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European Biophysics Journal: EBJ

Dalila Khemili, Carmen Valenzuela, Fatima Laraba-Djebari, Djelila Hammoudi-Triki
Neurotoxins of scorpion venoms modulate ion channels. Voltage-gated potassium (KV ) channels regulate the membrane potential and are involved in the activation and proliferation of immune cells. Macrophages are key components of the inflammatory response induced by scorpion venom. The present study was undertaken to investigate the effect of Androctonus australis hector (Aah) venom on KV channels in murine resident peritoneal macrophages. The cytotoxicity of the venom was assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) -based assay and electrophysiological recordings were performed using the whole-cell patch clamp technique...
July 13, 2018: European Biophysics Journal: EBJ
Robert T Wright, David Hayes, Peter J Sherwood, Walter F Stafford, John J Correia
The goal of this work is to develop a preclinical method for quantitative hydrodynamic and thermodynamic analysis of therapeutic proteins in crowded environments like human serum. The method utilizes tracer amounts of fluorescently labeled monoclonal antibodies and the Aviv AU-FDS optical system. We have performed sedimentation velocity experiments as a function of mAb, human serum albumin and human IgG concentration to extract self- and cross-term hydrodynamic nonideality effects. SV measurements are consistently complicated by weak mAb-mAb and mAb-IgG interactions (Wright et al...
July 12, 2018: European Biophysics Journal: EBJ
Emilie Vanhove, Marc Vanhove
Equilibrium titration curves have been used to determine the affinity of biomolecules using a variety of platforms and technologies. Such measurements, however, are experimentally limited by the time that is needed for the system to reach the equilibrium, which may exceed the time during which the studied biomolecules are stable. We propose here a kinetic model to analyze titration curves obtained prior to full equilibration of the system.
July 10, 2018: European Biophysics Journal: EBJ
Sagheer A Onaizi
Protein fouling is a serious problem in many food, pharmaceutical and household industries. In this work, the removal of rubisco protein fouling from cellulosic surfaces using a protease (subtilisin A) has been investigated experimentally and mathematically. The cellulosic surfaces were prepared using self-assembled monolayers (SAMs) on a surface plasmon resonance biosensor (chip) surface after conjugating cellulose to α-lipoic acid. Rubisco adsorption on the prepared cellulosic SAMs was found to be irreversible, leading to the creation of a tough protein fouling...
July 9, 2018: European Biophysics Journal: EBJ
Khair Bux, Syed Abid Ali, Syed Tarique Moin
Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein...
July 4, 2018: European Biophysics Journal: EBJ
Abbas Yousefpour, Sepideh Amjad-Iranagh, Fatemeh Goharpey, Hamid Modarress
In this work, the effects of the anti-hypertensive drug amlodipine in native and PEGylated forms on the malfunctioning of negatively charged lipid bilayer cell membranes constructed from DMPS or DMPS + DMPC were studied by molecular dynamics simulation. The obtained results indicate that amlodipine alone aggregates and as a result its diffusion into the membrane is retarded. In addition, due to their large size aggregates of the drug can damage the cell, rupturing the cell membrane. It is shown that PEGylation of amlodipine prevents this aggregation and facilitates its diffusion into the lipid membrane...
July 3, 2018: European Biophysics Journal: EBJ
Mohan Kumar, Mahima Kaushik, Shrikant Kukreti
Human telomeric G-rich sequences can fold back into various conformations depending upon the salt (Na+ or K+ ) at physiological pH. On the basis of results obtained by native PAGE electrophoresis, circular dichroism, and UV-melting experiments, we report here that truncated sequences of human telomere (d-GGGTTAGGG; GM9, d-AGGGTTAGGG; GM10, d-TAGGGTTAGGG; GM11) adopt a varied range of quadruplex conformations as a function of the cation present. By correlating CD and gel electrophoresis experiments; it was concluded that the GM9 oligonucleotide can self-associate to form a tetramer quadruplex (antiparallel; AP) in Na+ solution and a mixture of G-triplex (AP) or tri-G-quadruplex (parallel; P) along with a tetramer G-quadruplex structure (AP) in K+ ...
