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European Biophysics Journal: EBJ

Ewelina Nowak, Anna Wisła-Świder, Gohar Khachatryan, Maciej Fiedorowicz, Krzysztof Danel
Although much research has been performed on DNA complexes carrying long alkyl chains (C10, C16, and C18), there is no information about physicochemical characterization of synthesized composites with allyl imidazole-based ionic liquids and quaternary ammonium salts with n-butyl chains. Here, complexes were synthesized by ion-exchange reactions between sonicated DNA and three ionic liquids (ILs) formed from two imidazole-based compounds, 1-allyl-3-methylimidazolium bromide (Amim) or 1-butyl-3-methylimidazolium bromide (Bmim), and from the quaternary ammonium salt tetra-n-butylammonium bromide (TBAB)...
April 19, 2019: European Biophysics Journal: EBJ
Gabor Steinbach, David Nagy, Gábor Sipka, Erik Manders, Győző Garab, László Zimányi
Confocal laser scanning microscopy is probably the most widely used and one of the most powerful techniques in basic biology, medicine and material sciences that is employed to elucidate the architecture of complex cellular structures and molecular macro-assemblies. It has recently been shown that the information content, signal-to-noise ratio and resolution of such microscopes (LSMs) can be improved significantly by adding different attachments or modifying their design, while retaining their user-friendly features and relatively moderate costs...
April 13, 2019: European Biophysics Journal: EBJ
Marko Djordjevic, Andjela Rodic, Stefan Graovac
Recent decades brought a revolution to biology, driven mainly by exponentially increasing amounts of data coming from "'omics" sciences. To handle these data, bioinformatics often has to combine biologically heterogeneous signals, for which methods from statistics and engineering (e.g. machine learning) are often used. While such an approach is sometimes necessary, it effectively treats the underlying biological processes as a black box. Similarly, systems biology deals with inherently complex systems, characterized by a large number of degrees of freedom, and interactions that are highly non-linear...
April 9, 2019: European Biophysics Journal: EBJ
Seyedeh Akram Shirdel, Khosrow Khalifeh
Thermodynamics of protein folding refers to the stability measurements where structural changes of a given protein in the presence of a denaturing agent are monitored by spectroscopic or calorimetric techniques. In macroscopic point of view, protein stability represents the ratio of the population of its unfolded state to that of folded one in equilibrium condition, while in microscopic point of view, the stability is actually a net value from a combination of favorable and unfavorable contributions that affect the structural integrity of a protein molecule...
April 3, 2019: European Biophysics Journal: EBJ
Kei Segawa, Miki Watanabe-Matsui, Kengo Tsuda, Toshitaka Matsui, Mikako Shirouzu, Kazuhiko Igarashi, Kazutaka Murayama
Transcriptional repressor Bach1 plays an important role in antioxidant response. Bach1 function is regulated by heme binding to the four cysteine-proline (CP) motifs in Bach1, which leads to inhibition of its activity. Three of these CP motifs are located N-terminal to the bZip (basic leucine zipper) domain that is responsible for DNA binding. Based on sequence analysis, the region surrounding these CP motifs was expected to be intrinsically disordered. Bach1 is one of few known intrinsically disordered proteins that accept multiple heme molecules for functional regulation, but the molecular mechanisms of heme binding and functional regulation remain unclear...
April 1, 2019: European Biophysics Journal: EBJ
Valeria A Risso, Mario R Ermácora
[Formula: see text]-Lactamases (penicillinases) facilitate bacterial resistance to antibiotics and are excellent theoretical and experimental models in protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class A [Formula: see text]-lactamase with three tryptophan residues located one in each of its two domains and one in the interface between domains. The conformational landscape of three well-characterized ESP Trp[Formula: see text]Phe mutants was characterized in equilibrium unfolding experiments by measuring tryptophan fluorescence, far-UV CD, activity, hydrodynamic radius, and limited proteolysis...
