The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties.
ani M Abstract Mutations in the gelsolin protein are responsible for a rare conformational disease known as AGel amyloidosis. Four of these mutations are hosted by the second domain of the protein (G2): D187N/Y, G167R and N184K. The impact of the latter has been so far evaluated only by studies on the isolated G2. Here we report the characterization of full-length gelsolin carrying the N184K mutation and compare the findings with those obtained on the wild type and the other variants. The crystallographic structure of the N184K variant in the Ca2+-free conformation shows remarkable similarities with the wild type ...
Source: European Biophysics Journal : EBJ - November 13, 2019 Category: Physics Authors: de Rosa M, Barbiroli A, Bonì F, Scalone E, Mattioni D, Vanoni MA, Patrone M, Bollati M, Mastrangelo E, Giorgino T, Milani M Tags: Eur Biophys J Source Type: research

Distance measurements in the F0F1-ATP synthase from E. coli using smFRET and PELDOR spectroscopy.
k S Abstract Fluorescence resonance energy transfer in single enzyme molecules (smFRET, single-molecule measurement) allows the measurement of multicomponent distance distributions in complex biomolecules similar to pulsed electron-electron double resonance (PELDOR, ensemble measurement). Both methods use reporter groups: FRET exploits the distance dependence of the electric interaction between electronic transition dipole moments of the attached fluorophores, whereas PELDOR spectroscopy uses the distance dependence of the interaction between the magnetic dipole moments of attached spin labels. Such labels can be ...
Source: European Biophysics Journal : EBJ - November 8, 2019 Category: Physics Authors: Burger M, Rein S, Weber S, Gräber P, Kacprzak S Tags: Eur Biophys J Source Type: research

Thermodynamics of DNA: heat capacity changes on duplex unfolding.
Abstract The heat capacity change, ΔCp, accompanying the folding/unfolding of macromolecules reflects their changing state of hydration. Thermal denaturation of the DNA duplex is characterized by an increase in ΔCp but of much lower magnitude than observed for proteins. To understand this difference, the changes in solvent accessible surface area (ΔASA) have been determined for unfolding the B-form DNA duplex into disordered single strands. These showed that the polar component represents ~ 55% of the total increase in ASA, in contrast to globular proteins of similar molec...
Source: European Biophysics Journal : EBJ - November 5, 2019 Category: Physics Authors: Dragan A, Privalov P, Crane-Robinson C Tags: Eur Biophys J Source Type: research

Experimental determination of second virial coefficients by small-angle X-ray scattering: a problem revisited.
Abstract This investigation examines the validity of employing single-solute theory to interpret SAXS measurements on buffered protein solutions-the current practice despite the necessity to regard the buffer components as additional non-scattering solutes rather than as part of the solvent. The present study of bovine serum albumin in phosphate-buffered saline supplemented with 20-100 g/L sucrose as small cosolute has certainly verified the prediction that the experimentally obtained second virial coefficient should contain protein-cosolute contributions. Nevertheless, the second virial coefficient determine...
Source: European Biophysics Journal : EBJ - October 31, 2019 Category: Physics Authors: Mrozowich T, Winzor DJ, Scott DJ, Patel TR Tags: Eur Biophys J Source Type: research

Study of the complex coacervation mechanism between ovalbumin and the strong polyanion PSSNa: influence of temperature and pH.
Abstract We studied the complex between ovalbumin and long flexible poly-(sodium 4-styrene sulfonate) as a function of pH and temperature. We used various techniques [turbidimetry, conductometry, dynamic light scattering, viscosimetry, and ultra-small-angle light scattering (USALS)] to fully characterize the coacervate complex. Different phases of complexation versus temperature were determined by turbidimetric analysis (pHc, pHϕ1, and pHϕ2). The optimal protein/polyelectrolyte interaction occurred at pHopt 4. An increase in temperature made the hydrophobic interactions more favorable in the case of the soluble ...
Source: European Biophysics Journal : EBJ - October 26, 2019 Category: Physics Authors: Feddaoui W, Aschi A, Bey H, Othman T Tags: Eur Biophys J Source Type: research

Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations.
Abstract Aggregation of amyloid-[Formula: see text] (Aβ) peptides, cleaved from the amyloid precursor protein, is known as a precursor of the Alzheimer's disease (AD). It is also known that Alzheimer's disease is characterized by a substantial decrease of the amount of polyunsaturated lipids in the neuronal membranes of the frontal gray matter. To get insight into possible interconnection of these phenomena, we have carried out molecular dynamics simulations of two fragments of A[Formula: see text] peptide, A[Formula: see text][Formula: see text] and A[Formula: see text][Formula: see text], in four different ...
Source: European Biophysics Journal : EBJ - October 26, 2019 Category: Physics Authors: Ntarakas N, Ermilova I, Lyubartsev AP Tags: Eur Biophys J Source Type: research

