PMC biophysics最新文献_第2页

Assembly dynamics of PML nuclear bodies in living cells. PML核体在活细胞中的装配动力学。

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

Peter Brand, Thorsten Lenser, Peter Hemmerich

{"title":"Assembly dynamics of PML nuclear bodies in living cells.","authors":"Peter Brand, Thorsten Lenser, Peter Hemmerich","doi":"10.1186/1757-5036-3-3","DOIUrl":"https://doi.org/10.1186/1757-5036-3-3","url":null,"abstract":" The mammalian cell nucleus contains a variety of organelles or nuclear bodies which contribute to key nuclear functions. Promyelocytic leukemia nuclear bodies (PML NBs) are involved in the regulation of apoptosis, antiviral responses, the DNA damage response and chromatin structure, but their precise biochemical function in these nuclear pathways is unknown. One strategy to tackle this problem is to assess the biophysical properties of the component parts of these macromolecular assemblies in living cells. In this study we determined PML NB assembly dynamics by live cell imaging, combined with mathematical modeling. For the first time, dynamics of PML body formation were measured in cells lacking endogenous PML. We show that all six human nuclear PML isoforms are able to form nuclear bodies in PML negative cells. All isoforms exhibit individual exchange rates at NBs in PML positive cells but PML I, II, III and IV are static at nuclear bodies in PML negative cells, suggesting that these isoforms require additional protein partners for efficient exchange. PML V turns over at PML Nbs very slowly supporting the idea of a structural function for this isoform. We also demonstrate that SUMOylation of PML at Lysine positions K160 and/or K490 are required for nuclear body formation in vivo.We propose a model in which the isoform specific residence times of PML provide both, structural stability to function as a scaffold and flexibility to attract specific nuclear proteins for efficient biochemical reactions at the surface of nuclear bodies.MCS code: 92C37.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2010-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28755571","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: 74

Nanoscopy of the cellular response to hypoxia by means of fluorescence resonance energy transfer (FRET) and new FRET software. 利用荧光共振能量转移(FRET)和新的FRET软件的细胞对缺氧反应的纳米显微镜。

PMC biophysics Pub Date : 2010-03-05 DOI: 10.1186/1757-5036-3-5

Christoph Wotzlaw, Silke Gneuss, Rebecca Konietzny, Joachim Fandrey

{"title":"Nanoscopy of the cellular response to hypoxia by means of fluorescence resonance energy transfer (FRET) and new FRET software.","authors":"Christoph Wotzlaw, Silke Gneuss, Rebecca Konietzny, Joachim Fandrey","doi":"10.1186/1757-5036-3-5","DOIUrl":"https://doi.org/10.1186/1757-5036-3-5","url":null,"abstract":"Background: Cellular oxygen sensing is fundamental to all mammalian cells to adequately respond to a shortage of oxygen by increasing the expression of genes that will ensure energy homeostasis. The transcription factor Hypoxia-Inducible-Factor-1 (HIF-1) is the key regulator of the response because it coordinates the expression of hypoxia inducible genes. The abundance and activity of HIF-1 are controlled through posttranslational modification by hydroxylases, the cellular oxygen sensors, of which the activity is oxygen dependent.Methods: Fluorescence resonance energy transfer (FRET) was established to determine the assembly of the HIF-1 complex and to study the interaction of the alpha-subunit of HIF-1 with the O2-sensing hydroxylase. New software was developed to improve the quality and reliability of FRET measurements.Results: FRET revealed close proximity between the HIF-1 subunits in multiple cells. Data obtained by sensitized FRET in this study were fully compatible with previous work using acceptor bleaching FRET. Interaction between the O2-sensing hydroxylase PHD1 and HIF-1alpha was demonstrated and revealed exclusive localization of O2-sensing in the nucleus. The new software FRET significantly improved the quality and speed of FRET measurements.Conclusion: FRET measurements do not only allow following the assembly of the HIF-1 complex under hypoxic conditions but can also provide important information about the process of O2-sensing and its localisation within a cell.MCS codes: 92C30, 92C05, 92C40.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2010-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28755574","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

Conformational preference of ChaK1 binding peptides: a molecular dynamics study. ChaK1结合肽的构象偏好:分子动力学研究。

