BMC Biophysics最新文献

{"title":"Correction to: Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.","authors":"Paolo Mereghetti,&nbsp;Michael Martinez,&nbsp;Rebecca C Wade","doi":"10.1186/s13628-020-0026-z","DOIUrl":"https://doi.org/10.1186/s13628-020-0026-z","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1186/2046-1682-7-4.].</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-020-0026-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37745374","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":"Covalent linkage of bacterial voltage-gated sodium channels.","authors":"Huaping Sun,&nbsp;Zeyu Zheng,&nbsp;Olena A Fedorenko,&nbsp;Stephen K Roberts","doi":"10.1186/s13628-019-0049-5","DOIUrl":"https://doi.org/10.1186/s13628-019-0049-5","url":null,"abstract":"<p><strong>Background: </strong>Bacterial sodium channels are important models for understanding ion permeation and selectivity. However, their homotetrameric structure limits their use as models for understanding the more complex eukaryotic voltage-gated sodium channels (which have a pseudo-heterotetrameric structure formed from an oligomer composed of four domains). To bridge this gap we attempted to synthesise oligomers made from four covalently linked bacterial sodium channel monomers and thus resembling their eukaryotic counterparts.</p><p><strong>Results: </strong>Western blot analyses revealed NaChBac oligomers to be inherently unstable whereas intact expression of NavMs oligomers was possible. Immunodectection using confocal microscopy and electrophysiological characterisation of NavMs tetramers confirmed plasma membrane localisation and equivalent functionality with wild type NavMs channels when expressed in human embryonic kidney cells.</p><p><strong>Conclusion: </strong>This study has generated new tools for the investigation of eukaryotic channels. The successful covalent linkage of four bacterial Nav channel monomers should permit the introduction of radial asymmetry into the structure of bacterial Nav channels and enable the known structures of these channels to be used to gain unique insights into structure-function relationships of their eukaryotic counterparts.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-019-0049-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37215881","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":"Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.","authors":"Asli Yildirim,&nbsp;Nathalie Brenner,&nbsp;Robert Sutherland,&nbsp;Michael Feig","doi":"10.1186/s13628-018-0048-y","DOIUrl":"https://doi.org/10.1186/s13628-018-0048-y","url":null,"abstract":"<p><strong>Background: </strong>Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied extensively, very little is known how cellular crowding affects the conformational sampling of nucleic acids.</p><p><strong>Results: </strong>The effect of protein crowding on the conformational preferences of DNA (deoxyribonucleic acid) is described from fully atomistic molecular dynamics simulations of systems containing a DNA dodecamer surrounded by protein crowders. From the simulations, it was found that DNA structures prefer to stay in B-like conformations in the presence of the crowders. The preference for B-like conformations results from non-specific interactions of crowder proteins with the DNA sugar-phosphate backbone. Moreover, the simulations suggest that the crowder interactions narrow the conformational sampling to canonical regions of the conformational space.</p><p><strong>Conclusions: </strong>The overall conclusion is that crowding effects may stabilize the canonical features of DNA that are most important for biological function. The results are complementary to a previous study of DNA in reduced dielectric environments where reduced dielectric environments alone led to a conformational shift towards A-DNA. Such a shift was not observed here suggested that the reduced dielectric response of cellular environments is counteracted by non-specific interactions with protein crowders under in vivo conditions.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0048-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36830700","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 discontinuous Galerkin model for fluorescence loss in photobleaching of intracellular polyglutamine protein aggregates.","authors":"Christian V Hansen,&nbsp;Hans J Schroll,&nbsp;Daniel Wüstner","doi":"10.1186/s13628-018-0046-0","DOIUrl":"https://doi.org/10.1186/s13628-018-0046-0","url":null,"abstract":"<p><strong>Background: </strong>Intracellular phase separation and aggregation of proteins with extended poly-glutamine (polyQ) stretches are hallmarks of various age-associated neurodegenerative diseases. Progress in our understanding of such processes heavily relies on quantitative fluorescence imaging of suitably tagged proteins. Fluorescence loss in photobleaching (FLIP) is particularly well-suited to study the dynamics of protein aggregation in cellular models of Chorea Huntington and other polyQ diseases, as FLIP gives access to the full spatio-temporal profile of intensity changes in the cell geometry. In contrast to other methods, also dim aggregates become visible during time evolution of fluorescence loss in cellular compartments. However, methods for computational analysis of FLIP data are sparse, and transport models for estimation of transport and diffusion parameters from experimental FLIP sequences are missing.