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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...
October 17, 2016: 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...
October 15, 2016: European Biophysics Journal: EBJ
Apolinary Sobieszek
In early studies on smooth muscle, I described a crude myosin fraction (CMF) in which self-assembly of myosin filaments was observed. For the first time, the 14-nm periodicity stemming from regular arrangement of myosin heads on the filament surface was observed (Sobieszek in J Mol Biol 70:741-744, 1972). In this fraction, we also observed formation of long ribbon-shaped aggregates exhibiting a 5.6-nm periodicity, characteristic of tropomyosin (TM) paracrystals (Sobieszek and Small in Phil Trans R Soc Lond B 265:203-212, 1973)...
September 27, 2016: 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...
September 23, 2016: 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...
September 19, 2016: 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...
September 17, 2016: European Biophysics Journal: EBJ
Natalia A Koubassova, Sergey Y Bershitsky, Michael A Ferenczi, Theyencheri Narayanan, Andrey K Tsaturyan
Contraction of skeletal and cardiac muscle is controlled by Ca(2+) ions via regulatory proteins, troponin (Tn) and tropomyosin (Tpm) associated with the thin actin filaments in sarcomeres. In the absence of Ca(2+), Tn-C binds actin and shifts the Tpm strand to a position where it blocks myosin binding to actin, keeping muscle relaxed. According to the three-state model (McKillop and Geeves Biophys J 65:693-701, 1993), upon Ca(2+) binding to Tn, Tpm rotates about the filament axis to a 'closed state' where some myosin heads can bind actin...
September 17, 2016: European Biophysics Journal: EBJ
Anil A Sonkamble, Rahul P Sonsale, Mahesh S Kanshette, Komal B Kabara, Kunal H Wananje, Ashok C Kumbharkhane, Arvind V Sarode
Dielectric relaxation studies of vegetable oils are important for insights into their hydrogen bonding and intermolecular dynamics. The dielectric relaxation and thermo physical properties of triglycerides present in some vegetable oils have been measured over the frequency range of 10 MHz to 7 GHz in the temperature region 25 to 10 °C using a time-domain reflectometry approach. The frequency and temperature dependence of dielectric constants and dielectric loss factors were determined for coconut, peanut, soya bean, sunflower, palm, and olive oils...
September 7, 2016: European Biophysics Journal: EBJ
Konstantin S Usachev, Olga A Kolosova, Evelina A Klochkova, Aidar R Yulmetov, Albert V Aganov, Vladimir V Klochkov
Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16...
September 2, 2016: European Biophysics Journal: EBJ
Seifollah Jalili, Marzieh Saeedi
Despite available experimental results, the molecular mechanism of action of local anesthetics upon the nervous system and contribution of the cell membrane to the process are still controversial. In this work, molecular dynamics simulations were performed to investigate the effect of two clinically used local anesthetics, procaine and tetracaine, on the structure and dynamics of a fully hydrated dimyristoylphosphatidylcholine lipid bilayer. We focused on comparing the main effects of uncharged and charged drugs on various properties of the lipid membrane: mass density distribution, diffusion coefficient, order parameter, radial distribution function, hydrogen bonding, electrostatic potential, headgroup angle, and water dipole orientation...
August 24, 2016: European Biophysics Journal: EBJ
Eamonn F Healy, Luis Cervantes
Superoxide dismutase [Cu-Zn], or SOD1, is a homo-dimeric protein that functions as an antioxidant by scavenging for superoxides. A wide range of SOD1 variants are linked to inherited, or familial, amyotrophic lateral sclerosis, a progressive and fatal neurodegenerative disease. Aberrant SOD1 oligomerization has been strongly implicated in disease causation, even for sporadic ALS, or SALS, which accounts for ~90 % of ALS cases. Small heat shock proteins (sHSP) have been shown to protect against amyloid fibril formation in vitro, and the sHSP αB-crystallin suppresses in vitro aggregation of SOD1...
August 5, 2016: European Biophysics Journal: EBJ
Muhammad S Khan, Noura S Dosoky, Bakhrom K Berdiev, John D Williams
Black lipid membranes (BLMs) have been used for detecting single-channel activities of pore-forming peptides and ion channels. However, the short lifetimes and poor mechanical stability of suspended bilayers limit their applications in high throughput electrophysiological experiments. In this work, we present a synthetic solid-state nanopore functionalized with BLM fused with channel protein. A nanopore with diameter of ~180 nm was electrochemically fabricated in a thin silicon membrane. Folding and painting techniques were demonstrated for production of stable suspended BLMs followed by incorporation of transmembrane protein, ENaC...