March 30, 2019: European Biophysics Journal: EBJ
Chibin Zhang, Zhiwei Cheng, Xiaohui Lin, Wenquan Chu
A microscopic transport model of a polymer translocating through a nuclear pore complex (NPC) is presented based on self-consistent field theory (SCFT), with the NPC and its nucleoporins mimicked by a hairy channel. Multiple cell environment effects (electrolyte effect, excluded volume effect, NPC drag effect, and hydrophobic effect) are all considered in this hairy channel model. The influence of various parameters (polymer chain length, length of NPC, strength of hydrophobic effect, and excluded volume effect) on translocation time is studied through theoretical analysis and numerical calculation...
March 29, 2019: European Biophysics Journal: EBJ
Lilia Anghel, Andrey Rogachev, Alexander Kuklin, Raul Victor Erhan
β-Lactoglobulin is one of the most notable representatives of the lipocalin family of proteins that are mainly involved in the transportation of small hydrophobic molecules. Therefore, the conformation stability of these proteins represents an important step for several industrial applications. In this study, the β-lactoglobulin (β-lg) conformation stability in solution was studied as a function of the protein concentration, pH, NaCl and temperature when the protein concentration is significantly higher in the buffer solution...
March 28, 2019: European Biophysics Journal: EBJ
Zicong Zhou, Chen-Xu Wu
We explore the effects of two typical torques on the mechanical property of the helical configuration for an intrinsically straight filament or biopolymer either in three-dimensional space or on a cylinder. One torque is parallel to the direction of a uniaxial applied force, and is coupled to the cross section of the filament. We obtain some algebraic equations for the helical configuration and find that the boundary conditions are crucial. In three-dimensional space, we show that the extension is always a monotonic function of the applied force...
March 27, 2019: European Biophysics Journal: EBJ
Mohammad Abu Sayem Karal, Mostafizur Rahman, Md Kabir Ahamed, Sayed Ul Alam Shibly, Marzuk Ahmed, Md Mostofa Shakil
Lipid membranes of giant unilamellar vesicles (GUVs) with diameters greater than 10 μm are promising model membranes for investigating the physical and biological properties of the biomembranes of cells. These are extensively used for the study of the interaction of various membrane-active agents, where purified and similar-size oil-free GUVs are necessary. Although the existing membrane filtering method provides the required quality and quantity of GUVs, it includes a relatively expensive double-headed peristaltic pump...
March 27, 2019: European Biophysics Journal: EBJ
Szilvia Krekic, Dávid Nagy, Stefka G Taneva, László Fábián, László Zimányi, András Dér
In this paper, the photocycle of the dried photoactive yellow protein film has been investigated in different humidity environments, in order to characterize its nonlinear optical properties for possible integrated optical applications. The light-induced spectral changes of the protein films were monitored by an optical multichannel analyser set-up, while the accompanying refractive index changes were measured with the optical waveguide lightmode spectroscopy method. To determine the number and kinetics of spectral intermediates in the photocycle, the absorption kinetic data were analysed by singular value decomposition and multiexponential fitting methods, whose results were used in a subsequent step of fitting a photocycle model to the data...
March 23, 2019: European Biophysics Journal: EBJ
Vladimir P Zhdanov
After a short perturbation of a bistable genetic network, it returns to its initial steady state or transits to another steady state. The time scale characterizing such transient regimes can be appreciably longer compared to those of the degradation of the perturbed mRNAs and proteins. The author shows in detail the specifics of this slowdown of the transient kinetics using mean-field kinetic equations and Monte Carlo simulations. Attention is focused on nanocarrier-mediated delivery and release of short non-coding RNA (e...
March 22, 2019: European Biophysics Journal: EBJ
Ishay Wohl, Naomi Zurgil, Yaron Hakuk, Maria Sobolev, Mordechai Deutsch
We introduce a simple, label-free cytometry technique, based on the spatio-temporal fluctuation analysis of pixel gray levels of a cell image utilizing the Gray Level Information Entropy (GLIE) function. In this study, the difference in GLIE random fluctuations and its biophysical etiology in a comparison cell model of leukemic Jurkat cells and human healthy donor lymphocytes was explored. A combination of common bright field microscopy and a unique imaging dish wherein cells are individually held untethered in a picoliter volume matrix of optical chambers was used...
