Biophysics (Nagoya-shi, Japan)最新文献_第5页

Information-to-free-energy conversion: Utilizing thermal fluctuations. 信息到自由能的转换:利用热波动。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-08-07 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.107

Shoichi Toyabe, Eiro Muneyuki

引用次数: 3

Difference in hydration structures between F-actin and myosin subfragment-1 detected by small-angle X-ray and neutron scattering. 用小角x射线和中子散射检测F-actin和myosin亚片段-1水化结构的差异。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-07-23 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.99

Tatsuhito Matsuo, Toshiaki Arata, Toshiro Oda, Satoru Fujiwara

{"title":"Difference in hydration structures between F-actin and myosin subfragment-1 detected by small-angle X-ray and neutron scattering.","authors":"Tatsuhito Matsuo, Toshiaki Arata, Toshiro Oda, Satoru Fujiwara","doi":"10.2142/biophysics.9.99","DOIUrl":"https://doi.org/10.2142/biophysics.9.99","url":null,"abstract":"Hydration structures around F-actin and myosin subfragment-1 (S1), which play central roles as counterparts in muscle contraction, were investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The radius of gyration of chymotryptic S1 was evaluated to be 41.3±1.1 Å for SAXS, 40.1±3.0 Å for SANS in H2O, and 37.8±0.8 Å for SANS in D2O, respectively. The values of the cross-sectional radius of gyration of F-actin were 25.4±0.03 Å for SAXS, 23.4±2.4 Å for SANS in H2O, and 22.6 ± 0.6 Å for SANS in D2O, respectively. These differences arise from different contributions of the hydration shell to the scattering curves. Analysis by model calculations showed that the hydration shell of S1 has the average density 10-15% higher than bulk water, being the typical hydration shell. On the other hand, the hydration shell of F-actin has the average density more than 19% higher than bulk water, indicating that F-actin has a denser, unusual hydration structure. The results indicate a difference in the hydration structures around F-actin and S1. The unusual hydration structure around F-actin may have the structural property of so-called \"hyper-mobile water\" around F-actin. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"99-106"},"PeriodicalIF":0.0,"publicationDate":"2013-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.9.99","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34343845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Experimental thermodynamics of single molecular motor. 单分子马达的实验热力学。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-07-12 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.91

Shoichi Toyabe, Eiro Muneyuki

引用次数: 16

Contribution of a visual pigment absorption spectrum to a visual function: depth perception in a jumping spider. 视觉色素吸收光谱对视觉功能的贡献:跳蜘蛛的深度感知。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-07-09 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.85

Takashi Nagata, Kentaro Arikawa, Akihisa Terakita

引用次数: 1

A new approach to detect small peptides clearly and sensitively by Western blotting using a vacuum-assisted detection method. 利用真空辅助检测方法，Western blotting检测小肽清晰、灵敏的新方法。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-06-21 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.79

Satoshi Tomisawa, Chiharu Abe, Masakatsu Kamiya, Takashi Kikukawa, Makoto Demura, Keiichi Kawano, Tomoyasu Aizawa

{"title":"A new approach to detect small peptides clearly and sensitively by Western blotting using a vacuum-assisted detection method.","authors":"Satoshi Tomisawa, Chiharu Abe, Masakatsu Kamiya, Takashi Kikukawa, Makoto Demura, Keiichi Kawano, Tomoyasu Aizawa","doi":"10.2142/biophysics.9.79","DOIUrl":"https://doi.org/10.2142/biophysics.9.79","url":null,"abstract":"Western blotting is a widely used technique for the detection and quantification of proteins and peptides. However, it is challenging to detect small peptides efficiently by the conventional Western blotting method with shaking, in part because the peptides readily detach from the blotted membrane. Although some modified Western blotting protocols have been developed to overcome this problem, it remains difficult to prevent peptide detachment from the membrane. In this study, we show that the previously developed vacuum-assisted detection method greatly improves the detection of small peptides without additional protocol modification. The vacuum-assisted method was developed to shorten the time required for all immunodetection steps, and all the Western blotting solutions penetrated the membrane quickly and efficiently by this method. By using this vacuum method, we succeeded in detecting small peptides that were completely undetectable by the conventional Western blotting method. We also confirmed that peptide detachment was induced even by gentle shaking in the case of the conventional method, and the detachment was accelerated when detergent was present in the buffer. Unlike in the conventional method, there is no need to shake the membrane in solution in the vacuum method. Therefore, it is thought that the small peptides could be detected sensitively only by the vacuum method. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"79-83"},"PeriodicalIF":0.0,"publicationDate":"2013-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.9.79","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34343842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Responses of chromosome segregation machinery to mechanical perturbations. 染色体分离机制对机械扰动的响应。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-06-08 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.73

