BMC Biophysics最新文献

{"title":"A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.","authors":"Phuong H Nguyen,&nbsp;Anna M Popova,&nbsp;Kálmán Hideg,&nbsp;Peter Z Qin","doi":"10.1186/s13628-015-0019-5","DOIUrl":"https://doi.org/10.1186/s13628-015-0019-5","url":null,"abstract":"<p><strong>Background: </strong>Spin labels, which are chemically stable radicals attached at specific sites of a bio-molecule, enable investigations on structure and dynamics of proteins and nucleic acids using techniques such as site-directed spin labeling and paramagnetic NMR. Among spin labels developed, the class of rigid labels have limited or no independent motions between the radical bearing moiety and the target, and afford a number of advantages in measuring distances and monitoring local dynamics within the parent bio-molecule. However, a general method for attaching a rigid label to nucleic acids in a nucleotide-independent manner has not been reported.</p><p><strong>Results: </strong>We developed an approach for installing a nearly rigid nitroxide spin label, designated as R5c, at a specific site of the nucleic acid backbone in a nucleotide-independent manner. The method uses a post-synthesis approach to covalently attach the nitroxide moiety in a cyclic fashion to phosphorothioate groups introduced at two consecutive nucleotides of the target strand. R5c-labeled nucleic acids are capable of pairing with their respective complementary strands, and the cyclic nature of R5c attachment significantly reduced independence motions of the label with respect to the parent duplex, although it may cause distortion of the local environment at the site of labeling. R5c yields enhanced sensitivity to the collective motions of the duplex, as demonstrated by its capability to reveal changes in collective motions of the substrate recognition duplex of the 120-kDa Tetrahymena group I ribozyme, which elude detection by a flexible label.</p><p><strong>Conclusions: </strong>The cyclic R5c nitroxide can be efficiently attached to a target nucleic acid site using a post-synthetic coupling approach conducted under mild biochemical conditions, and serves as a viable label for experimental investigation of segmental motions in nucleic acids, including large folded RNAs.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0019-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33118656","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}

{"title":"A flexible approach to assess fluorescence decay functions in complex energy transfer systems.","authors":"Christoph Roethlein,&nbsp;Markus S Miettinen,&nbsp;Zoya Ignatova","doi":"10.1186/s13628-015-0020-z","DOIUrl":"https://doi.org/10.1186/s13628-015-0020-z","url":null,"abstract":"<p><strong>Background: </strong>Time-correlated Förster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions.</p><p><strong>Results: </strong>Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems.</p><p><strong>Conclusion: </strong>This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0020-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33118655","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}

{"title":"Life at the mesoscale: the self-organised cytoplasm and nucleoplasm.","authors":"Richard P Sear,&nbsp;Ignacio Pagonabarraga,&nbsp;Andrew Flaus","doi":"10.1186/s13628-015-0018-6","DOIUrl":"https://doi.org/10.1186/s13628-015-0018-6","url":null,"abstract":"<p><p>The cell contains highly dynamic structures exploiting physical principles of self-organisation at the mesoscale (100 nm to 10 μm). Examples include non-membrane bound cytoplasmic bodies, cytoskeleton-based motor networks and multi-scale chromatin organisation. The challenges of mesoscale self-organisation were discussed at a CECAM workshop in July 2014. Biologists need approaches to observe highly dynamic, low affinity, low specificity associations and to perturb single structures, while biological physicists and biomathematicians need to work closely with biologists to build and validate quantitative models. A table of terminology is included to facilitate multidisciplinary efforts to reveal the richness and diversity of mesoscale cell biology. </p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0018-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33166615","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}