Electrostatic interactions of alkaline earth cations with 1,2-dimyristoyl-sn-glycero-3-phosphatidic acid (DMPA) model membranes at neutral and acidic pH.
Abstract The binding of alkaline earth cations Mg2+, Ca2+, and Sr2+ (M2+) to unilamellar 1,2-dimyristoyl-sn-glycero-3-phosphatidic acid (DMPA) vesicles was analysed by pH potentiometry, differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC) and FT-IR spectroscopy. The binding of alkaline earth cations induces deprotonation of the DMPA headgroup even at very low concentration of divalent cations (~ 100 µM). The amount of deprotonated DMPA was measured by pH potentiometry as a function of divalent cation concentration. The thermotropic phase behaviour of DMPA:M2+ complexes ...
Source: European Biophysics Journal : EBJ - October 26, 2019 Category: Physics Authors: Garidel P, Blume A Tags: Eur Biophys J Source Type: research

Denaturation studies of Clarias gariepinus glutathione transferase in dilute and crowded solutions.
Abstract It is important to understand the effect of crowding conditions on the native structure and functional state of enzymes. Equilibrium denaturation studies of Clarius gariepinus GST (CgGST) by guanidine hydrochloride (GdHCl) under dilute conditions and in separate solutions of 0-100 g dm-3 Ficoll 70, polyethylene glycol 6000 (PEG 6000) and equal w/v mixtures of the two polymers at 25 °C and pH 7.4 were studied fluorometrically. The data were analyzed based on a two-state model assuming the native protein dimer separates into two monomers and then unfolds. The standard free energy of unfol...
Source: European Biophysics Journal : EBJ - October 25, 2019 Category: Physics Authors: Ogunmoyole T, Fodeke AA, Adewale IO Tags: Eur Biophys J Source Type: research

Investigation of spectral and kinetic properties of polymer films based on some analogs of bacteriorhodopsin.
Abstract We investigated the characteristics of modified forms of bacteriorhodopsin in which the native retinal chromophore is replaced by a chemical analog ("bacteriorhodopsin analogs"), embedded in a polymer film. We found they displayed differential absorption spectra and kinetic curves for the most long-lived intermediates of the BR photocycle. We also studied the influence of chemical reagents on the functioning of bacteriorhodopsin analogs in polymeric films. We found that the immobilization of BR analogs in polymer leads, as in the case of native BR, to a slowing down of their photocycles. Kinetic...
Source: European Biophysics Journal : EBJ - October 23, 2019 Category: Physics Authors: Druzhko AB, Pirutin SK Tags: Eur Biophys J Source Type: research

A statistical model for activation of Factor C by binding to LPS aggregates.
Abstract Published data on Factor C activity at various LPS and Lipid A concentrations (Nakamura et al. in Eur J Biochem 176:89, 1988; Kobayashi et al. in J Biol Chem 37:25987, 2014) were rearranged to show that Factor C exhibited its maximum activity at a specific concentration of LPS. A statistical model was proposed for examining whether a single LPS molecule binding activates Factor C (monomeric activation) or dimerization of Factor C is necessary for the activation (dimeric activation). In the monomeric activation model the plots of the relative activity of Factor C against the molar ratio of LPS to Factor C ...
Source: European Biophysics Journal : EBJ - October 19, 2019 Category: Physics Authors: Miyagawa Y, Kikuchi K, Tsuchiya M, Adachi S Tags: Eur Biophys J Source Type: research

Obtaining precise and accurate results by ITC.
Abstract Acquisition of precise and accurate results by isothermal titration calorimetry (ITC) can be achieved through thoughtful experimental design and modeling and careful experimental operations. Large reported errors in ITC results in determinations of stoichiometries, equilibrium constants and enthalpy changes for ligand binding to proteins are the consequence of poor experiment design, failure to properly calibrate and test instruments and protocols, lack of controls, errors in solution preparation, and incorrect data analyses. Analysis of a recent report that claimed to have determined the "repeatabil...
Source: European Biophysics Journal : EBJ - September 25, 2019 Category: Physics Authors: Hansen LD, Quinn C Tags: Eur Biophys J Source Type: research

