PMC biophysics最新文献

Combined use of steady-state fluorescence emission and anisotropy of merocyanine 540 to distinguish crystalline, gel, ripple, and liquid crystalline phases in dipalmitoylphosphatidylcholine bilayers. 结合稳态荧光发射和merocyanine 540的各向异性来区分双棕榈酰磷脂酰胆碱双层中的结晶、凝胶、波纹和液晶相。

PMC biophysics Pub Date : 2010-11-05 DOI: 10.1186/1757-5036-3-14

Hannabeth A Franchino, Brett C Johnson, Steven K Neeley, Rajeev B Tajhya, Mai P Vu, Heather A Wilson-Ashworth, John D Bell

{"title":"Combined use of steady-state fluorescence emission and anisotropy of merocyanine 540 to distinguish crystalline, gel, ripple, and liquid crystalline phases in dipalmitoylphosphatidylcholine bilayers.","authors":"Hannabeth A Franchino, Brett C Johnson, Steven K Neeley, Rajeev B Tajhya, Mai P Vu, Heather A Wilson-Ashworth, John D Bell","doi":"10.1186/1757-5036-3-14","DOIUrl":"https://doi.org/10.1186/1757-5036-3-14","url":null,"abstract":" The various lamellar phases of dipalmitoylphosphadtidylcholine bilayers with and without cholesterol were used to assess the versatility of the fluorescent probe merocyanine 540 through simultaneous measurements of emission intensity, spectral shape, and steady-state anisotropy. Induction of the crystalline phase (Lc') by pre-incubation at 4°C produced a wavelength dependence of anisotropy which was strong at 15 and 25°C, weak at 38°C, and minimal above the main transition (>~41.5°C) or after returning the temperature from 46 to 25°C. The profile of anisotropy values across this temperature range revealed the ability of the probe to detect crystalline, gel (Lβ'), and liquid crystalline (Lα) phases. The temperature dependence of fluorescence intensity was additionally able to distinguish between the ripple (Pβ') and gel phases. In contrast, the shape of the emission spectrum, quantified as the ratio of merocyanine monomer and dimer peaks (585 and 621 nm), was primarily sensitive to the crystalline and gel phases because dimer fluorescence requires a highly-ordered environment. This requirement also explained the diminution of anisotropy wavelength dependence above 25°C. Repetition of experiments with vesicles containing cholesterol allowed creation of a phase map. Superimposition of data from the three simultaneous measurements provided details about the various phase regions in the map not discernible from any one of the three alone. The results were applied to assessment of calcium-induced membrane changes in living cells.PACS Codes: 87.16.dt.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2010-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29450271","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

Tubulohelical membrane arrays: From the initial observation to the elucidation of nanophysical properties and cellular function. 管螺旋膜阵列:从最初的观察到纳米物理性质和细胞功能的阐明。

PMC biophysics Pub Date : 2010-06-28 DOI: 10.1186/1757-5036-3-13

Siegfried Reipert, Józefa Wesierska-Gadek, Sebastian Wienerroither

{"title":"Tubulohelical membrane arrays: From the initial observation to the elucidation of nanophysical properties and cellular function.","authors":"Siegfried Reipert, Józefa Wesierska-Gadek, Sebastian Wienerroither","doi":"10.1186/1757-5036-3-13","DOIUrl":"https://doi.org/10.1186/1757-5036-3-13","url":null,"abstract":" Lipids undergo self-assembly to form ordered nonlamellar, nanoperiodic arrays both in vitro and in vivo. While engineering of such membrane arrays for technical devices is envisaged, we know little about their cellular function. Do they represent building blocks of an inherent cellular nanotechnology? Prospects for answering this question could be improved if the nanophysical properties of the membrane arrays could be studied in the context of specific cellular functions. Therefore, we draw attention to exceptional complex membrane arrays found in the renal epithelial cell line PtK2 that could provide perfect conditions for both biophysical and cell functional studies. The so-called tubulohelical membrane arrays (TUHMAs) combine nanoperiodicity of lipid membranes with that of helix-like proteinaceous core structures. Strikingly, they show several characteristics of dynamic, microtubule-associated single organelles. Our initial data indicate that TUHMA formation occurs in the depth of the cytoplasm under participation of cytoplasmic nucleoporins. Once matured, they may fuse with the nuclear membrane in polarized positions, either perpendicularly or in parallel to the nucleus. As a starting point for the initiation of functional studies we found a connection between TUHMAs and primary cilia, indicated by immunolabeling patterns of detyrosynated tubulin and cytoplasmic nucleoporins. We discuss these observations in the context of the ciliary cycle and of the specific requirement of ciliated renal epithelial cells for oriented cell division. Finally, we raise the question of whether putative nanooptical properties of TUHMAs could serve for communicating orientation between dividing cells.MCS codes: 92C37, 92C05, 92C50.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2010-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29087786","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: 2

