Biophysics (Nagoya-shi, Japan)最新文献_第4页

Mapping of the local environmental changes in proteins by cysteine scanning. 用半胱氨酸扫描绘制局部环境变化的蛋白质图谱。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-01-16 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.1

Yoichi Yamazaki, Tomoko Nagata, Akihisa Terakita, Hideki Kandori, Yoshinori Shichida, Yasushi Imamoto

{"title":"Mapping of the local environmental changes in proteins by cysteine scanning.","authors":"Yoichi Yamazaki, Tomoko Nagata, Akihisa Terakita, Hideki Kandori, Yoshinori Shichida, Yasushi Imamoto","doi":"10.2142/biophysics.10.1","DOIUrl":"https://doi.org/10.2142/biophysics.10.1","url":null,"abstract":"Protein conformational changes, which regulate the activity of proteins, are induced by the alternation of intramolecular interactions. Therefore, the detection of the local environmental changes around the key amino acid residues is essential to understand the activation mechanisms of functional proteins. Here we developed the methods to scan the local environmental changes using the vibrational band of cysteine S-H group. We validated the sensitivity of this method using bathorhodopsin, a photoproduct of rhodopsin trapped at liquid nitrogen temperature, which undergoes little conformational changes from the dark state as shown by the X-ray crystallography. The cysteine residues were individually introduced into 15 positions of Helix III, which contains several key amino acid residues for the light-induced conformational changes of rhodopsin. The shifts of S-H stretching modes of these cysteine residues and native cysteine residues upon the formation of bathorhodopsin were measured by Fourier transform infrared spectroscopy. While most of cysteine residues demonstrated no shift of S-H stretching mode, cysteine residues introduced at positions 117, 118, and 122, which are in the vicinity of the chromophore, demonstrated the significant changes. The current results are consistent with the crystal structure of bathorhodopsin, implying that the cysteine scanning is sensitive enough to detect the tiny conformational changes. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2014-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.10.1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732702","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: 5

Physical aspects of sensory transduction on seeing, hearing and smelling. 关于视觉、听觉和嗅觉的感官传导的物理方面。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-12-26 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.183

Tohru Yoshioka, Manabu Sakakibara

{"title":"Physical aspects of sensory transduction on seeing, hearing and smelling.","authors":"Tohru Yoshioka, Manabu Sakakibara","doi":"10.2142/biophysics.9.183","DOIUrl":"10.2142/biophysics.9.183","url":null,"abstract":"What is the general principle of sensory transduction? Sensory transduction is defined as energy transformation from the external world to the internal world. The energy of the external world, such as thermal energy (heat), electro-magnetic energy (light), mechanical energy (sound) and the energy from molecules (chemicals), is converted into electrochemical events in the animal nervous system. The following five classes of special sense receptors are utilized for energy conversion: vision (photo); audition (sound); taste and smell (chemo); and tactile (mechano). There are also other special sense receptors, including thermo and noxious receptors. The focus of this study is on photoreceptors, sound-receptors and odorant-receptors because the transduction mechanisms of these receptors are explained biochemically and understood by a common physical principle; these biochemical models are well known in neuroscience. The following notable problems are inherent in these biochemical models: the cGMP ionophore model of the vertebrate photoreceptor cannot explain the fast photo-response (∼msec); the tip links connection model of stereocilia in the basilar membrane for opening the K(+) channel on the tip of a hair has difficulty explaining the high frequency vibration of hair cells without a damping of the oscillation, and the odorant shape-specific receptor model for olfactory transduction has difficulty in discriminating the minute differences among similar fragrant smells of essential oils with different molecular shapes. These difficulties might arise from a lack of the physical sense when the transduction models were proposed. This article will reconsider these problems and propose rational models for visual, olfactory and auditory transduction. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"183-91"},"PeriodicalIF":0.0,"publicationDate":"2013-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34734073","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: 0

The C-terminal periplasmic domain of MotB is responsible for load-dependent control of the number of stators of the bacterial flagellar motor. MotB的c端周质结构域负责细菌鞭毛马达定子数量的负载依赖性控制。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-12-26 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.173

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

{"title":"The C-terminal periplasmic domain of MotB is responsible for load-dependent control of the number of stators of the bacterial flagellar motor.","authors":"David J Castillo, Shuichi Nakamura, Yusuke V Morimoto, Yong-Suk Che, Nobunori Kami-Ike, Seishi Kudo, Tohru Minamino, Keiichi Namba","doi":"10.2142/biophysics.9.173","DOIUrl":"https://doi.org/10.2142/biophysics.9.173","url":null,"abstract":"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 mechano-sensor 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. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"173-81"},"PeriodicalIF":0.0,"publicationDate":"2013-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732717","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: 39

Detection of a protein-bound water vibration of halorhodopsin in aqueous solution. 水溶液中盐紫红质蛋白结合水振动的检测。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-12-21 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.167