Effects of electrically-induced constant tension on giant unilamellar vesicles using irreversible electroporation.
Abstract Stretching in membranes of cells and vesicles plays important roles in various physiological and physicochemical phenomena. Irreversible electroporation (IRE) is the irreversible permeabilization of the membrane through the application of a series of electrical field pulses of micro- to millisecond duration. IRE induces lateral tension due to stretching in the membranes of giant unilamellar vesicles (GUVs). However, the effects of electrically induced (i.e., IRE) constant tension in the membranes of GUVs have not been investigated yet in detail. To explore the effects of electrically induced tension on GU...
Source: European Biophysics Journal : EBJ - September 24, 2019 Category: Physics Authors: Karal MAS, Ahamed MK, Rahman M, Ahmed M, Shakil MM, Siddique-E-Rabbani K Tags: Eur Biophys J Source Type: research

Effects of bovine serum albumin (BSA) on the excited-state properties of meso-tetrakis(sulfonatophenyl) porphyrin (TPPS4).
ssevitch IE Abstract To infer changes in the photophysical properties of porphyrins due to complexation with albumin, a combination of Z-scan and conventional spectroscopic techniques was employed. We measured the characteristics of excited states of meso-tetrakis(sulfonatophenyl) porphyrin bound to bovine serum albumin and observed that the binding reduces the intersystem crossing quantum yield and increases the internal conversion one. A reverse saturable absorption process was observed in the nanosecond timescale. These results are important for prediction of the efficiency of this complex in medical and optica...
Source: European Biophysics Journal : EBJ - September 23, 2019 Category: Physics Authors: Gonçalves PJ, Bezerra FC, Almeida LM, Alonso L, Souza GRL, Alonso A, Zílio SC, Borissevitch IE Tags: Eur Biophys J Source Type: research

A new six-electrode electrical impedance technique for probing deep organs in the human body.
Abstract Electrical impedance measurements of biological tissue have many potential applications and tetrapolar impedance measurement (TPIM) with four electrodes is traditionally used which eliminates high skin contact impedance. A linear array of four electrodes for TPIM on the horizontal plane of a cylindrical volume conductor of diameter D, where the length of the array is πD/2 with potential electrodes near the centre of the array, will give a high sensitivity near the surface which reduces rapidly with depth. A recently proposed six-electrode variation of TPIM uses an additional pair of potential electrode...
Source: European Biophysics Journal : EBJ - September 16, 2019 Category: Physics Authors: Roy SK, Karal MAS, Kadir MA, Rabbani KS Tags: Eur Biophys J Source Type: research

Insights into conformation and membrane interactions of the acyclic and dicarba-bridged brevinin-1BYa antimicrobial peptides.
Abstract Brevinin-1BYa is a 24-amino acid residue host-defense peptide, first isolated from skin secretions of the foothill yellow-legged frog Rana boylii. The peptide is of interest, as it shows broad-spectrum antimicrobial activity, and is particularly effective against opportunistic yeast pathogens. Its potential for clinical use, however, is hindered by its latent haemolytic activity. The structures of two analogues, the less haemolytic [C18S,C24S]brevinin-1BYa and the more potent cis-dicarba-brevinin-1BYa, were investigated in various solution and membrane-mimicking environments by [Formula: see text] spectro...
Source: European Biophysics Journal : EBJ - September 12, 2019 Category: Physics Authors: Timmons PB, O'Flynn D, Conlon JM, Hewage CM Tags: Eur Biophys J Source Type: research

On the motion of magnetotactic bacteria: theoretical predictions and experimental observations.
Abstract The movement of magnetotactic bacteria is done in a viscous media in the low Reynolds number regime. In the present research, the simple model for magnetotactic bacteria motion, proposed by Nogueira and Lins de Barros (Eur Biophys J 24:13-21, 1995), was used to numerically simulate their trajectory. The model was done considering a spherical bacterium with a single flagellum and a magnetic moment positioned in the sphere center and parallel to the flagella. The numerical solution shows that the trajectory is a cylindrical helix and that the body Euler angles have linear dependencies on time. Using that in...
Source: European Biophysics Journal : EBJ - September 11, 2019 Category: Physics Authors: Acosta-Avalos D, Rodrigues E Tags: Eur Biophys J Source Type: research