PMC biophysics Pub Date : 2010-01-21 DOI: 10.1186/1757-5036-3-2

Jiajing Zhang, Christopher A King, Kevin Dalby, Pengyu Ren

{"title":"Conformational preference of ChaK1 binding peptides: a molecular dynamics study.","authors":"Jiajing Zhang, Christopher A King, Kevin Dalby, Pengyu Ren","doi":"10.1186/1757-5036-3-2","DOIUrl":"https://doi.org/10.1186/1757-5036-3-2","url":null,"abstract":" TRPM7/ChaK1 is a recently discovered atypical protein kinase that has been suggested to selectively phosphorylate the substrate residues located in alpha-helices. However, the actual structure of kinase-substrate complex has not been determined experimentally and the recognition mechanism remains unknown. In this work we explored possible kinase-substrate binding modes and the likelihood of an alpha-helix docking interaction, within a kinase active site, using molecular modeling. Specifically kinase ChaK1 and its two peptide substrates were examined; one was an 11-residue segment from the N-terminal domain of annexin-1, a putative endogenous substrate for ChaK1, and the other was an engineered 16-mer peptide substrate determined via peptide library screening. Simulated annealing (SA), replica-exchange molecular dynamics (REMD) and steered molecular dynamics (SMD) simulations were performed on the two peptide substrates and the ChaK1-substrate complex in solution. The simulations indicate that the two substrate peptides are unlikely to bind and react with the ChaK1 kinase in a stable alpha-helical conformation overall. The key structural elements, sequence motifs, and amino acid residues in the ChaK1 and their possible functions involved in the substrate recognition are discussed.PACS Codes: 87.15.A-","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2010-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28736444","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

Kinetics of diffusion-controlled enzymatic reactions with charged substrates. 带电荷底物的扩散控制酶促反应动力学。

PMC biophysics Pub Date : 2010-01-18 DOI: 10.1186/1757-5036-3-1

Benzhuo Lu, J Andrew McCammon

{"title":"Kinetics of diffusion-controlled enzymatic reactions with charged substrates.","authors":"Benzhuo Lu, J Andrew McCammon","doi":"10.1186/1757-5036-3-1","DOIUrl":"https://doi.org/10.1186/1757-5036-3-1","url":null,"abstract":"The Debye-Hückel limiting law (DHL) has often been used to estimate rate constants of diffusion-controlled reactions under different ionic strengths. Two main approximations are adopted in DHL: one is that the solution of the linearized Poisson-Boltzmann equation for a spherical cavity is used to estimate the excess electrostatic free energy of a solution; the other is that details of electrostatic interactions of the solutes are neglected. This makes DHL applicable only at low ionic strengths and dilute solutions (very low substrate/solute concentrations). We show in this work that through numerical solution of the Poisson-Nernst-Planck equations, diffusion-reaction processes can be studied at a variety of conditions including realistically concentrated solutions, high ionic strength, and certainly with non-equilibrium charge distributions. Reaction rate coefficients for the acetylcholine-acetylcholinesterase system are predicted to strongly depend on both ionic strength and substrate concentration. In particular, they increase considerably with increase of substrate concentrations at a fixed ionic strength, which is open to experimental testing. This phenomenon is also verified on a simple model, and is expected to be general for electrostatically attracting enzyme-substrate systems.PACS Codes: 82.45.Tv, 87.15.VvMSC Codes: 92C30.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"3 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2010-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-3-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28715113","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: 23

Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins. 通过改变设计的钙结合蛋白中的带电配位残基对金属结合亲和力和蛋白质稳定性的反向调节。

PMC biophysics Pub Date : 2009-12-21 DOI: 10.1186/1757-5036-2-11

Anna Wilkins Maniccia, Wei Yang, Julian A Johnson, Shunyi Li, Harianto Tjong, Huan-Xiang Zhou, Lev A Shaket, Jenny J Yang