June 22, 2018: European Biophysics Journal: EBJ
Cornelia M Schneider, Helmut Cölfen
Analytical band centrifugation (ABC) is a powerful tool for the analysis of macromolecules and nanoparticles. Although it offers several advantages over the sedimentation velocity (SV) experiment like a physical separation of the individual components and the possibility to perform chemical reactions, its analysis is still very restricted. Therefore, we investigated the integration of ABC data as an alternative approach, as this results in data similar to SV, which can then be evaluated by many established evaluation programs...
June 21, 2018: European Biophysics Journal: EBJ
Simon E Wawra, Martin Thoma, Johannes Walter, Christian Lübbert, Thaseem Thajudeen, Cornelia Damm, Wolfgang Peukert
By combining analytical ultracentrifugation (AUC) in liquid phase and scanning mobility particle sizer (SMPS) in the gas phase, additional information on the particle size and morphology has been obtained for rigid particles. In this paper, we transfer this concept to soft particles, allowing us to analyze the size and molar mass of the short side chain perfluorosulfonic acid ionomer Aquivion® in a dilute aqueous suspension. The determination of the primary size and exact molar mass of this class of polymers is challenging since they are optically transparent and due to the formation of different aggregate structures depending on the concentration and solvent properties...
June 16, 2018: European Biophysics Journal: EBJ
S V Efimov, Yu O Zgadzay, N B Tarasova, V V Klochkov
The protein hormone insulin exists in several forms in nature, and a large number of modified sequences are used in pharmacy. They differ by physicochemical properties and efficiency of biological action. Pancreatic bovine insulin was studied in an acidic solution by nuclear magnetic resonance spectroscopy. [Formula: see text]H and [Formula: see text]C NMR signal assignment of backbone and side chains was made by analysis of a set of 2D spectra obtained on a sample with natural isotope abundance. The presence of certain secondary structure elements was revealed on a qualitative level based on nuclear Overhauser effect spectroscopy, which are similar to those observed in the crystal structure...
June 1, 2018: European Biophysics Journal: EBJ
Oleksii Zdorevskyi, Sergey N Volkov
Single-molecule experiments on DNA unzipping are analyzed on the basis of the mobility of nucleic bases in complementary pairs. Two possible scenarios of DNA double-helix unzipping are proposed and studied, using the atom-atom potential function method. According to the first scenario, the base pairs transit into a 'preopened' metastable state and then fully open along the 'stretch' pathway. In this case, the DNA unzipping takes place slowly and as an equilibrium process, with the opening energies being similar to the energies obtained in thermodynamic experiments on DNA melting...
May 31, 2018: European Biophysics Journal: EBJ
Shenggen Yao, Thomas G Meikle, Ashish Sethi, Frances Separovic, Jeffrey J Babon, David W Keizer
Pulsed-field gradient nuclear magnetic resonance has seen an increase in applications spanning a broad range of disciplines where molecular translational diffusion properties are of interest. The current study introduces and experimentally evaluates the measurement of translational diffusion coefficients of 15 N-enriched biomolecules using a 1 H-15 N HMQC-filtered band-selective excitation short transient (BEST) sequence as an alternative to the previously described SOFAST-XSTE sequence. The results demonstrate that accurate translational diffusion coefficients of 15 N-labelled peptides and proteins can be obtained using this alternative 1 H-15 N HMQC-filtered BEST sequence which is implementable on NMR spectrometers equipped with probes fitted with a single-axis field gradient, including most cryoprobes dedicated to bio-NMR...
May 21, 2018: European Biophysics Journal: EBJ
Haram Kim, Emre Brookes, Weiming Cao, Borries Demeler
Sedimentation velocity experiments performed in the analytical ultracentrifuge are modeled using finite-element solutions of the Lamm equation. During modeling, three fundamental parameters are optimized: the sedimentation coefficients, the diffusion coefficients, and the partial concentrations of all solutes present in a mixture. A general modeling approach consists of fitting the partial concentrations of solutes defined in a two-dimensional grid of sedimentation and diffusion coefficient combinations that cover the range of possible solutes for a given mixture...