Phenotypic, structural, and ultrastructural analysis of triple-negative breast cancer cell lines and breast cancer stem cell subpopulation.
Abstract Triple negative breast cancer (TNBC) is a highly heterogeneous disease, which influences the therapeutic response and makes difficult the discovery of effective targets. This heterogeneity is attributed to the presence of breast cancer stem cells (BCSCs), which determines resistance to chemotherapy and subsequently disease recurrence and metastasis. In this context, this work aimed to evaluate the morphological and phenotypic cellular heterogeneity of two TNBC cell lines cultured in monolayer and tumorsphere (TS) models by fluorescence and electron microscopy and flow cytometry. The BT-549 and Hs 578T ana...
Source: European Biophysics Journal : EBJ - September 4, 2019 Category: Physics Authors: Moreira MP, Brayner FA, Alves LC, Cassali GD, Silva LM Tags: Eur Biophys J Source Type: research

Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions.
Abstract Cells are crowded with various macromolecules and metabolites, which affect biochemical reactions in many ways, from the diffusion of substrates to catalytic activities of enzymes. We herein investigated the proteolytic activity of the human immunodeficiency virus type 1 protease (HIV-1 PR) under non-crowded and crowded conditions. The latter environment was mimicked with various (poly)ethylene glycol molecules as crowding agents. We found that these crowding agents affect the kinetic parameters of the HIV-1 PR catalyzed reaction by increasing the Michaelis-Menten constant and decreasing the maximum veloc...
Source: European Biophysics Journal : EBJ - August 28, 2019 Category: Physics Authors: Maximova K, Wojtczak J, Trylska J Tags: Eur Biophys J Source Type: research

Impact of semen-derived amyloid (SEVI) on sperm viability and motility: its implication in male reproductive fitness.
Abstract Human semen contains a large number of macromolecules, including proteins/enzymes and carbohydrates, regulating and protecting sperm cells. Proteomic analysis of human seminal fluid led to the discovery of semen amyloids derived from short peptide fragments of the proteins prostatic acid phosphatase (PAP) and semenogelin (SG) which are known to play a crucial role in enhancing HIV infection. However, the relevance of their existence in human semen and role in maintaining sperm behavior remains unclear. Distinct physiological, biochemical, and biophysical attributes might cause these amyloids to influence ...
Source: European Biophysics Journal : EBJ - August 7, 2019 Category: Physics Authors: Kumar V, Kumar PG, Yadav JK Tags: Eur Biophys J Source Type: research

Liposome production and concurrent loading of drug simulants by microfluidic hydrodynamic focusing.
In this study, nanoscale liposomes are fabricated using the microfluidic hydrodynamic focusing (MHF) approach, and the effects of flow rate ratio (FRR) on liposome size and drug loading efficiency are studied. Fluorescein isothiocyanate modified dextran is used as a hydrophilic drug simulant and Nile red is used as a hydrophobic drug simulant. The experiment results show that hydrophilic drug simulant loading efficiency increases as FRR increases and eventually plateaues at around 90% loading efficiency. The hydrophobic drug simulant loading efficiency and FRR have a positive linear correlation when FRR varies from 10 to 5...
Source: European Biophysics Journal : EBJ - July 20, 2019 Category: Physics Authors: Lin WS, Malmstadt N Tags: Eur Biophys J Source Type: research

Unveiling the binding and orientation of the antimicrobial peptide Plantaricin 149 in zwitterionic and negatively charged membranes.
In this study, the interactions of Pln149 with model membranes composed of zwitterionic and/or anionic phospholipids were investigated using a range of biophysical techniques, including isothermal titration calorimetry, surface tension measurements, synchrotron radiation circular dichroism spectroscopy, oriented circular dichroism spectroscopy, and optical microscopy, to elucidate these peptides' mode of interactions and provide insight into their functional roles. In anionic model membranes, the binding of Pln149 to lipid bilayers is an endothermic process and induces a helical secondary structure in the peptide. The heli...
Source: European Biophysics Journal : EBJ - July 19, 2019 Category: Physics Authors: Kumagai PS, Sousa VK, Donato M, Itri R, Beltramini LM, Araujo APU, Buerck J, Wallace BA, Lopes JLS Tags: Eur Biophys J Source Type: research

Biophysical characterization and molecular phylogeny of human KIN protein.
Seixas FAV Abstract The DNA/RNA-binding KIN protein was discovered in 1989, and since then, it has been found to participate in several processes, e.g., as a transcription factor in bacteria, yeasts, and plants, in immunoglobulin isotype switching, and in the repair and resolution of double-strand breaks caused by ionizing radiation. However, the complete three-dimensional structure and biophysical properties of KIN remain important information for clarifying its function and to help elucidate mechanisms associated with it not yet completely understood. The present study provides data on phylogenetic analyses of ...
Source: European Biophysics Journal : EBJ - July 15, 2019 Category: Physics Authors: Pattaro Júnior JR, Caruso ÍP, de Lima Neto QA, Duarte Junior FF, Dos Santos Rando F, Gerhardt ECM, Fernandez MA, Seixas FAV Tags: Eur Biophys J Source Type: research