{"title":"Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins.","authors":"Anna Wilkins Maniccia, Wei Yang, Julian A Johnson, Shunyi Li, Harianto Tjong, Huan-Xiang Zhou, Lev A Shaket, Jenny J Yang","doi":"10.1186/1757-5036-2-11","DOIUrl":"https://doi.org/10.1186/1757-5036-2-11","url":null,"abstract":"Ca(2+ )binding proteins are essential for regulating the role of Ca(2+ )in cell signaling and maintaining Ca(2+ )homeostasis. Negatively charged residues such as Asp and Glu are often found in Ca(2+ )binding proteins and are known to influence Ca(2+ )binding affinity and protein stability. In this paper, we report a systematic investigation of the role of local charge number and type of coordination residues in Ca(2+ )binding and protein stability using de novo designed Ca(2+ )binding proteins. The approach of de novo design was chosen to avoid the complications of cooperative binding and Ca(2+)-induced conformational change associated with natural proteins. We show that when the number of negatively charged coordination residues increased from 2 to 5 in a relatively restricted Ca(2+)-binding site, Ca(2+ )binding affinities increased by more than 3 orders of magnitude and metal selectivity for trivalent Ln(3+ )over divalent Ca(2+ )increased by more than 100-fold. Additionally, the thermal transition temperatures of the apo forms of the designed proteins decreased due to charge repulsion at the Ca(2+ )binding pocket. The thermal stability of the proteins was regained upon Ca(2+ )and Ln(3+ )binding to the designed Ca(2+ )binding pocket. We therefore observe a striking tradeoff between Ca(2+)/Ln(3+ )affinity and protein stability when the net charge of the coordination residues is varied. Our study has strong implications for understanding and predicting Ca(2+)-conferred thermal stabilization of natural Ca(2+ )binding proteins as well as for designing novel metalloproteins with tunable Ca(2+ )and Ln(3+ )binding affinity and selectivity.PACS codes: 05.10.-a.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"2 ","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2009-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-2-11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28606426","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

Amplitude distribution of stochastic oscillations in biochemical networks due to intrinsic noise. 生物化学网络内禀噪声随机振荡的振幅分布。

PMC biophysics Pub Date : 2009-11-17 DOI: 10.1186/1757-5036-2-10

Moritz Lang, Steffen Waldherr, Frank Allgöwer

{"title":"Amplitude distribution of stochastic oscillations in biochemical networks due to intrinsic noise.","authors":"Moritz Lang, Steffen Waldherr, Frank Allgöwer","doi":"10.1186/1757-5036-2-10","DOIUrl":"https://doi.org/10.1186/1757-5036-2-10","url":null,"abstract":" Intrinsic noise is a common phenomenon in biochemical reaction networks and may affect the occurence and amplitude of sustained oscillations in the states of the network. To evaluate properties of such oscillations in the time domain, it is usually required to conduct long-term stochastic simulations, using for example the Gillespie algorithm. In this paper, we present a new method to compute the amplitude distribution of the oscillations without the need for long-term stochastic simulations. By the derivation of the method, we also gain insight into the structural features underlying the stochastic oscillations. The method is applicable to a wide class of non-linear stochastic differential equations that exhibit stochastic oscillations. The application is exemplified for the MAPK cascade, a fundamental element of several biochemical signalling pathways. This example shows that the proposed method can accurately predict the amplitude distribution for the stochastic oscillations even when using further computational approximations.PACS Codes: 87.10.Mn, 87.18.Tt, 87.18.VfMSC Codes: 92B05, 60G10, 65C30.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"2 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2009-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-2-10","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28514385","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: 10

Two-dimensional nanosecond electric field mapping based on cell electropermeabilization. 基于细胞电渗透的二维纳秒电场映射。

PMC biophysics Pub Date : 2009-11-11 DOI: 10.1186/1757-5036-2-9

Meng-Tse Chen, Chunqi Jiang, P Thomas Vernier, Yu-Hsuan Wu, Martin A Gundersen

{"title":"Two-dimensional nanosecond electric field mapping based on cell electropermeabilization.","authors":"Meng-Tse Chen, Chunqi Jiang, P Thomas Vernier, Yu-Hsuan Wu, Martin A Gundersen","doi":"10.1186/1757-5036-2-9","DOIUrl":"https://doi.org/10.1186/1757-5036-2-9","url":null,"abstract":" Nanosecond, megavolt-per-meter electric pulses cause permeabilization of cells to small molecules, programmed cell death (apoptosis) in tumor cells, and are under evaluation as a treatment for skin cancer. We use nanoelectroporation and fluorescence imaging to construct two-dimensional maps of the electric field associated with delivery of 15 ns, 10 kV pulses to monolayers of the human prostate cancer cell line PC3 from three different electrode configurations: single-needle, five-needle, and flat-cut coaxial cable. Influx of the normally impermeant fluorescent dye YO-PRO-1 serves as a sensitive indicator of membrane permeabilization. The level of fluorescence emission after pulse exposure is proportional to the applied electric field strength. Spatial electric field distributions were compared in a plane normal to the center axis and 15-20 mum from the tip of the center electrode. Measurement results agree well with models for the three electrode arrangements evaluated in this study. This live-cell method for measuring a nanosecond pulsed electric field distribution provides an operationally meaningful calibration of electrode designs for biological applications and permits visualization of the relative sensitivities of different cell types to nanoelectropulse stimulation. PACS Codes: 87.85.M-","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"2 1","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2009-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-2-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28500950","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: 28