May 17, 2018: European Biophysics Journal: EBJ
Tayler L Williams, Gary E Gorbet, Borries Demeler
Recent developments in the UltraScan-III software make it possible to model multi-speed analytical ultracentrifugation sedimentation velocity experiments using finite-element solutions of the Lamm equation. Using simulated data, we demonstrate here how these innovations can be used to enhance the resolution of sedimentation velocity experiments when compared to single-speed experiments. Using heterogeneous systems covering as much as five orders of magnitude in molar mass and fivefold in anisotropy, we compare results from runs performed at multiple speeds to those obtained from single-speed experiments, fitted individually and analyzed globally over multiple speeds, and quantify resolution for sample heterogeneous in size and anisotropy...
May 10, 2018: European Biophysics Journal: EBJ
Konstantin A Okotrub, Nikolay V Surovtsev
We applied a Raman spectroscopy approach to investigate the effect of a cryoprotectant on the redox state of cytochromes on freezing yeast cells. The redox activity of cytochromes was studied using time-resolved photobleaching of the resonance Raman lines. It is found that ice formation causes a drastic change in the redox state of cytochromes in cells frozen without cryoprotectant, whereas in the presence of glycerol the effects of ice formation are more gradual. The photobleaching rate of cells frozen in glycerol solution shows a gradual slowing with temperature decrease and an abrupt slowdown below - 48 °C...
April 27, 2018: European Biophysics Journal: EBJ
Kim Potvin-Fournier, Geneviève Valois-Paillard, Marie-Claude Gagnon, Thierry Lefèvre, Pierre Audet, Line Cantin, Jean-François Paquin, Christian Salesse, Michèle Auger
Recoverin is a protein involved in the phototransduction cascade by regulating the activity of rhodopsin kinase through a calcium-dependent binding process at the surface of rod outer segment disk membranes. We have investigated the interaction of recoverin with zwitterionic phosphatidylcholine bilayers, the major lipid component of the rod outer segment disk membranes, using both 31 P and 19 F solid-state nuclear magnetic resonance (NMR) and infrared spectroscopy. In particular, several novel approaches have been used, such as the centerband-only detection of exchange (CODEX) technique to investigate lipid lateral diffusion and 19 F NMR to probe the environment of the recoverin myristoyl group...
April 24, 2018: European Biophysics Journal: EBJ
Uğur Çetiner, Andriy Anishkin, Sergei Sukharev
Adaptive desensitization and inactivation are common properties of most ion channels and receptors. The mechanosensitive channel of small conductance MscS, which serves as a low-threshold osmolyte release valve in most bacteria, inactivates not from the open, but from the resting state under moderate tensions. This mechanism enables the channel to respond differently to slow tension ramps versus abruptly applied stimuli. In this work, we present a reconstruction of the energy landscape for MscS transitions based on patch current kinetics recorded under special pressure protocols...
April 23, 2018: European Biophysics Journal: EBJ
Andreas Dress
In this paper, it is argued that the fact that, so far, even the worst and most far-reaching epidemics-from the Plague of Athens in 430 BC and the Plague of Justinian in 541/542 AD to the Hong Kong Flu from 1968/69-always finally petered out can be explained using Manfred Eigen's quasispecies concept: Indeed, as the infectious agents, while duplicating themselves in the infected organisms, mutate all the time, these infected organisms carry along quite a multitude of mutational variants or-in Manfred Eigen's terms-a whole quasispecies of infectious agents implying that, within that quasispecies, those variants that differ from the wild type may actually serve as some kind of vaccination program when infecting some previously uninfected persons...
May 2018: European Biophysics Journal: EBJ
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May 2018: European Biophysics Journal: EBJ
Eberhard Neumann, Sergej Kakorin
The chemical thermodynamic concept for membrane electroporation is critically revisited. The hysteresis in the electric field dependence of the rapid in-field electroporation events (on the in-field hysteresis branch) and the slower post-field pore resealing process (zero-field hysteresis branch) is a typical ensemble property involving rapid single-pore opening-closing events that are temporally and spatially distributed. In the case of spherical membrane shells in homogeneous external fields, the acting local field is dependent on the polar-angular position...
May 2018: European Biophysics Journal: EBJ
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