Tetsuya Fukuda, Kosuke Muroda, Hideki Kandori

{"title":"Detection of a protein-bound water vibration of halorhodopsin in aqueous solution.","authors":"Tetsuya Fukuda, Kosuke Muroda, Hideki Kandori","doi":"10.2142/biophysics.9.167","DOIUrl":"https://doi.org/10.2142/biophysics.9.167","url":null,"abstract":"Protein-bound water molecules play crucial roles in their structure and function, but their detection is an experimental challenge, particularly in aqueous solution at room temperature. By applying attenuated total reflection (ATR) Fourier-transform infrared (FTIR) spectroscopy to a light-driven Cl(-) pump pharaonis halorhodopsin (pHR), here we detected an O-H stretching vibration of protein-bound water molecules in the active center. The pHR(Cl(-)) minus pHR(Br(-)) ATR-FTIR spectra show random fluctuation at 3600-3000 cm(-1), frequency window of water vibration, which can be interpreted in terms of dynamical fluctuation of aqueous water at room temperature. On the other hand, we observed a reproducible spectral feature at 3617 (+)/3630 (-) cm(-1) in the pHR(Cl(-)) minus pHR(Br(-)) spectrum, which is absent in the pHR(Cl(-)) minus pHR(Cl(-)) and in the pHR(Br(-)) minus pHR(Br(-)) spectra. The water O-H stretching vibrations of pHR(Cl(-)) and pHR(Br(-)) at 3617 and 3630 cm(-1), respectively, are confirmed by light-induced difference FTIR spectra in isotope water (H2 (18)O) at 77 K. The observed water molecule presumably binds to the active center of pHR, and alter its hydrogen bond during the Cl(-) pumping photocycle. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"167-72"},"PeriodicalIF":0.0,"publicationDate":"2013-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732716","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

Increase in cyclic AMP concentration in a cerebral giant interneuron mimics part of a memory trace for conditioned taste aversion of the pond snail. 在一个巨大的大脑中间神经元中，环AMP浓度的增加模拟了田螺条件性味觉厌恶的部分记忆痕迹。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-11-13 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.161

Emi Otsuka, Miho Matsunaga, Ryuichi Okada, Miki Yamagishi, Akiko Okuta, Ken Lukowiak, Etsuro Ito

{"title":"Increase in cyclic AMP concentration in a cerebral giant interneuron mimics part of a memory trace for conditioned taste aversion of the pond snail.","authors":"Emi Otsuka, Miho Matsunaga, Ryuichi Okada, Miki Yamagishi, Akiko Okuta, Ken Lukowiak, Etsuro Ito","doi":"10.2142/biophysics.9.161","DOIUrl":"https://doi.org/10.2142/biophysics.9.161","url":null,"abstract":"Conditioned taste aversion (CTA) can be classically conditioned in the pond snail Lymnaea stagnalis and subsequently be consolidated into long-term memory (LTM). The neural trace that subserves CTA-LTM can be summarized as follows: A polysynaptic inhibitory postsynaptic potential recorded in the neuron 1 medial (N1M) cell in the conditioned snails as a result of activation of the cerebral giant cell (CGC) is larger and lasts longer than that in control snails. The N1M cell is ultimately activated by the CGC via the neuron 3 tonic (N3t) cell. That is, the inhibitory monosynaptic inputs from the N3t cell to the N1M cell are facilitated. The N1M and N3t cells are the members of feeding central pattern generator, whereas the CGC is a multimodal interneuron thought to play a key role in feeding behavior. Here we examined the involvement of a second messenger, cAMP, in the establishment of the memory trace. We injected cAMP into the CGC and monitored the potentials of the B3 motor neuron activated by the CGC. B3 activity is used as an index for the synaptic inputs from the N3t cell to the N1M cell. We found that the B3 potentials were transiently enlarged. Thus, when the cAMP concentration is increased in the CGC by taste aversion training, cAMP-induced changes may play a key role in the establishment of a memory trace in the N3t cell. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"161-6"},"PeriodicalIF":0.0,"publicationDate":"2013-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732715","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: 20

Single molecule FRET observation of kinesin-1's head-tail interaction on microtubule. 微管上驱动蛋白-1正反相互作用的单分子FRET观察。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-11-07 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.149

Takahiro Aoki, Michio Tomishige, Takayuki Ariga

引用次数: 7

3D structure of eukaryotic flagella/cilia by cryo-electron tomography. 真核生物鞭毛/纤毛的低温电子断层扫描三维结构。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-10-17 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.141

Takashi Ishikawa

引用次数: 4

Recent structural studies on Dom34/aPelota and Hbs1/aEF1α: important factors for solving general problems of ribosomal stall in translation. 最近对Dom34/aPelota和Hbs1/aEF1α的结构研究:解决翻译中核糖体失速问题的重要因素。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-09-07 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.131

Kan Kobayashi, Ryuichiro Ishitani, Osamu Nureki

引用次数: 5

Development of a rapid Buffer-exchange system for time-resolved ATR-FTIR spectroscopy with the step-scan mode. 步进扫描模式下时间分辨ATR-FTIR光谱快速缓冲交换系统的研制。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-08-10 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.123

Yuji Furutani, Tetsunari Kimura, Kido Okamoto

{"title":"Development of a rapid Buffer-exchange system for time-resolved ATR-FTIR spectroscopy with the step-scan mode.","authors":"Yuji Furutani, Tetsunari Kimura, Kido Okamoto","doi":"10.2142/biophysics.9.123","DOIUrl":"https://doi.org/10.2142/biophysics.9.123","url":null,"abstract":"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 re-action 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. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"123-9"},"PeriodicalIF":0.0,"publicationDate":"2013-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732711","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: 13

LigandBox: A database for 3D structures of chemical compounds. LigandBox:一个化合物三维结构的数据库。

Biophysics (Nagoya-shi, Japan) Pub Date : 2013-08-07 eCollection Date: 2013-01-01 DOI: 10.2142/biophysics.9.113

Takeshi Kawabata, Yusuke Sugihara, Yoshifumi Fukunishi, Haruki Nakamura

{"title":"LigandBox: A database for 3D structures of chemical compounds.","authors":"Takeshi Kawabata, Yusuke Sugihara, Yoshifumi Fukunishi, Haruki Nakamura","doi":"10.2142/biophysics.9.113","DOIUrl":"https://doi.org/10.2142/biophysics.9.113","url":null,"abstract":"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. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"9 ","pages":"113-21"},"PeriodicalIF":0.0,"publicationDate":"2013-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.9.113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732710","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: 24