</p><p><strong>Results: </strong>In this paper, we present a computational method for analysis of FLIP imaging experiments of intracellular polyglutamine protein aggregates also called inclusion bodies (IBs). By this method, we can determine the diffusion constant and nuclear membrane transport coefficients of polyQ proteins as well as the exchange rates between aggregates and the cytoplasm. Our method is based on a reaction-diffusion multi-compartment model defined on a mesh obtained by segmentation of the cell images from the FLIP sequence. The discontinuous Galerkin (DG) method is used for numerical implementation of our model in FEniCS, which greatly reduces the computing time. The method is applied to representative experimental FLIP sequences, and consistent estimates of all transport parameters are obtained.</p><p><strong>Conclusions: </strong>By directly estimating the transport parameters from live-cell image sequences using our new computational FLIP approach surprisingly fast exchange dynamics of mutant Huntingtin between cytoplasm and dim IBs could be revealed. This is likely relevant also for other polyQ diseases. Thus, our method allows for quantifying protein dynamics at different stages of the protein aggregation process in cellular models of neurodegeneration.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0046-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36754338","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":"Phenylalanine intercalation parameters for liquid-disordered phase domains - a membrane model study.","authors":"Paulina Adamczewski,&nbsp;Valeria Tsoukanova","doi":"10.1186/s13628-018-0047-z","DOIUrl":"10.1186/s13628-018-0047-z","url":null,"abstract":"<p><strong>Background: </strong>Propensity of phenylalanine (Phe) for nonpolar environments drives its intercalation into phospholipid membranes, which has been implicated in metabolic and neurological disorders. The knowledge of Phe intercalation parameters can be instrumental in understanding various membrane processes triggered by interactions with Phe, in particular the early events leading to the formation of nucleation/docking sites for the self-assembly of Phe amyloid fibrils at the membrane surface.</p><p><strong>Results: </strong>In this study, we used monolayers of phosphatidylethanolamine (DPPE) and phosphatidylcholine (DPPC) to mimic the membrane outer leaflet. Its initial interaction with Phe was modeled by injecting Phe into the aqueous phase underneath the monolayer. Constant pressure insertion assays augmented with epifluorescence microscopy imaging were used to monitor Phe intercalation. Our primary goal was to determine the Phe intercalation area, <i>A</i> _Phe. Two values were obtained for <i>A</i> _Phe, 33 ± 2 and 48 ± 3 Å².</p><p><strong>Conclusions: </strong>Phe appeared to discriminate between DPPE and DPPC packing, and use two modes of intercalation. The area of <i>A</i> _Phe 33 ± 2 Å² is consistent with a Phe monomer intercalating into membrane by inserting the phenyl ring nearly normal to the membrane surface. This mode has been found to operate in DPPE membranes. For DPPC membranes however, the value of <i>A</i> _Phe = 48 ± 3 Å² suggests that, from saline, Phe tends to intercalate as a larger species plausibly dragging along a counterion, Na⁺, in a Na⁺(Phe) complex.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0047-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36713906","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":"Jörg Langowski: his scientific legacy and the future it promises.","authors":"Giuseppe Chirico,&nbsp;Alexander Gansen,&nbsp;Sanford H Leuba,&nbsp;Ada L Olins,&nbsp;Donald E Olins,&nbsp;Jeremy C Smith,&nbsp;Katalin Tóth","doi":"10.1186/s13628-018-0045-1","DOIUrl":"https://doi.org/10.1186/s13628-018-0045-1","url":null,"abstract":"<p><strong>Background: </strong>With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for the creation of effective scientific research networks.</p><p><strong>Methods: </strong>Here, after reviewing some of Jörg's key research contributions and ideas, we offer through the personal remembrance of his closest collaborators, a deep analysis of the major results of his research and the future directions they have engendered.