57Fe enrichment in mice for β-thalassaemia studies via Mössbauer spectroscopy of blood samples.
57Fe enrichment in mice for β-thalassaemia studies via Mössbauer spectroscopy of blood samples. Eur Biophys J. 2019 Jul 13;: Authors: Charitou G, Tsertos C, Parpottas Y, Kleanthous M, Lederer CW, Phylactides M Abstract In this work, wild-type and heterozygous β-thalassaemic mice were enriched with 57Fe via gastrointestinal absorption to characterize in greater detail the iron complexes then identifiable via Mössbauer spectroscopy. The 57Fe enrichment method was validated and Mössbauer spectra were obtained at 80 K from blood samples from wild-type and β-thalassaemic ...
Source: European Biophysics Journal : EBJ - July 13, 2019 Category: Physics Authors: Charitou G, Tsertos C, Parpottas Y, Kleanthous M, Lederer CW, Phylactides M Tags: Eur Biophys J Source Type: research

Growth of a gas bubble in a perfused tissue in an unsteady pressure field with source or sink.
Abstract In the context of decompression sickness, this paper presents analytical formulae and explanations for growth of a gas bubble in blood and other tissues in an unsteady diffusion field with a source or a sink. The formulae are valid for variable (through decompression) and constant (concerning diving stops/at sea level) ambient pressure. Under a linear decompression regime for ambient pressure, the gas bubble growth is proportional to ascent rate, tissue diffusivity and initial tissue tension and inversely proportional to surface tension, initial ambient pressure and the strength of the source/sink paramet...
Source: European Biophysics Journal : EBJ - July 9, 2019 Category: Physics Authors: Mohamed KG, Mohammadein SA Tags: Eur Biophys J Source Type: research

Are cell membrane nanotubes the ancestors of the nervous system?
Abstract Cell membrane nanotubes, variously referred to as tunneling nanotubes and cytonemes, are currently the focus of much interest. They are of ancient origin, as indicated by their opportunistic use for cell invasion by pathogens, including bacteria and virus, and by their employment in bacterial networking. They play a significant role in cancer invasion and in the explanation of glioblastoma resistance to treatment. Their structure and properties have been investigated with optical tweezers. They have been detected in vivo. Their role in the immune system was early verified. Very recently, it was shown that...
Source: European Biophysics Journal : EBJ - July 6, 2019 Category: Physics Authors: Nussenzveig HM Tags: Eur Biophys J Source Type: research

Viscoelasticity variation in a biofilm-mediated Bacillus subtilis suspension induced by adding polyethylene glycol.
Abstract Recent experiments show that synthetic polymers can influence the degree of microbial aggregation and the rheological properties of bacterial suspensions, the study of which can help us control biofilm formation. In this article, we add polyethylene glycol (PEG) with various molecular weights and concentrations into two types Bacillus subtilis cell cultures, Luria Broth (LB) and Minimal Salts glutamate glycerol (MSgg), respectively. We first observe cell clusters in cell suspensions with various concentrations of PEG, and measure cluster size in both static and dynamic fluid environments. We find that cel...
Source: European Biophysics Journal : EBJ - July 6, 2019 Category: Physics Authors: Wang X, Shen X, Wang Z, Kong Y Tags: Eur Biophys J Source Type: research

A model for the chemomechanical coupling of the mammalian cytoplasmic dynein molecular motor.
Abstract Available single-molecule data have shown that some mammalian cytoplasmic dynein dimers move on microtubules with a constant step size of about 8.2 nm. Here, a model is presented for the chemomechanical coupling of these mammalian cytoplasmic dynein dimers. In contrast to the previous models, a peculiar feature of the current model is that the rate constants of ATPase activity are independent of the external force. Based on this model, analytical studies of the motor dynamics are presented. With only four adjustable parameters, the theoretical results reproduce quantitatively diverse available single...
Source: European Biophysics Journal : EBJ - July 5, 2019 Category: Physics Authors: Xie P Tags: Eur Biophys J Source Type: research

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes.
rti S Abstract According to the generalized conformational selection model, ligand binding involves the co-existence of at least two conformers with different ligand-affinities in a dynamical equilibrium. Conformational transitions between them should be guaranteed by intramolecular vibrational dynamics associated to each conformation. These motions are, therefore, related to the biological function of a protein. Positions whose mutations are found to alter these vibrations the most can be defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. In a ...
Source: European Biophysics Journal : EBJ - July 4, 2019 Category: Physics Authors: Saldaño TE, Tosatto SCE, Parisi G, Fernandez-Alberti S Tags: Eur Biophys J Source Type: research