Bistability in the actin cortex. 肌动蛋白皮层的双稳定性。

PMC biophysics Pub Date : 2010-06-24 DOI: 10.1186/1757-5036-3-12

Carsten Beta

引用次数: 7

Monte Carlo Simulations indicate that Chromati: Nanostructure is accessible by Light Microscopy. 蒙特卡罗模拟表明，Chromati：可以通过光学显微镜观察到纳米结构。

PMC biophysics Pub Date : 2010-06-10 DOI: 10.1186/1757-5036-3-11

Philipp M Diesinger, Dieter W Heermann

{"title":"Monte Carlo Simulations indicate that Chromati: Nanostructure is accessible by Light Microscopy.","authors":"Philipp M Diesinger, Dieter W Heermann","doi":"10.1186/1757-5036-3-11","DOIUrl":"10.1186/1757-5036-3-11","url":null,"abstract":" A long controversy exists about the structure of chromatin. Theoretically, this structure could be resolved by scattering experiments if one determines the scattering function - or equivalently the pair distribution function - of the nucleosomes. Unfortunately, scattering experiments with live cells are very difficult and limited to only a couple of nucleosomes.Nevertheless, new techniques like the high-resolution light microscopy supply a new approach to this problem. In this work we determine the radial pair distribution function of chromatin described by our E2A model and find that the dominant peaks which characterize the chromatin structure are very robust in several ways: They can still be identified in the case of chromatin fibers with reasonable linker histone and nucleosome defect rates as well as in the 2D case after a projection like in most high-res light microscopy experiments. This might initiate new experimental approaches like optical microscopy to finally determine the nanostructure of chromatin.Furthermore, we examine the statistics of random chromatin collisions and compare it with 5C data of a gene desert. We find that only chromatin fibers with histone depletion show a significant amount of contacts on the kbp-scale which play a important role in gene regulation. Therefore, linker histone and nucleosome depletion might not only be chromatin defects but even be necessary to facilitate transcription.PACS codes: 82.35.Pq, 87.16.A-, 87.16.af.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 ","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2010-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29043501","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

Combined molecular dynamics and continuum solvent studies of the pre-pore Cry4Aa trimer suggest its stability in solution and how it may form pore. 结合分子动力学和连续溶剂对预孔Cry4Aa三聚体的研究，揭示了其在溶液中的稳定性及其形成孔的机理。