</p><p><strong>Conclusions: </strong>The legacy of Jörg Langowski has been to propel a way of viewing biological function that considers living systems as dynamic and in three dimensions. This physical view of biology that he pioneered is now, finally, becoming established also because of his great effort.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0045-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36327774","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":"Transport of charged small molecules after electropermeabilization - drift and diffusion.","authors":"Esin B Sözer,&nbsp;C Florencia Pocetti,&nbsp;P Thomas Vernier","doi":"10.1186/s13628-018-0044-2","DOIUrl":"https://doi.org/10.1186/s13628-018-0044-2","url":null,"abstract":"<p><strong>Background: </strong>Applications of electric-field-induced permeabilization of cells range from cancer therapy to wastewater treatment. A unified understanding of the underlying mechanisms of membrane electropermeabilization, however, has not been achieved. Protocols are empirical, and models are descriptive rather than predictive, which hampers the optimization and expansion of electroporation-based technologies. A common feature of existing models is the assumption that the permeabilized membrane is passive, and that transport through it is entirely diffusive. To demonstrate the necessity to go beyond that assumption, we present here a quantitative analysis of the post-permeabilization transport of three small molecules commonly used in electroporation research - YO-PRO-1, propidium, and calcein - after exposure of cells to minimally perturbing, 6 ns electric pulses.</p><p><strong>Results: </strong>Influx of YO-PRO-1 from the external medium into the cell exceeds that of propidium, consistent with many published studies. Both are much greater than the influx of calcein. In contrast, the normalized molar <i>efflux</i> of calcein from pre-loaded cells into the medium after electropermeabilization is roughly equivalent to the <i>influx</i> of YO-PRO-1 and propidium. These relative transport rates are correlated not with molecular size or cross-section, but rather with molecular charge polarity.</p><p><strong>Conclusions: </strong>This comparison of the kinetics of molecular transport of three small, charged molecules across electropermeabilized cell membranes reveals a component of the mechanism of electroporation that is customarily taken into account only for the time during electric pulse delivery. The large differences between the influx rates of propidium and YO-PRO-1 (cations) and calcein (anion), and between the influx and efflux of calcein, suggest a significant role for the post-pulse transmembrane potential in the migration of ions and charged small molecules across permeabilized cell membranes, which has been largely neglected in models of electroporation.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0044-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35949892","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":"Synaptic neuron-astrocyte communication is supported by an order of magnitude analysis of inositol tris-phosphate diffusion at the nanoscale in a model of peri-synaptic astrocyte projection.","authors":"Pavel Montes de Oca Balderas,&nbsp;Horacio Montes de Oca Balderas","doi":"10.1186/s13628-018-0043-3","DOIUrl":"https://doi.org/10.1186/s13628-018-0043-3","url":null,"abstract":"<p><strong>Background: </strong>Astrocytes were conceived for decades only as supporting cells of the brain. However, the observation of Ca2+ waves in astrocyte synctitia, their neurotransmitter receptor expression and gliotransmitter secretion suggested a role in information handling, conception that has some controversies. <i>Synaptic Neuron-Astrocyte metabotropic communication mediated by Inositol tris-phosphate</i> (SN-AmcIP3) is supported by different reports. However, some models contradict this idea and Ca2+ stores are 1000 ± 325 nm apart from the Postsynaptic Density in the Perisynaptic Astrocyte Projections (PAP's), suggesting that SN-AmcIP3 is extrasynaptic. However, this assumption does not consider IP3 Diffusion Coefficient (<i>Dab</i>), that activates IP3 Receptor (IP3R) releasing Ca2+ from intracellular stores.</p><p><strong>Results: </strong>In this work we idealized a model of a PAP (PAPm) to perform an order of magnitude analysis of IP3 diffusion using a transient mass diffusion model. This model shows that IP3 forms a concentration gradient along the PAPm that reaches the steady state in milliseconds, three orders of magnitude before IP3 degradation. The model predicts that IP3 concentration near the Ca2+ stores may activate IP3R, depending upon Phospholipase C (PLC) number and activity. Moreover, the PAPm supports that IP3 and extracellular Ca2+ entry synergize to promote global Ca2+ transients.</p><p><strong>Conclusion: </strong>The model presented here indicates that Ca2+ stores position in PAP's does not limit SN-AmcIP3.