Regional Biophysics Conference: RBC2018.
PMID: 31267213 [PubMed - as supplied by publisher] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - July 2, 2019 Category: Physics Authors: Arsov Z, Koklič T Tags: Eur Biophys J Source Type: research

JOINT 12th EBSA congress and 10th ICBP - IUPAP congress, July 20-24, 2019, Madrid, Spain - Abstracts.
Authors: PMID: 31257549 [PubMed] (Source: European Biophysics Journal : EBJ)
Source: European Biophysics Journal : EBJ - July 1, 2019 Category: Physics Tags: Eur Biophys J Source Type: research

Synchrotron radiation-based FTIR spectro-microscopy of the brainstem of the hSOD1 G93A rat model of amyotrophic lateral sclerosis.
Abstract Pathological mechanisms in amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease, are still poorly understood. One subset of familial ALS cases is caused by mutations in the metallo-enzyme copper-zinc superoxide dismutase (SOD1), increasing the susceptibility of the SOD1 protein to form insoluble intracellular aggregates. Here, we employed synchrotron radiation-based Fourier transform infrared spectroscopy and microscopy to investigate brainstem cross-sections from the transgenic hSOD1 G93A rat model of ALS that overexpresses human-mutated SOD1. We compared the biomacromolecular organic c...
Source: European Biophysics Journal : EBJ - June 26, 2019 Category: Physics Authors: Andjus P, Stamenković S, Dučić T Tags: Eur Biophys J Source Type: research

Stochastic and deterministic approaches to modelling calcium release in cardiac myocytes at different spatial arrangements of ryanodine receptors.
ute;ková A Abstract Calcium release sites (CRSs) play a key role in excitation-contraction coupling of cardiac myocytes. Recent studies based on electron tomography and super-resolution imaging revealed that CRSs are not completely filled with ryanodine receptors (RyRs) and that the spatial arrangement of RyRs is neither uniform nor static. In this work, we studied the effect of spatial arrangement of RyRs on RyR activation using simulations based on Monte Carlo (MC) and mean-field (MF) approaches. Both approaches showed that activation of RyRs is sensitive to the arrangement of RyRs in the CRS. However, th...
Source: European Biophysics Journal : EBJ - June 24, 2019 Category: Physics Authors: Iaparov BI, Moskvin AS, Zahradník I, Zahradníková A Tags: Eur Biophys J Source Type: research

Study of the mechanical properties of fresh and cryopreserved individual human oocytes.
Abstract In assisted reproduction technologies, the cryopreservation of oocytes is a common procedure used to circumvent female infertility. However, some morphological and functional alterations of oocytes have been observed depending on the protocol applied. In this work, the mechanical response of individual human oocytes before and after a freeze-thawing procedure was characterised. Oocytes, immediately after retrieval, were morphologically evaluated by bright-field optical microscopy and their elasticity measured by indentation measurements using atomic force microscopy. Oocytes were then frozen according to ...
Source: European Biophysics Journal : EBJ - June 22, 2019 Category: Physics Authors: Giolo E, Martinelli M, Luppi S, Romano F, Ricci G, Lazzarino M, Andolfi L Tags: Eur Biophys J Source Type: research

Inhibition of influenza virus activity by the bovine seminal plasma protein PDC-109.
;ller P Abstract A number of viruses causing sexually transmissible diseases are transmitted via mammalian seminal plasma. Several components of seminal plasma have been shown to influence those viruses and their physiological impact. To unravel whether components of seminal plasma could affect viruses transmitted via other pathways, it was investigated here whether the bovine seminal plasma protein PDC-109, belonging to the Fn-type 2 protein family, influences the activity of influenza A viruses, used as a model for enveloped viruses. We found that PDC-109 inhibits the fusion of influenza virus with human erythro...
Source: European Biophysics Journal : EBJ - June 20, 2019 Category: Physics Authors: Welke RW, Haralampiev I, Schröter F, Braun BC, Herrmann A, Sieben C, Müller P Tags: Eur Biophys J Source Type: research

Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy.
In this study we examined microenvironment of Trp residues in "dry" sets of nonhomologous proteins that belong to four structural classes, as well as in a "wet" set. In silico experiments showed that residues of Trp demonstrate higher surface accessibility in proteins of "alpha/beta" class where they are rarely included in beta strands. However, this feature has not caused "red" shift in fluorescence spectra in "alpha/beta" proteins in vitro, since there are several factors that should be combined together to cause it: high surface accessibility and high hydrophilicity of t...
Source: European Biophysics Journal : EBJ - June 15, 2019 Category: Physics Authors: Khrustalev VV, Poboinev VV, Stojarov AN, Khrustaleva TA Tags: Eur Biophys J Source Type: research