{"title":"BMC Biophysics reviewer acknowledgement 2014","authors":"Catherine J. Potenski","doi":"10.1186/s13628-015-0017-7","DOIUrl":"https://doi.org/10.1186/s13628-015-0017-7","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-015-0017-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vesicle biomechanics in a time-varying magnetic field.","authors":"Hui Ye,&nbsp;Austen Curcuru","doi":"10.1186/s13628-014-0016-0","DOIUrl":"https://doi.org/10.1186/s13628-014-0016-0","url":null,"abstract":"<p><strong>Background: </strong>Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a time-varying magnetic field. Following previous publications and to simplify the calculation, this model treated the inner and suspending media as lossy dielectrics, the membrane thickness set at zero, and the electric resistance of the membrane assumed to be negligible. This work provided the first analytical solutions for the surface charges, electric field, radial pressure, overall translational forces, and rotational torques introduced on a vesicle by the time-varying magnetic field. Frequency responses of these measures were analyzed, particularly the frequency used clinically by transcranial magnetic stimulation (TMS).</p><p><strong>Results: </strong>The induced surface charges interacted with the electric field to produce a biomechanical impact upon the vesicle. The distribution of the induced surface charges depended on the orientation of the coil and field frequency. The densities of these charges were trivial at low frequency ranges, but significant at high frequency ranges. The direction of the radial force on the vesicle was dependent on the conductivity ratio between the vesicle and the medium. At relatively low frequencies (<200 KHz), including the frequency used in TMS, the computed radial pressure and translational forces on the vesicle were both negligible.</p><p><strong>Conclusions: </strong>This work provides an analytical framework and insight into factors affecting cellular biomechanics under a time-varying magnetic field. Biological effects of clinical TMS are not likely to occur via alteration of the biomechanics of brain cells.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-014-0016-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33026399","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}

{"title":"Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric.","authors":"Renmin Han,&nbsp;Liansan Wang,&nbsp;Fan Xu,&nbsp;Yongdeng Zhang,&nbsp;Mingshu Zhang,&nbsp;Zhiyong Liu,&nbsp;Fei Ren,&nbsp;Fa Zhang","doi":"10.1186/s13628-014-0015-1","DOIUrl":"https://doi.org/10.1186/s13628-014-0015-1","url":null,"abstract":"<p><strong>Background: </strong>The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with conventional light microscopy. These techniques utilize the stochastic switching of probe molecules to overcome the diffraction limit and determine the precise localizations of molecules, which often requires a long image acquisition time. However, long acquisition times increase the risk of sample drift. In the case of high resolution microscopy, sample drift would decrease the image resolution.</p><p><strong>Results: </strong>In this paper, we propose a novel metric based on the distance between molecules to solve the drift correction. The proposed metric directly uses the position information of molecules to estimate the frame drift. We also designed an algorithm to implement the metric for the general application of drift correction. There are two advantages of our method: First, because our method does not require space binning of positions of molecules but directly operates on the positions, it is more natural for single molecule imaging techniques. Second, our method can estimate drift with a small number of positions in each temporal bin, which may extend its potential application.</p><p><strong>Conclusions: </strong>The effectiveness of our method has been demonstrated by both simulated data and experiments on single molecular images.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-014-0015-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33027746","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}

{"title":"A novel delta current method for transport stoichiometry estimation.","authors":"Xuesi M Shao,&nbsp;Liyo Kao,&nbsp;Ira Kurtz","doi":"10.1186/s13628-014-0014-2","DOIUrl":"https://doi.org/10.1186/s13628-014-0014-2","url":null,"abstract":"<p><strong>Background: </strong>The ion transport stoichiometry (q) of electrogenic transporters is an important determinant of their function. q can be determined by the reversal potential (Erev) if the transporter under study is the only electrogenic transport mechanism or a specific inhibitor is available. An alternative approach is to calculate delta reversal potential (ΔErev) by altering the concentrations of the transported substrates. This approach is based on the hypothesis that the contributions of other channels and transporters on the membrane to Erev are additive. However, Erev is a complicated function of the sum of different conductances rather than being additive.</p><p><strong>Results: </strong>We propose a new delta current (ΔI) method based on a simplified model for electrogenic secondary active transport by Heinz (Electrical Potentials in Biological Membrane Transport, 1981). ΔI is the difference between two currents obtained from altering the external concentration of a transported substrate thereby eliminating other currents without the need for a specific inhibitor. q is determined by the ratio of ΔI at two different membrane voltages (V1 and V2) where q = 2RT/(F(V2 -V1))ln(ΔI2/ΔI1) + 1. We tested this ΔI methodology in HEK-293 cells expressing the elctrogenic SLC4 sodium bicarbonate cotransporters NBCe2-C and NBCe1-A, the results were consistent with those obtained with the Erev inhibitor method. Furthermore, using computational simulations, we compared the estimates of q with the ΔErev and ΔI methods. The results showed that the ΔErev method introduces significant error when other channels or electrogenic transporters are present on the membrane and that the ΔI equation accurately calculates the stoichiometric ratio.</p><p><strong>Conclusions: </strong>We developed a ΔI method for estimating transport stoichiometry of electrogenic transporters based on the Heinz model. This model reduces to the conventional reversal potential method when the transporter under study is the only electrogenic transport process in the membrane. When there are other electrogenic transport pathways, ΔI method eliminates their contribution in estimating q. Computational simulations demonstrated that the ΔErev method introduces significant error when other channels or electrogenic transporters are present and that the ΔI equation accurately calculates the stoichiometric ratio. This new ΔI method can be readily extended to the analysis of other electrogenic transporters in other tissues.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-014-0014-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32948529","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}