Takeshi Itabashi, Jun Takagi, Kazuya Suzuki, Shin'ichi Ishiwata

{"title":"Responses of chromosome segregation machinery to mechanical perturbations.","authors":"Takeshi Itabashi, Jun Takagi, Kazuya Suzuki, Shin'ichi Ishiwata","doi":"10.2142/biophysics.9.73","DOIUrl":"https://doi.org/10.2142/biophysics.9.73","url":null,"abstract":"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.","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"73-8"},"PeriodicalIF":0.0,"publicationDate":"2013-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.9.73","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34343841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Role of the Dc domain of the bacterial hook protein FlgE in hook assembly and function. 细菌钩蛋白FlgE Dc结构域在钩蛋白组装和功能中的作用。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-06-06 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.63

Nao Moriya, Tohru Minamino, Hedda U Ferris, Yusuke V Morimoto, Masamichi Ashihara, Takayuki Kato, Keiichi Namba

{"title":"Role of the Dc domain of the bacterial hook protein FlgE in hook assembly and function.","authors":"Nao Moriya, Tohru Minamino, Hedda U Ferris, Yusuke V Morimoto, Masamichi Ashihara, Takayuki Kato, Keiichi Namba","doi":"10.2142/biophysics.9.63","DOIUrl":"https://doi.org/10.2142/biophysics.9.63","url":null,"abstract":"The bacterial flagellar hook acts as a universal joint to smoothly transmit torque produced by the motor to the filament. The hook protein FlgE assembles into a 55 nm tubular structure with the help of the hook cap (FlgD). FlgE consists of four domains, D0, Dc, D1 and D2, arranged from the inner to the outer part of the tubular structure of the hook. The Dc domain contributes to the structural stability of the hook, but it is unclear how this Dc domain is responsible for the universal joint mechanism. Here, we carried out a deletion analysis of the FlgE Dc domain. FlgEΔ4/5 with deletion of residues 30 to 49 was not secreted into the culture media. FlgEΔ5 and FlgEΔ6 with deletions of residues 40 to 49 and 50 to 59, respectively, still formed hooks, allowing the export apparatus to export the hook-filament junction proteins FlgK and FlgL and flagellin FliC. However, these deletions inhibited the replacement of the FlgD hook cap by FlgK at the hook tip, thereby abolishing filament formation. Deletion of residues 50 to 59 significantly affected hook morphology. These results suggest that the Dc domain is responsible not only for hook assembly but also for FlgE export, the interaction with FlgK, and the polymorphic supercoiling mechanism of the hook. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"63-72"},"PeriodicalIF":0.0,"publicationDate":"2013-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.9.63","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34343840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Rotary catalysis of FoF1-ATP synthase. FoF1-ATP合酶的旋转催化作用。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-05-22 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.51

Rikiya Watanabe

引用次数: 4

Crystal structure of channelrhodopsin, a light-gated cation channel - all cations lead through the monomer. 通道视紫红质的晶体结构，一个光门控阳离子通道-所有阳离子通过单体。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-05-22 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.57

Hideaki E Kato, Osamu Nureki

引用次数: 7

Characterization of the ordered phase formed by sphingomyelin analogues and cholesterol binary mixtures. 鞘磷脂类似物与胆固醇二元混合物形成有序相的表征。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-05-22 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.37

Masanao Kinoshita, Sarah Goretta, Hiroshi Tsuchikawa, Nobuaki Matsumori, Michio Murata

{"title":"Characterization of the ordered phase formed by sphingomyelin analogues and cholesterol binary mixtures.","authors":"Masanao Kinoshita, Sarah Goretta, Hiroshi Tsuchikawa, Nobuaki Matsumori, Michio Murata","doi":"10.2142/biophysics.9.37","DOIUrl":"https://doi.org/10.2142/biophysics.9.37","url":null,"abstract":"The influences of structural alterations of sphingomyelin (SM) on its interactions with cholesterol (chol) and on ordered phase formation were examined by density measurements and surface pressure vs. molecular area isotherm measurements. In addition, we quantitatively characterized the ordered phase formed in each SM and chol binary mixture on the basis of the molecular compressional modulus of SM ( [Formula: see text]). Density measurements demonstrated that the ordered phase formation in threo-SM (tSM)/chol and dihydrosphingomyelin (DHSM)/chol binary bilayers shows similar chol concentration-dependency to that of natural erythro-SM (eSM)/chol bilayers; the ordered phase formation was completed in the presence of 25 mol% chol. In contrast, SM bearing a triple bond in the place of a double bond (tripleSM) required a greater concentration of chol to completely transform the bilayer into the ordered phase (at 40 mol% chol). Surface pressure vs. molecular area isotherms showed that the DHSM molecule ( [Formula: see text] = 290 mN/m) is more rigid than eSM ( [Formula: see text] = 240 mN/m) above 30 mol% chol (in the ordered phase), although these values are similar (140-150 mN/m) in the absence of chol (liquid condensed phase). Most likely, the DHSM/chol mixture forms a more ordered membrane than the eSM/chol mixture does. Moreover, in the absence of chol, the rigidity of the tripleSM molecule ( [Formula: see text] = 250 mN/m) is significantly higher as compared with that of the eSM molecule ( [Formula: see text] = 150 mN/m), which is probably due to the presence of a triple bond. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"37-49"},"PeriodicalIF":0.0,"publicationDate":"2013-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.9.37","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34637173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11