U-turn trajectories of magnetotactic cocci allow the study of the correlation between their magnetic moment, volume and velocity.
OC, Abreu F Abstract Magnetotactic bacteria are microorganisms that present intracellular chains of magnetic nanoparticles, the magnetosome chain. A challenge in the study of magnetotactic bacteria is the measurement of the magnetic moment associated with the magnetosome chain. Several techniques have been used to estimate the average magnetic moment of a population of magnetotactic bacteria, and others permit the measurement of the magnetic moment of individual bacteria. The U-turn technique allows the measurement of the individual magnetic moment and other parameters associated with the movement and magnetotaxis...
Source: European Biophysics Journal : EBJ - June 15, 2019 Category: Physics Authors: Acosta-Avalos D, de Figueiredo AC, Conceição CP, da Silva JJP, Aguiar KJMSP, de Lima Medeiros M, do Nascimento M, de Melo RD, Sousa SMM, de Barros HL, Alves OC, Abreu F Tags: Eur Biophys J Source Type: research

Biophysical modeling of wave propagation phenomena: experimental determination of pulse wave velocity in viscous fluid-filled elastic tubes in a gravitation field.
Abstract Biophysical understanding of arterial hemodynamics plays an important role in proper medical diagnosis and investigation of cardiovascular disease pathogens. One of the major cardiovascular parameters is pulse wave velocity (PWV), which depends on the mechanical properties of the arterial wall. The PWV contains information on the condition of the cardiovascular system as well as its physiological age. In humans and most animals, blood flow through the blood vessels is affected by several internal and external forces. The most influencing external force on blood flow is gravity. In the upright position of ...
Source: European Biophysics Journal : EBJ - June 14, 2019 Category: Physics Authors: Žikić D, Stojadinović B, Nestorović Z Tags: Eur Biophys J Source Type: research

Solution structure and backbone dynamics for S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis.
Abstract The pro-drug pyrazinamide is hydrolyzed to pyrazinoic acid (POA) in its use for the treatment of tuberculosis. As a molecule with bactericidal activity, POA binds to the C-terminal S1 domain of ribosomal protein S1 from Mycobacterium tuberculosis (MtRpsACTD_S1) to inhibit trans-translation. Trans-translation is a critical component of protein synthesis quality control, and is mediated by transfer-messenger RNA. Here, we have determined the solution structure of MtRpsACTD_S1(280-368), and analyzed its structural dynamics by NMR spectroscopy. The solution structure of MtRpsACTD_S1(280-368) mainly consists o...
Source: European Biophysics Journal : EBJ - June 5, 2019 Category: Physics Authors: Huang B, Fan S, Liu Y, Zhao Y, Lin D, Liao X Tags: Eur Biophys J Source Type: research

An estimate to the first approximation of microtubule rupture force.
Abstract Microtubule mechanical properties are essential for understanding basic cellular processes, including cell motility and division, but the forces that result in microtubule rupture or breakage have not yet been measured directly. These forces are essential to understand the mechanical properties of the cytoskeleton and responses by cells to both normal conditions and stress caused by injury or disease. Here we estimate the force required to rupture a microtubule by analyzing kinesin-14 Ncd motor-induced microtubule breakage in ensemble motility assays. We model the breakage events as caused by Ncd motors p...
Source: European Biophysics Journal : EBJ - May 27, 2019 Category: Physics Authors: Endow SA, Marszalek PE Tags: Eur Biophys J Source Type: research

Application of small-angle neutron diffraction to the localization of general anesthetics in model membranes.
rka N Abstract We set out to explore the applicability of small-angle neutron diffraction (SAND) to the localization of biomembrane components by studying the general anesthetic n-decane in a model lipid bilayer system composed of dioleoyl-phosphocholine (DOPC). Samples in the form of planar membrane multilayers were hydrated by varied mixtures of deuterated and protonated water, and examined by the means of SAND. Neutron scattering length density (NSLD) profiles of the system were then reconstructed from the experimental data. We exploited the significantly different neutron scattering properties of hydrogen and ...
Source: European Biophysics Journal : EBJ - May 14, 2019 Category: Physics Authors: Hrubovčák P, Kondela T, Ermakova E, Kučerka N Tags: Eur Biophys J Source Type: research