{"title":"Langevin dynamics simulations of charged model phosphatidylinositol lipids in the presence of diffusion barriers: toward an atomic level understanding of corralling of PIP2 by protein fences in biological membranes.","authors":"Kyu Il Lee,&nbsp;Wonpil Im,&nbsp;Richard W Pastor","doi":"10.1186/s13628-014-0013-3","DOIUrl":"https://doi.org/10.1186/s13628-014-0013-3","url":null,"abstract":"<p><strong>Background: </strong>The polyvalent acidic lipid phosphatidylinositol, 4,5-bisphosphate (PIP2) is important for many cellular functions. It has been suggested that different pools of PIP2 exist in the cytoplasmic leaflet of the plasma membrane, and that such pooling could play a role in the regulation of PIP2. The mechanism of fencing, however, is not understood.</p><p><strong>Results: </strong>This study presents the results of Langevin dynamics simulations of PIP2 to elucidate some of the molecular level considerations that must be applied to models for fencing. For each simulation, a pool of PIP2 (modeled as charged spheres) was placed in containments with boundaries modeled as a single row of rods (steric or electrostatic) or rigid protein filaments. It is shown that even a small gap (20 Å, which is 1.85 times larger than the diameter of a PIP2 sphere) leads to poor steric blocking, and that electrostatic blockage is only effective at very high charge density. Filaments of human septin, yeast septin, and actin also failed to provide adequate blockage when placed on the membrane surface. The two septins do provide high blockage consistent with experiment and with phenomenological considerations of permeability when they are buried 9 Å and 12 Å below the membrane surface, respectively. In contrast, burial does not improve blockage by the \"arch-shaped\" actin filaments. Free energy estimates using implicit membrane-solvent models indicate that burial of the septins to about 10 Å can be achieved without penetration of charged residues into the hydrophobic region of the membrane.</p><p><strong>Conclusions: </strong>These results imply that a functioning fence assembled from protein filaments must either be buried well below the membrane surface, have more than a single row, or contain additional components that fill small gaps in the filaments.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-014-0013-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33132814","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}

{"title":"Origin of multiple intersubunit rotations before EF-G-catalyzed ribosomal translocation through the mRNA with a downstream secondary structure","authors":"P. Xie","doi":"10.1186/S13628-014-0012-4","DOIUrl":"https://doi.org/10.1186/S13628-014-0012-4","url":null,"abstract":"","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/S13628-014-0012-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65859814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation tools for particle-based reaction-diffusion dynamics in continuous space.","authors":"Johannes Schöneberg,&nbsp;Alexander Ullrich,&nbsp;Frank Noé","doi":"10.1186/s13628-014-0011-5","DOIUrl":"https://doi.org/10.1186/s13628-014-0011-5","url":null,"abstract":"<p><p>Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics. </p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-014-0011-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33102978","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}