻号頁・発行日

vol.48, no.1, pp.S171-S171, 2008

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rights: 日本生物物理学会rights: 本文データは学協会の許諾に基づきCiNiiから複製したものであるrelation: IsVersionOf: http://ci.nii.ac.jp/naid/110007014122/

著者

Ken Nishikawa Akira R. Kinjo

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.10, pp.99-108, 2014 (Released:2014-12-17)

参考文献数

50

被引用文献数

1 12

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We propose the cooperative model of phenotype-driven evolution, in which natural selection operates on a phenotype caused by both genetic and epigenetic factors. The conventional theory of evolutionary synthesis assumes that a phenotypic value (P) is the sum of genotypic value (G) and environmental deviation (E), P=G+E, where E is the fluctuations of the phenotype among individuals in the absence of environmental changes. In contrast, the cooperative model assumes that an evolution is triggered by an environmental change and individuals respond to the change by phenotypic plasticity (epigenetic changes). The phenotypic plasticity, while essentially qualitative, is denoted by a quantitative value F which is modeled as a normal random variable like E, but with a much larger variance. Thus, the fundamental equation of the cooperative model is given as P=G+F where F includes the effect of E. Computer simulations using a genetic algorithm demonstrated that the cooperative model realized much faster evolution than the evolutionary synthesis. This accelerated evolution was found to be due to the cumulative evolution made possible by a ratchet mechanism due to the epigenetic contribution to the phenotypic value. The cooperative model can well account for the phenomenon of genetic assimilation, which, in turn, suggests the mechanism of cumulative selection. The cooperative model may also serve as a theoretical basis to understand various ideas and phenomena of the phenotypedriven evolution such as genetic assimilation, the theory of facilitated phenotypic variation, and epigenetic inheritance over generations.

著者

Keisuke Fujita Mitsuhiro Iwaki

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.10, pp.69-75, 2014 (Released:2014-11-01)

参考文献数

36

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Myosin V is a vesicle transporter that unidirectionally walks along cytoskeletal actin filaments by converting the chemical energy of ATP into mechanical work. Recently, it was found that myosin V force generation is a composition of two processes: a lever-arm swing, which involves a conformational change in the myosin molecule, and a Brownian search-and-catch, which involves a diffusive “search” by the motor domain that is followed by an asymmetric “catch” in the forward actin target such that Brownian motion is rectified. Here we developed a system that combines optical tweezers with DNA nano-material to show that the Brownian search-and-catch mechanism is the energetically dominant process at near stall force, providing 13 kBT of work compared to just 3 kBT by the lever-arm swing. Our result significantly reconsiders the lever-arm swinging model, which assumes the swing dominantly produces work (>10 kBT), and sheds light on the Brownian search-and-catch as a driving process.

著者

Hideki Itoh Kotaro Oyama Madoka Suzuki Shin’ichi Ishiwata

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.10, pp.109-119, 2014 (Released:2014-12-17)

参考文献数

41

被引用文献数

5 18

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Temperature-sensitive Ca2+ dynamics occur primarily through transient receptor potential channels, but also by means of Ca2+ channels and pumps on the endoplasmic reticulum membrane. As such, cytoplasmic Ca2+ concentration ([Ca2+]cyt) is re-equilibrated by changes in ambient temperature. The present study investigated the effects of heat pulses (heating duration: 2 s or 150 s) on [Ca2+]cyt in single WI-38 fibroblasts, which are considered as normal cells. We found that Ca2+ burst occurred immediately after short (2 s) heat pulse, which is similar to our previous report on HeLa cells, but with less thermosensitivity. The heat pulses originated from a focused 1455-nm infrared laser light were applied in the vicinity of cells under the optical microscope. Ca2+ bursts induced by the heat pulse were suppressed by treating cells with inhibitors for sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) or inositol trisphosphate receptor (IP3R). Long (150 s) heat pulses also induced Ca2+ bursts after the onset of heating and immediately after re-cooling. Cells were more thermosensitive at physiological (37°C) than at room (25°C) temperature; however, at 37°C, cells were responsive at a higher temperature (ambient temperature+heat pulse). These results strongly suggest that the heat pulse-induced Ca2+ burst is caused by a transient imbalance in Ca2+ flow between SERCA and IP3R, and offer a potential new method for thermally controlling Ca2+-regulated cellular functions.

著者

David J. Castillo Shuichi Nakamura Yusuke V. Morimoto Yong-Suk Che Nobunori Kami-ike Seishi Kudo Tohru Minamino Keiichi Namba

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.9, pp.173-181, 2013 (Released:2013-12-26)

参考文献数

46

被引用文献数

4 34

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The bacterial flagellar motor is made of a rotor and stators. In Salmonella it is thought that about a dozen MotA/B complexes are anchored to the peptidoglycan layer around the motor through the C-terminal peptidoglycan-binding domain of MotB to become active stators as well as proton channels. MotB consists of 309 residues, forming a single transmembrane helix (30-50), a stalk (51-100) and a C-terminal peptidoglycan-binding domain (101-309). Although the stalk is dispensable for torque generation by the motor, it is required for efficient motor performance. Residues 51 to 72 prevent premature proton leakage through the proton channel prior to stator assembly into the motor. However, the role of residues 72-100 remains unknown. Here, we analyzed the torque-speed relationship of the MotB(Δ72-100) motor. At a low speed near stall, this mutant motor produced torque at the wild-type level. Unlike the wild-type motor, however, torque dropped off drastically by slight decrease in external load and then showed a slow exponential decay over a wide range of load by its further reduction. Since it is known that the stator is a mechanosensor and that the number of active stators changes in a load-dependent manner, we interpreted this unusual torque-speed relationship as anomaly in load-dependent control of the number of active stators. The results suggest that residues 72-100 of MotB is required for proper load-dependent control of the number of active stators around the rotor.