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0043-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35842630","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":"Thermal decomposition of the amino acids glycine, cysteine, aspartic acid, asparagine, glutamic acid, glutamine, arginine and histidine.","authors":"Ingrid M Weiss,&nbsp;Christina Muth,&nbsp;Robert Drumm,&nbsp;Helmut O K Kirchner","doi":"10.1186/s13628-018-0042-4","DOIUrl":"https://doi.org/10.1186/s13628-018-0042-4","url":null,"abstract":"<p><strong>Background: </strong>The pathways of thermal instability of amino acids have been unknown. New mass spectrometric data allow unequivocal quantitative identification of the decomposition products.</p><p><strong>Results: </strong>Calorimetry, thermogravimetry and mass spectrometry were used to follow the thermal decomposition of the eight amino acids G, C, D, N, E, Q, R and H between 185 °C and 280 °C. Endothermic heats of decomposition between 72 and 151 kJ/mol are needed to form 12 to 70% volatile products. This process is neither melting nor sublimation. With exception of cysteine they emit mainly H₂O, some NH₃ and no CO₂. Cysteine produces CO₂ and little else. The reactions are described by polynomials, AA→<i>a</i> NH₃+<i>b</i> H₂O+<i>c</i> CO₂+<i>d</i> H₂S+<i>e</i> residue, with integer or half integer coefficients. The solid monomolecular residues are rich in peptide bonds.</p><p><strong>Conclusions: </strong>Eight of the 20 standard amino acids decompose at well-defined, characteristic temperatures, in contrast to commonly accepted knowledge. Products of decomposition are simple. The novel quantitative results emphasize the impact of water and cyclic condensates with peptide bonds and put constraints on hypotheses of the origin, state and stability of amino acids in the range between 200 °C and 300 °C.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-018-0042-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35836585","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":"GPMVs in variable physiological conditions: could they be used for therapy delivery?","authors":"Špela Zemljič Jokhadar,&nbsp;Urška Klančnik,&nbsp;Maja Grundner,&nbsp;Tjaša Švelc Kebe,&nbsp;Saša Vrhovec Hartman,&nbsp;Mirjana Liović,&nbsp;Jure Derganc","doi":"10.1186/s13628-017-0041-x","DOIUrl":"https://doi.org/10.1186/s13628-017-0041-x","url":null,"abstract":"<p><strong>Background: </strong>Cell based carriers are increasingly recognized as a good system for cargo delivery to cells. One of the reasons is their biocompatibility and low toxicity compared to artificial systems. Giant plasma membrane vesicles (GPMV) derive from the cell plasma membrane. Thus they offer the closest approximation to it, which makes them good candidates for potential drug delivery systems. To evaluate the applicability of GPMVs as carriers, we analyzed their basic biophysical properties to test their robustness in the face of changeable physiological conditions, as well as their ability to translocate across the membrane into cells.</p><p><strong>Results: </strong>GPMVs formed from human umbilical vein endothelial cells (HUVEC) sustain a drastic osmotic challenge (50-500 mOsmoL/kg) unlike giant unilamelar vesicles (GUVs). In hyper-osmotic solutions the average volume decreases and membrane invaginations form, while in the hypo-osmolar buffer the volume of GPMVs increases and these changes were not reversible. The membranes of flaccid GPMVs started to wrinkle unevenly giving rise to buds after exposure to lipopolysaccharide (LPS). The shape changes in GUVs are reversible in contrast to GPMVs after LPS removal. GPMVs exposed to fluorescent LPS exhibited a signal that remained visible in some GPMVs even after LPS removal, which was never the case with GUVs. Calcein penetrated both into GUVs and GPMVs, however after the removal from the bulk solution some of the GPMVs still exhibited very bright signal, while in GUVs only a weak fluorescent signal was detected. We could also see that practically all GPMVs incorporated dextran initially, but after the dextran solution was changed with the initial non-fluorescent solution it remained only in 20% of them. The majority of HUVEC cells displayed a fluorescent signal after the incubation with GPMVs that contained fluorescently labeled dextran.</p><p><strong>Conclusion: </strong>Our findings indicate that GPMVs behave quite differently from artificially made giant phospholipid vesicles and the changes induced by the different treatments we subjected them to are not reversible. We also demonstrate that different substances can be both loaded into them and delivered into cells, so GPMVs may be of potential use as cargo/therapy delivery systems.</p>","PeriodicalId":9045,"journal":{"name":"BMC Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13628-017-0041-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35714816","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}