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European Biophysics Journal: EBJ

Carla Pallavicini, Alejandro Monastra, Nicolás González Bardeci, Diana Wetzler, Valeria Levi, Luciana Bruno
Microtubules are filamentous biopolymers involved in essential biological processes. They form key structures in eukaryotic cells, and thus it is very important to determine the mechanisms involved in the formation and maintenance of the microtubule network. Microtubule bucklings are transient and localized events commonly observed in living cells and characterized by a fast bending and its posterior relaxation. Active forces provided by molecular motors have been indicated as responsible for most of these rapid deformations...
April 19, 2017: European Biophysics Journal: EBJ
G Kopylova, S Nabiev, D Shchepkin, S Bershitsky
Carbonylation induced by hyperthyroidism suppresses force generation of skeletal myosin and sliding velocity of actin filaments in an in vitro motility assay. However, its effects on cardiac myosin at the molecular level have not been studied. Hyperthyroidism induces a change in expression of myosin heavy chains in ventricles, which may mask the effect of oxidation. In contrast to ventricular myosin, expression of myosin heavy chains in the atrium does not change upon hyperthyroidism and enables investigation of the effect of oxidation on cardiac myosin...
April 13, 2017: European Biophysics Journal: EBJ
Martin B Ulmschneider, Jakob P Ulmschneider, J Alfredo Freites, Gunnar von Heijne, Douglas J Tobias, Stephen H White
Hydrophobic amino acids are abundant in transmembrane (TM) helices of membrane proteins. Charged residues are sparse, apparently due to the unfavorable energetic cost of partitioning charges into nonpolar phases. Nevertheless, conserved arginine residues within TM helices regulate vital functions, such as ion channel voltage gating and integrin receptor inactivation. The energetic cost of arginine in various positions along hydrophobic helices has been controversial. Potential of mean force (PMF) calculations from atomistic molecular dynamics simulations predict very large energetic penalties, while in vitro experiments with Sec61 translocons indicate much smaller penalties, even for arginine in the center of hydrophobic TM helices...
April 13, 2017: European Biophysics Journal: EBJ
Akira Sato, Chiemi Ueda, Ryu Kimura, Chisato Kobayashi, Yoji Yamazaki, Keiichi Ebina
Modifications of low-density lipoprotein (LDL), such as oxidation and aggregation, and angiotensin (Ang) peptides are involved in the pathogenesis of atherosclerosis. Here, we investigated the relationship between one of the Ang peptides, AngII, and two LDL modifications, oxidation and aggregation. Using polyacrylamide gel electrophoresis and aggregation assays, we noted that AngII markedly induced the aggregation of LDL and oxidized LDL (Ox-LDL), and bound to both the aggregated and non-aggregated forms. In contrast, a peptide (AngIII) formed by deletion of N-terminal Asp of AngII induced the aggregation of Ox-LDL but not LDL...
April 11, 2017: European Biophysics Journal: EBJ
Robert W Janes
Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution...
April 3, 2017: European Biophysics Journal: EBJ
A Steuer, K Wende, P Babica, J F Kolb
Nanosecond pulsed electric fields (nsPEFs) applied to cells can induce different biological effects depending on pulse duration and field strength. One known process is the induction of apoptosis whereby nsPEFs are currently investigated as a novel cancer therapy. Another and probably related change is the breakdown of the cytoskeleton. We investigated the elasticity of rat liver epithelial cells WB-F344 in a monolayer using atomic force microscopy (AFM) with respect to the potential of cells to undergo malignant transformation or to develop a potential to metastasize...
April 1, 2017: European Biophysics Journal: EBJ
Maïwenn Beaugrand, Alexandre A Arnold, Steve Bourgault, Philip T F Williamson, Isabelle Marcotte
The hERG channel is a voltage-gated potassium channel found in cardiomyocytes that contributes to the repolarization of the cell membrane following the cardiac action potential, an important step in the regulation of the cardiac cycle. The lipids surrounding K(+) channels have been shown to play a key role in their regulation, with anionic lipids shown to alter gating properties. In this study, we investigate how anionic lipids interact with the pore helix of hERG and compare the results with those from Kv1...
March 17, 2017: European Biophysics Journal: EBJ
Patricia S Kumagai, Ricardo DeMarco, Jose L S Lopes
The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others...
March 3, 2017: European Biophysics Journal: EBJ
Ying Wang, Helene Schellenberg, Volker Walhorn, Katja Toensing, Dario Anselmetti
Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules...
March 1, 2017: European Biophysics Journal: EBJ
Yu Ishibashi, Shusuke Oura, Kazuo Umemura
We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH2 groups (CONH2-SWNT) exhibited very strong interactions between the CONH2-SWNT and DNA binding proteins. Instead, when these SWNT surfaces were wrapped with DNA molecules (thymine 30-mers), protein binding was a little decreased. Our results revealed that DNA wrapped PEG-SWNT was one of the most promising candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces...
February 15, 2017: European Biophysics Journal: EBJ
Zhicheng Li, Yang Li, Qiang Lei, Qing Zhao
Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage...
February 6, 2017: European Biophysics Journal: EBJ
Roger Duarte de Melo, Daniel Acosta-Avalos
Magnetotactic microorganisms are characterized by swimming in the direction of an applied magnetic field. In nature, two types of swimming polarity have been observed: north-seeking microorganisms that swim in the same direction as the magnetic field, and south-seeking microorganisms that swim in the opposite direction. The present work studies the reversal in the swimming polarity of the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis following an isolation process using high magnetic fields from magnets...