著者

Yuji Furutani Tetsunari Kimura Kido Okamoto

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.9, pp.123-129, 2013 (Released:2013-08-10)

参考文献数

20

被引用文献数

5 10

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Attenuated total reflectance (ATR)-FTIR spectroscopy has been widely used to probe protein structural changes under various stimuli, such as light absorption, voltage change, and ligand binding, in aqueous conditions. Time-resolved measurements require a trigger, which can be controlled electronically; therefore, light and voltage changes are suitable. Here we developed a novel, rapid buffer-exchange system for time-resolved ATR-FTIR spectroscopy to monitor the ligand- or ion-binding reaction of a protein. By using the step-scan mode (time resolution; 2.5 ms), we confirmed the completion of the buffer-exchange reaction within ~25 ms; the process was monitored by the infrared absorption change of a nitrate band at 1,350 cm-1. We also demonstrated the anion-binding reaction of a membrane protein, Natronomonas pharaonis halorhodopsin (pHR), which binds a chloride ion in the initial anion-binding site near the retinal chromophore. The formation of chloride- or nitrate-bound pHR was confirmed by an increase of the retinal absorption band at 1,528 cm-1. It also should be noted that low sample consumption (~1 μg of protein) makes this new method a powerful technique to understand ligand-protein and ion-protein interactions, particularly for membrane proteins.

著者

Takeshi Itabashi Jun Takagi Kazuya Suzuki Shin'ichi Ishiwata

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.9, pp.73-78, 2013 (Released:2013-06-08)

参考文献数

36

被引用文献数

3

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For genome stability, the proper segregation of chromosomes is required. The exquisite process of chromosome segregation has charmed a lot of cell- and molecular biologists into watching what happens inside a mitotic cell and how each molecule contributes to this process for the accomplishment of accurate cell division1. The process to partition the duplicated genome to the daughter cells in each cell division is mediated by a self-organized structure called the mitotic spindle. It is well known that the mitotic spindle is a multi-component macromolecular machine composed of microtubules, molecular motors (kinesins, cytoplasmic dynein), and other regulatory molecules (microtubule-associated proteins, kinases, etc.). In recent years, most of the protein components of the mitotic spindle have been identified and the functions of these proteins have been characterized using molecular perturbations2,3. Thus, the mechanisms for spindle assembly and chromosome segregation are being revealed rapidly. However, the chromosome segregation machinery is poorly understood from the mechanical point of view, such as how the mitotic spindle within a cell responds to a variety of mechanical forces, originating from cell-cell interactions or environmental fluctuations. Recent advances in the controlled mechanical perturbation have indicated that the mitotic spindle possesses a structural pliability, size adaptability to the applied external forces, and a strong self-organizing ability. Mechanical perturbations revealed also the mechanochemical regulation of chromosome segregation machinery, which responds to the applied forces. Here, we discuss the current progress in the biophysical research on the architectural and functional dynamics of the mitotic spindle.

著者

Hajime Fukuoka Yuichi Inoue Akihiko Ishijima

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.8, pp.59-66, 2012 (Released:2012-03-03)

参考文献数

49

被引用文献数

8

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Escherichia coli cells swim toward a favorable environment by chemotaxis. The chemotaxis system regulates the swimming behavior of the bacteria by controlling the rotational direction of their flagellar motors. Extracellular stimuli sensed by chemoreceptors are transduced to an intracellular signal molecule, phosphorylated CheY (CheY-P), that switches the rotational direction of the flagellar motors from counterclockwise (CCW) to clockwise (CW) or from CW to CCW. Many studies have focused on identifying the proteins involved in the chemotaxis system, and findings on the structures and intracellular localizations of these proteins have largely elucidated the molecular pathway. On the other hand, quantitative evaluations of the chemotaxis system, including the process of intracellular signaling by the propagation of CheY-P and the rotational switching of flagellar motor by binding of CheY-P molecules, are still uncertain. For instance, scientific consensus has held that the flagellar motors of an E. coli cell switch rotational direction asynchronously. However, recent work shows that the rotational switching of any two different motors on a single E. coli cell is highly coordinated; a sub-second switching delay between motors is clearly correlated with the relative distance of each motor from the chemoreceptor patch located at one pole of the cell. In this review of previous studies and our recent findings, we discuss the regulatory mechanism of the multiple flagellar motors on an individual E. coli cell and the intracellular signaling process that can be inferred from this coordinated switching.

著者

Tomoya Tsukazaki Osamu Nureki

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.7, pp.129-133, 2011 (Released:2011-11-30)

参考文献数

26

被引用文献数

6

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Protein transport across membranes is a fundamental and essential cellular activity in all organisms. In bacteria, protein export across the cytoplasmic membrane, driven by dynamic interplays between the protein-conducting SecYEG channel (Sec translocon) and the SecA ATPase, is enhanced by the proton motive force (PMF) and a membrane-integrated Sec component, SecDF. However, the structure and function of SecDF have remained unclear. We solved the first crystal structure of SecDF, consisting of a pseudo-symmetrical 12-helix transmembrane domain and two protruding periplasmic domains. Based on the structural features, we proposed that SecDF functions as a membrane-integrated chaperone, which drives protein movement without using the major energetic currency, ATP, but with remarkable cycles of conformational changes, powered by the proton gradient across the membrane. By a series of biochemical and biophysical approaches, several functionally important residues in the transmembrane region have been identified and our model of the SecDF function has been verified.