Simple modeling of FtsZ polymers on flat and curved surfaces: correlation with experimental in vitro observations. 平面和曲面上 FtsZ 聚合物的简单建模：与体外实验观察结果的相关性。

PMC biophysics Pub Date : 2009-10-22 DOI: 10.1186/1757-5036-2-8

Alfonso Paez, Pablo Mateos-Gil, Ines Hörger, Jesús Mingorance, Germán Rivas, Miguel Vicente, Marisela Vélez, Pedro Tarazona

{"title":"Simple modeling of FtsZ polymers on flat and curved surfaces: correlation with experimental in vitro observations.","authors":"Alfonso Paez, Pablo Mateos-Gil, Ines Hörger, Jesús Mingorance, Germán Rivas, Miguel Vicente, Marisela Vélez, Pedro Tarazona","doi":"10.1186/1757-5036-2-8","DOIUrl":"10.1186/1757-5036-2-8","url":null,"abstract":" FtsZ is a GTPase that assembles at midcell into a dynamic ring that constricts the membrane to induce cell division in the majority of bacteria, in many archea and several organelles. In vitro, FtsZ polymerizes in a GTP-dependent manner forming a variety of filamentous flexible structures. Based on data derived from the measurement of the in vitro polymerization of Escherichia coli FtsZ cell division protein we have formulated a model in which the fine balance between curvature, flexibility and lateral interactions accounts for structural and dynamic properties of the FtsZ polymers observed with AFM. The experimental results have been used by the model to calibrate the interaction energies and the values obtained indicate that the filaments are very plastic. The extension of the model to explore filament behavior on a cylindrical surface has shown that the FtsZ condensates promoted by lateral interactions can easily form ring structures through minor modulations of either filament curvature or longitudinal bond energies. The condensation of short, monomer exchanging filaments into rings is shown to produce enough force to induce membrane deformations.PACS codes: 87.15.ak, 87.16.ka, 87.17.Ee.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"2 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2009-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28080611","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 influence of membrane physical properties on microvesicle release in human erythrocytes. 膜物理性质对人红细胞微泡释放的影响。

PMC biophysics Pub Date : 2009-08-24 DOI: 10.1186/1757-5036-2-7

Laurie J Gonzalez, Elizabeth Gibbons, Rachel W Bailey, Jeremy Fairbourn, Thaothanh Nguyen, Samantha K Smith, Katrina B Best, Jennifer Nelson, Allan M Judd, John D Bell

{"title":"The influence of membrane physical properties on microvesicle release in human erythrocytes.","authors":"Laurie J Gonzalez, Elizabeth Gibbons, Rachel W Bailey, Jeremy Fairbourn, Thaothanh Nguyen, Samantha K Smith, Katrina B Best, Jennifer Nelson, Allan M Judd, John D Bell","doi":"10.1186/1757-5036-2-7","DOIUrl":"https://doi.org/10.1186/1757-5036-2-7","url":null,"abstract":" Exposure of human erythrocytes to elevated intracellular calcium causes fragments of the cell membrane to be shed as microvesicles. This study tested the hypothesis that microvesicle release depends on microscopic membrane physical properties such as lipid order, fluidity, and composition. Membrane properties were manipulated by varying the experimental temperature, membrane cholesterol content, and the activity of the trans-membrane phospholipid transporter, scramblase. Microvesicle release was enhanced by increasing the experimental temperature. Reduction in membrane cholesterol content by treatment with methyl-beta-cyclodextrin also facilitated vesicle shedding. Inhibition of scramblase with R5421 impaired vesicle release. These data were interpreted in the context of membrane characteristics assessed previously by fluorescence spectroscopy with environment-sensitive probes such as laurdan, diphenylhexatriene, and merocyanine 540. The observations supported the following conclusions: 1) calcium-induced microvesicle shedding in erythrocytes relates more to membrane properties detected by diphenylhexatriene than by the other probes; 2) loss of trans-membrane phospholipid asymmetry is required for microvesicle release.PACS Codes: 87.16.dj, 87.16.dt.","PeriodicalId":88297,"journal":{"name":"PMC biophysics","volume":"2 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2009-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1757-5036-2-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28360225","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: 43

Zwanzig-Mori projection operators and EEG dynamics: deriving a simple equation of motion. zwanzi - mori投影算子和脑电图动力学:推导一个简单的运动方程。

PMC biophysics Pub Date : 2009-07-13 DOI: 10.1186/1757-5036-2-6

David Hsu, Murielle Hsu

引用次数: 12