February 4, 2017: European Biophysics Journal: EBJ
Patrizia Iavicoli, François Rossi, Baptiste Lamarre, Angelo Bella, Maxim G Ryadnov, Luigi Calzolai
Peptide-lipid interactions support a variety of biological functions. Of particular interest are those that underpin fundamental mechanisms of innate immunity that are programmed in host defense or antimicrobial peptide sequences found virtually in all multicellular organisms. Here we synthetically modulate antimicrobial peptide-lipid interactions using an archetypal helical antimicrobial peptide and synthetic membranes mimicking bacterial and mammalian membranes in solution. We probe these interactions as a function of membrane-induced folding, membrane stability and peptide-lipid ratios using a correlative approach encompassing light scattering and spectroscopy measurements such as circular dichroism spectroscopy, fluorescence and nuclear magnetic resonance spectroscopy...
May 2017: European Biophysics Journal: EBJ
Anatoliy I Dragan, Christopher M Read, Colyn Crane-Robinson
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed...
May 2017: European Biophysics Journal: EBJ
Wallance Moreira Pazin, Danilo da Silva Olivier, Neus Vilanova, Ana Paula Ramos, Ilja Karina Voets, Ademilson Espencer Egea Soares, Amando Siuiti Ito
Green propolis, a mixture of beeswax and resinous compounds processed by Apis mellifera, displays several pharmacological properties. Artepillin C, the major compound in green propolis, consists of two prenylated groups bound to a phenyl group. Several studies have focused on the therapeutic effects of Artepillin C, but there is no evidence that it interacts with amphiphilic aggregates to mimic cell membranes. We have experimentally and computationally examined the interaction between Artepillin C and model membranes composed of dimyristoylphosphatidylcholine (DMPC) because phosphatidylcholine (PC) is one of the most abundant phospholipids in eukaryotic cell membranes...
May 2017: European Biophysics Journal: EBJ
Anna Mularski, Jonathan Wilksch, Eric Hanssen, Jian Li, Takehiro Tomita, Sacha James Pidot, Tim Stinear, Frances Separovic, Dick Strugnell
Atomic force microscopy measurements of capsule thickness revealed that that the wild-type Klebsiella pneumoniae AJ218 capsular polysaccharides were rearranged by exposure to colistin. The increase in capsule thickness measured near minimum inhibitory/bactericidal concentration (MIC/MBC) is consistent with the idea that colistin displaces the divalent cations that cross-bridge adjacent lipopolysaccharide (LPS) molecules through the capsule network. Cryo-electron microscopy demonstrated that the measured capsule thickness at near MIC/MBC of 1...
May 2017: European Biophysics Journal: EBJ
Annick Renevey, Sereina Riniker
Polytheonamide B (pTB), a highly cytotoxic peptide produced by a symbiotic bacterium of the marine sponge Theonella swinhoei, forms a transmembrane pore consisting of 49 residues. More than half of its residues are posttranslationally modified. Epimerizations result in alternating L- and D-amino acids that allow the peptide to adopt a [Formula: see text]-helical conformation. Unusually, the wide [Formula: see text]-helix of pTB is stable in a polar environment, which is in contrast to gramicidin A, an antibiotic with similar function and structure...
May 2017: European Biophysics Journal: EBJ
MohammadMahdi Sahebifard, Alireza Shahidi, Saeed Ziaei-Rad
In the current article, the dynamic evolution of two-phase vesicles is presented as an extension to a previous stationary model and based on an equilibrium of local forces. In the simplified model, ignoring the effects of membrane inertia, a dynamic equilibrium between the membrane bending potential and local fluid friction is considered in each phase. The equilibrium equations at the domain borders are completed by extended introduction of membrane section reactions. We show that in some cases, the results of stationary and evolutionary models are in agreement with each other and also with experimental observations, while in others the two models differ markedly...
May 2017: European Biophysics Journal: EBJ
Carmela Rianna, Manfred Radmacher
We used atomic force microscopy (AFM) technique to measure the viscoelastic response of cancer and normal thyroid cells on different stiffness polyacrylamide gels. After applying a step in contact we recorded the stress relaxation of cells in order to measure their viscous and elastic properties. With the help of an extended version of the Hertz model, we could quantify for the first time by AFM the elastic modulus and the dynamic viscosity of cells on substrates with different stiffnesses. We have cultured anaplastic carcinoma and normal thyroid cells on three different substrates: polyacrylamide gels with elastic modulus in a range of 3-5 and 30-40 kPa and "infinitely" stiff Petri dishes...
May 2017: European Biophysics Journal: EBJ
Dariusz Man, Ryszard Olchawa
The effect of the surface layer of model membranes on their physical properties was discussed in this paper. The research involved a physical ESR experiment with the use of spin probes and computer simulation based on the Monte Carlo technique. Liposomes formed during the process of sonication of lecithin were scanned in an ESR spectrometer. The membrane surface layer model, represented by the system of electric dipoles arranged in rectangular or hexagonal matrices, was studied. The final states of computer simulations were presented as textures...
May 2017: European Biophysics Journal: EBJ
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