PMC biophysics Pub Date : 2010-05-13 DOI: 10.1186/1757-5036-3-10

Taveechai Taveecharoenkool, Chanan Angsuthanasombat, Chalermpol Kanchanawarin

{"title":"Combined molecular dynamics and continuum solvent studies of the pre-pore Cry4Aa trimer suggest its stability in solution and how it may form pore.","authors":"Taveechai Taveecharoenkool, Chanan Angsuthanasombat, Chalermpol Kanchanawarin","doi":"10.1186/1757-5036-3-10","DOIUrl":"https://doi.org/10.1186/1757-5036-3-10","url":null,"abstract":" Cry4Aa toxin is one of the highly specific mosquito-larvicidal proteins produced by the bacterium Bacillus thuringiensis subspecies israelensis. It is thought to form pores in the larval midgut membrane that cause membrane leakage and subsequent insect death. Therefore, Cry4Aa and other Cry toxins have been used as efficient and safe bacterial insecticides to control the disease-carrying mosquitoes such as Aedes, Anopheles, and Culex. However, we still do not clearly understand how Cry toxins kill mosquito-larvae at molecular details. Recent electron crystallographic images of Cry4Ba toxin, another toxin closely related to Cry4Aa toxin, have suggested that the protein forms trimer in aqueous solution and in lipid monolayer. Moreover, the unit cell of X-ray crystal structure of Cry4Ba toxin has been shown to be trimeric. In this study, we constructed the first full-atom structural model of Cry4Aa trimer using the trimeric unit cell structure of Cry4Ba toxin as a template and then used the methods of molecular dynamics (MD) and molecular mechanics combined with Poisson-Boltzmann and surface area (MM-PBSA) to show that the trimeric structure of Cry4Aa toxin is stable in 150 mM KCl solution on 10 ns timescale. The results reveal that Cry4Aa toxins use polar amino acid residues on alpha-helices 3, 4, and 6 to form trimer and suggest that the proteins form trimer to reduce their non-polar interactions with surrounding water. Based on the obtained trimeric structure of Cry4Aa toxins, we propose that pore formation of Cry toxins may involve a 90 degrees -hairpin rotation during the insertion of their three alpha4-alpha5 hairpins into the membrane. This process may be mediated by water and ions.PACS Codes: 87.15.ap, 87.15.bk, 87.14.ep.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2010-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-10","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28987460","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: 17

Live cell flattening - traditional and novel approaches. 活细胞扁平化--传统和新型方法。

PMC biophysics Pub Date : 2010-04-19 DOI: 10.1186/1757-5036-3-9

Christian Westendorf, Albert J Bae, Christoph Erlenkamper, Edouard Galland, Carl Franck, Eberhard Bodenschatz, Carsten Beta

引用次数: 0

Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study. 二维红外光谱探测迷你蛋白Beta3s的折叠仿真研究。

PMC biophysics Pub Date : 2010-03-19 DOI: 10.1186/1757-5036-3-8

Christopher Nj Marai, Shaul Mukamel, Jin Wang

引用次数: 6

Self-organizing actin waves that simulate phagocytic cup structures. 模拟吞噬杯结构的自组织肌动蛋白波。

PMC biophysics Pub Date : 2010-03-18 DOI: 10.1186/1757-5036-3-7

Günther Gerisch

{"title":"Self-organizing actin waves that simulate phagocytic cup structures.","authors":"Günther Gerisch","doi":"10.1186/1757-5036-3-7","DOIUrl":"https://doi.org/10.1186/1757-5036-3-7","url":null,"abstract":" This report deals with actin waves that are spontaneously generated on the planar, substrate-attached surface of Dictyostelium cells. These waves have the following characteristics. (1) They are circular structures of varying shape, capable of changing the direction of propagation. (2) The waves propagate by treadmilling with a recovery of actin incorporation after photobleaching of less than 10 seconds. (3) The waves are associated with actin-binding proteins in an ordered 3-dimensional organization: with myosin-IB at the front and close to the membrane, the Arp2/3 complex throughout the wave, and coronin at the cytoplasmic face and back of the wave. Coronin is a marker of disassembling actin structures. (4) The waves separate two areas of the cell cortex that differ in actin structure and phosphoinositide composition of the membrane. The waves arise at the border of membrane areas rich in phosphatidylinositol (3,4,5) trisphosphate (PIP3). The inhibition of PIP3 synthesis reversibly inhibits wave formation. (5) The actin wave and PIP3 patterns resemble 2-dimensional projections of phagocytic cups, suggesting that they are involved in the scanning of surfaces for particles to be taken up.PACS Codes: 87.16.Ln, 87.19.lp, 89.75.Fb.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2010-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28837401","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: 47

Two-color STED microscopy reveals different degrees of colocalization between hexokinase-I and the three human VDAC isoforms. 双色 STED 显微镜显示了 hexokinase-I 与三种人类 VDAC 异构体之间不同程度的共定位。