August 1, 2016: European Biophysics Journal: EBJ
Thittaya Kunthic, Wahyu Surya, Boonhiang Promdonkoy, Jaume Torres, Panadda Boonserm
Bacillus thuringiensis vegetative insecticidal proteins like Vip3A have been used for crop protection and to delay resistance to existing insecticidal Cry toxins. However, little is known about Vip3A's behavior or its mechanism of action, and a structural model is required. Herein, in an effort to facilitate future crystallization and functional studies, we have used the orthogonal biophysical techniques of light scattering and sedimentation to analyze the aggregation behavior and stability of trypsin-activated Vip3A toxin in solution...
July 29, 2016: European Biophysics Journal: EBJ
André F Ferreira, Akhilesh Rai, Lino Ferreira, Pedro N Simões
The immobilization of gold nanoparticles (AuNPs) with antimicrobial peptides (AMPs) is a new and promising way to enhance both the activity and targeting capabilities of AMPs. However, a full understanding of the adsorption process underlying these materials is still lacking. Cecropin-melittin is a peptide with a broad antimicrobial activity while displaying low hemolytic properties, whose conjugation with AuNPs has not been studied before. In this context, we report the investigation of the adsorption process of the cecropin-melittin peptide, with (CM-SH) and without (CM) cysteine at its C-terminus, onto a gold surface based on all-atom MD simulations...
July 28, 2016: European Biophysics Journal: EBJ
Oscar Björnham, Magnus Andersson
Dynamic force spectroscopy (DFS) is an experimental technique that is commonly used to assess information on the strength, energy landscape, and lifetime of noncovalent bio-molecular interactions. DFS traditionally requires an applied force that increases linearly with time so that the bio-complex under investigation is exposed to a constant loading rate. However, tethers or polymers can modulate the applied force in a nonlinear manner. For example, bacterial adhesion pili and polymers with worm-like chain properties are structures that show nonlinear force responses...
July 26, 2016: European Biophysics Journal: EBJ
Benedikt Fels, Nikolaj Nielsen, Albrecht Schwab
The tumor environment contributes importantly to tumor cell behavior and cancer progression. Aside from biochemical constituents, physical factors of the environment also influence the tumor. Growing evidence suggests that mechanics [e.g., tumor (stroma) elasticity, tissue pressure] are critical players of cancer progression. Underlying mechanobiological mechanisms involve among others the regulation of focal adhesion molecules, cytoskeletal modifications, and mechanosensitive (MS) ion channels of cancer- and tumor-associated cells...
October 2016: European Biophysics Journal: EBJ
Nahit Rizaner, Rustem Onkal, Scott P Fraser, Alessandro Pristerá, Kenji Okuse, Mustafa B A Djamgoz
The possible association of intracellular Ca(2+) with metastasis in human cancer cells is poorly understood. We have studied Ca(2+) signaling in human prostate and breast cancer cell lines of strongly versus weakly metastatic potential in a comparative approach. Intracellular free Ca(2+) was measured using a membrane-permeant fluorescent Ca(2+)-indicator dye (Fluo-4 AM) and confocal microscopy. Spontaneous Ca(2+) oscillations were observed in a proportion of strongly metastatic human prostate and breast cancer cells (PC-3M and MDA-MB-231, respectively)...
October 2016: European Biophysics Journal: EBJ
Oksana Iamshanova, Pascal Mariot, V'yacheslav Lehen'kyi, Natalia Prevarskaya
Sodium (Na(+)) ions are known to regulate many signaling pathways involved in both physiological and pathological conditions. In particular, alterations in intracellular concentrations of Na(+) and corresponding changes in membrane potential are known to be major actors of cancer progression to metastatic phenotype. Though the functionality of Na(+) channels and the corresponding Na(+) currents can be investigated using the patch-clamp technique, the latter is rather invasive and a technically difficult method to study intracellular Na(+) transients compared to Na(+) fluorescence imaging...
October 2016: European Biophysics Journal: EBJ
A Zaccagnino, C Pilarsky, D Tawfik, S Sebens, A Trauzold, I Novak, A Schwab, H Kalthoff
The altered expression and/or activity of ion channels and transporters (transportome) have been associated with malignant behavior of cancer cells and were proposed to be a hallmark of cancer. However, the impact of altered transportome in epithelial cancers, such as pancreatic ductal adenocarcinoma (PDAC), as well as its pathophysiological consequences, still remains unclear. Here, we report the in silico analysis of 840 transportome genes in PDAC patients' tissues. Our study was focused on the transportome changes and their correlation with functional and behavioral responses in PDAC tumor and stromal compartments...
October 2016: European Biophysics Journal: EBJ
Saverio Gentile
It has been well established that changes in ion fluxes across cellular membranes as a function of time is fundamental in maintaining cellular homeostasis of every living cell. Consequently, dysregulation of ion channels activity is a critical event in pathological conditions of several tissues, including cancer. Nevertheless, the role of ion channels in cancer biology is still not well understood and very little is known about the possible therapeutic opportunities offered by the use of the vast collection of drugs that target ion channels...
October 2016: European Biophysics Journal: EBJ
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