An insight into pH-induced changes in FAD conformational structure by means of time-resolved fluorescence and circular dichroism.
Abstract Optical properties of flavin adenine dinucleotide (FAD) moiety are widely used nowadays for biotechnological applications. Given the fundamental role played by FAD, additional structural information about this enzymatic cofactor can be extremely useful in order to obtain a greater insight into its functional role in proteins. For this purpose, we have investigated FAD behaviour in aqueous solutions at different pH values by a novel approach based on the combined use of time-resolved fluorescence and circular dichroism spectroscopies. The results showed that pH strongly affects time-resolved fluorescence e...
Source: European Biophysics Journal : EBJ - May 4, 2019 Category: Physics Authors: Esposito R, Delfino I, Portaccio M, Iannuzzi C, Lepore M Tags: Eur Biophys J Source Type: research

Moving average filtering with deconvolution (MAD) for hidden Markov model with filtering and correlated noise.
Abstract Ion channel data recorded using the patch clamp technique are low-pass filtered to remove high-frequency noise. Almanjahie et al. (Eur Biophys J 44:545-556, 2015) based statistical analysis of such data on a hidden Markov model (HMM) with a moving average adjustment for the filter but without correlated noise, and used the EM algorithm for parameter estimation. In this paper, we extend their model to include correlated noise, using signal processing methods and deconvolution to pre-whiten the noise. The resulting data can be modelled as a standard HMM and parameter estimates are again obtained using the E...
Source: European Biophysics Journal : EBJ - April 27, 2019 Category: Physics Authors: Almanjahie IM, Khan RN, Milne RK, Nomura T, Martinac B Tags: Eur Biophys J Source Type: research

Possible sensor applications of selected DNA-surfactant complexes.
Abstract 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). Sign...
Source: European Biophysics Journal : EBJ - April 19, 2019 Category: Physics Authors: Nowak E, Wisła-Świder A, Khachatryan G, Fiedorowicz M, Danel K Tags: Eur Biophys J Source Type: research

Fluorescence-detected linear dichroism imaging in a re-scan confocal microscope equipped with differential polarization attachment.
nyi L Abstract 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. Differential polarization (DP) attachments, using hig...
Source: European Biophysics Journal : EBJ - April 13, 2019 Category: Physics Authors: Steinbach G, Nagy D, Sipka G, Manders E, Garab G, Zimányi L Tags: Eur Biophys J Source Type: research

From biophysics to 'omics and systems biology.
Abstract 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-li...
Source: European Biophysics Journal : EBJ - April 9, 2019 Category: Physics Authors: Djordjevic M, Rodic A, Graovac S Tags: Eur Biophys J Source Type: research

Thermodynamics of protein folding: methodology, data analysis and interpretation of data.
Abstract 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. In this manuscript, the principles and methodol...
Source: European Biophysics Journal : EBJ - April 3, 2019 Category: Physics Authors: Shirdel SA, Khalifeh K Tags: Eur Biophys J Source Type: research

Biophysical characterization of heme binding to the intrinsically disordered region of Bach1.
Abstract 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...
Source: European Biophysics Journal : EBJ - April 1, 2019 Category: Physics Authors: Segawa K, Watanabe-Matsui M, Tsuda K, Matsui T, Shirouzu M, Igarashi K, Murayama K Tags: Eur Biophys J Source Type: research

Equilibrium partially folded states of B. licheniformis[Formula: see text]-lactamase.
ra MR Abstract [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, acti...
Source: European Biophysics Journal : EBJ - March 30, 2019 Category: Physics Authors: Risso VA, Ermácora MR Tags: Eur Biophys J Source Type: research

Polymer translocation through a hairy channel mimicking the inner plug of a nuclear pore complex.
Abstract 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. Numer...
Source: European Biophysics Journal : EBJ - March 29, 2019 Category: Physics Authors: Zhang C, Cheng Z, Lin X, Chu W Tags: Eur Biophys J Source Type: research

β-Lactoglobulin associative interactions: a small-angle scattering study.
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. Using small-angle X-ray and neutron scattering methods (SANS and SAXS), it was shown that β-lg forms dimeric structures in 50 mM HEPES buffer under various conditions of the medium. At pH 5.9, β-lg preserves its dimeric form in the high protein concentration range of 10-40 mg/mL. However, the conformation swelled with the addition of 50 mM NaCl in the syst...
Source: European Biophysics Journal : EBJ - March 28, 2019 Category: Physics Authors: Anghel L, Rogachev A, Kuklin A, Erhan RV Tags: Eur Biophys J Source Type: research