PMC biophysics Pub Date : 2010-03-05 DOI: 10.1186/1757-5036-3-4

Daniel Neumann, Johanna Bückers, Lars Kastrup, Stefan W Hell, Stefan Jakobs

{"title":"Two-color STED microscopy reveals different degrees of colocalization between hexokinase-I and the three human VDAC isoforms.","authors":"Daniel Neumann, Johanna Bückers, Lars Kastrup, Stefan W Hell, Stefan Jakobs","doi":"10.1186/1757-5036-3-4","DOIUrl":"10.1186/1757-5036-3-4","url":null,"abstract":" The voltage-dependent anion channel (VDAC, also known as mitochondrial porin) is the major transport channel mediating the transport of metabolites, including ATP, across the mitochondrial outer membrane. Biochemical data demonstrate the binding of the cytosolic protein hexokinase-I to VDAC, facilitating the direct access of hexokinase-I to the transported ATP. In human cells, three hVDAC isoforms have been identified. However, little is known on the distribution of these isoforms within the outer membrane of mitochondria and to what extent they colocalize with hexokinase-I. In this study we show that whereas hVDAC1 and hVDAC2 are localized predominantly within the same distinct domains in the outer membrane, hVDAC3 is mostly uniformly distributed over the surface of the mitochondrion. We used two-color stimulated emission depletion (STED) microscopy enabling a lateral resolution of ~40 nm to determine the detailed sub-mitochondrial distribution of the three hVDAC isoforms and hexokinase-I. Individual hVDAC and hexokinase-I clusters could thus be resolved which were concealed in the confocal images. Quantitative colocalization analysis of two-color STED images demonstrates that within the attained resolution, hexokinase-I and hVDAC3 exhibit a higher degree of colocalization than hexokinase-I with either hVDAC1 or hVDAC2. Furthermore, a substantial fraction of the mitochondria-bound hexokinase-I pool does not colocalize with any of the three hVDAC isoforms, suggesting a more complex interplay of these proteins than previously anticipated. This study demonstrates that two-color STED microscopy in conjunction with quantitative colocalization analysis is a powerful tool to study the complex distribution of membrane proteins in organelles such as mitochondria.PACS: 87.16.Tb, 87.85.Rs.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2010-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28755573","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

Geometric constrains for detecting short actin filaments by cryogenic electron tomography. 低温电子断层扫描检测肌动蛋白短丝的几何约束。

PMC biophysics Pub Date : 2010-03-05 DOI: 10.1186/1757-5036-3-6

Mikhail Kudryashev, Simone Lepper, Wolfgang Baumeister, Marek Cyrklaff, Friedrich Frischknecht

{"title":"Geometric constrains for detecting short actin filaments by cryogenic electron tomography.","authors":"Mikhail Kudryashev, Simone Lepper, Wolfgang Baumeister, Marek Cyrklaff, Friedrich Frischknecht","doi":"10.1186/1757-5036-3-6","DOIUrl":"https://doi.org/10.1186/1757-5036-3-6","url":null,"abstract":" Polymerization of actin into filaments can push membranes forming extensions like filopodia or lamellipodia, which are important during processes such as cell motility and phagocytosis. Similarly, small organelles or pathogens can be moved by actin polymerization. Such actin filaments can be arranged in different patterns and are usually hundreds of nanometers in length as revealed by various electron microscopy approaches. Much shorter actin filaments are involved in the motility of apicomplexan parasites. However, these short filaments have to date not been visualized in intact cells. Here, we investigated Plasmodium sporozoites, the motile forms of the malaria parasite that are transmitted by the mosquito, using cryogenic electron tomography. We detected filopodia-like extensions of the plasma membrane and observed filamentous structures in the supra-alveolar space underneath the plasma membrane. However, these filaments could not be unambiguously assigned as actin filaments. In silico simulations of EM data collection and tomographic reconstruction identify the limits in revealing the filaments due to their length, concentration and orientation.PACS Codes: 87.64.Ee.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2010-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28762794","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: 40