March 22, 2019: European Biophysics Journal: EBJ
Adéla Krizova, Lena Maltan, Isabella Derler
Ca2+ ions represent versatile second messengers that regulate a huge diversity of processes throughout the cell's life. One prominent Ca2+ entry pathway into the cell is the Ca2+ release-activated Ca2+ (CRAC) ion channel. It is fully reconstituted by the two molecular key players: the stromal interaction molecule (STIM1) and Orai. STIM1 is a Ca2+ sensor located in the membrane of the endoplasmic reticulum, and Orai, a highly Ca2+ selective ion channel embedded in the plasma membrane. Ca2+ store-depletion leads initially to the activation of STIM1 which subsequently activates Orai channels via direct binding...
March 21, 2019: European Biophysics Journal: EBJ
Yoelsy Leyva, Osmel Martin, Noel Perez, José Suarez-Lezcano, Manuel Fundora-Pozo
Potential constraints on protocell size are developed from simple entropic considerations. To do that, two new different indexes as measures of their structural and dynamic order were developed and applied to an elemental model of the heterotrophic protocell. According to our results, cell size should be a key factor determining the potential of these primitive systems to evolve and consequently to support life. Our analyses also suggest that the size of the optimal vesicles could be constrained to have radii in the interval [Formula: see text], where the two extreme limits [Formula: see text] and [Formula: see text] represent the states of maximum structural order (largest accumulation of substrate inside the vesicle) and the maximum flux of entropy production, respectively...
March 21, 2019: European Biophysics Journal: EBJ
Stane Pajk, Hana Majaron, Matej Novak, Boštjan Kokot, Janez Štrancar
The potential of live-cell stimulated emission depletion (STED) nanoscopy has not yet been fully exploited. Currently, the main limitation is the small number of fluorophores and probes that can sustain high light intensity/high dose employed in STED. Namely, fluorophores suitable for STED nanoscopy must be bright and highly photostable and exhibit a large Stokes shift. To expand the list of available probes, we synthesized and evaluated several new membrane probes for live-cell STED nanoscopy. Of the tested probes, probes MePyr500, ThiaCN545 and NB640 not only allow high-resolution STED images, but also partition into the intracellular membranes relatively quickly, thus lacking the selectivity of labelling solely the plasma membrane...
March 16, 2019: European Biophysics Journal: EBJ
Maria A van Agthoven, Yuko P Y Lam, Peter B O'Connor, Christian Rolando, Marc-André Delsuc
Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion-neutral, ion-electron, or ion-photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation...
March 13, 2019: European Biophysics Journal: EBJ
Oleksii Zdorevskyi, Sergey N Volkov
The original article was published with the following errors.
March 6, 2019: European Biophysics Journal: EBJ
Han Yan, Daming Zhou, Biao Shi, Ziyin Zhang, Haibing Tian, Leyong Yu, Yunjiao Wang, Xiyun Guan, Zuobin Wang, Deqiang Wang
Solid-state nanopores are considered an attractive basis for single-molecule DNA sequencing. At present, one obstacle to be overcome is the improvement of their temporal resolution, with the DNA molecules remaining in the sensing volume of the nanopore for a long period of time. Here, we used a composite system of a concentration gradient of LiCl in solution and a nanofiber mesh to slow the DNA perforation speed. Compared to different alkali metal solutions with the same concentration, LiCl can extend the dwell time to 20 ms, five times longer than NaCl and KCl...
March 2, 2019: European Biophysics Journal: EBJ
Nadica Ivošević DeNardis, Jadranka Pečar Ilić, Ivica Ružić, Nives Novosel, Tea Mišić Radić, Andreas Weber, Damir Kasum, Zuzana Pavlinska, Ria Katalin Balogh, Bálint Hajdu, Alžbeta Marček Chorvátová, Béla Gyurcsik
We examined the response of algal cells to laboratory-induced cadmium stress in terms of physiological activity, autonomous features (motility and fluorescence), adhesion dynamics, nanomechanical properties, and protein expression by employing a multimethod approach. We develop a methodology based on the generalized mathematical model to predict free cadmium concentrations in culture. We used algal cells of Dunaliella tertiolecta, which are widespread in marine and freshwater systems, as a model organism. Cell adaptation to cadmium stress is manifested through cell shape deterioration, slower motility, and an increase of physiological activity...
February 26, 2019: European Biophysics Journal: EBJ
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