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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
Nicola J Harris, Heather E Findlay, Michael R Sanders, Mateusz Kedzierski, Ália Dos Santos, Paula J Booth
Membrane transporters are a vital class of proteins for which there is little available structural and thermodynamic information. The Major Facilitator Superfamily (MFS) is a large group of transport proteins responsible for transporting a wide range of substrates in eukaryotes and prokaryotes. We have used far-UV circular dichroism (CD) to assess whether transporters from this superfamily have the same chemical and thermal stability. We have compared the stability of five different MFS transporters; PepTSo from Shewanella oneidensis and LacY, GalP, GlpT and XylE from Escherichia coli, as well as a known stable mutant of LacY, LacY-C154G...
January 23, 2017: European Biophysics Journal: EBJ
Patrick Voos, Mehtap Yazar, René Lautenschläger, Oliver Rauh, Anna Moroni, Gerhard Thiel
Apamin is frequently used as a specific blocker of small-conductance Ca(2+)-activated (SK type) K(+) channels. Here we show that the small neurotoxin is not as specific as anticipated. It is also a high-affinity inhibitor with an IC50 of 13 nM of the Kv1.3 channel; it blocks the latter with potency similar to the Kv1.3 blocker PAP-1. Since SK type channels and Kv1.3 channels are frequently coexpressed in different tissues such as cells of the immune system, apamin must be used with caution as a pharmacological tool...
January 20, 2017: European Biophysics Journal: EBJ
Linda M Field, T G Emyr Davies, Andrias O O'Reilly, Martin S Williamson, B A Wallace
The pyrethroid insecticides are a very successful group of compounds that have been used extensively for the control of arthropod pests of agricultural crops and vectors of animal and human disease. Unfortunately, this has led to the development of resistance to the compounds in many species. The mode of action of pyrethroids is known to be via interactions with the voltage-gated sodium channel. Understanding how binding to the channel is affected by amino acid substitutions that give rise to resistance has helped to elucidate the mode of action of the compounds and the molecular basis of their selectivity for insects vs mammals and between insects and other arthropods...
January 9, 2017: European Biophysics Journal: EBJ
Alfredo Sánchez-Solano, Angel A Islas, Thomas Scior, Bertin Paiz-Candia, Lourdes Millan-PerezPeña, Eduardo M Salinas-Stefanon
The mechanism of inactivation of mammalian voltage-gated Na(+) channels involves transient interactions between intracellular domains resulting in direct pore occlusion by the IFM motif and concomitant extracellular interactions with the β1 subunit. Navβ1 subunits constitute single-pass transmembrane proteins that form protein-protein associations with pore-forming α subunits to allosterically modulate the Na(+) influx into the cell during the action potential of every excitable cell in vertebrates. Here, we explored the role of the intracellular IFM motif of rNav1...
December 23, 2016: European Biophysics Journal: EBJ
Jian Tian, Chunlong Tu, Bobo Huang, Yitao Liang, Jian Zhou, Xuesong Ye
Electrophysiology and mechanics are two essential components in the functions of cardiomyocytes and skeletal muscle cells. The simultaneous recording of electrophysiological and mechanical activities is important for the understanding of mechanisms underlying cell functions. For example, on the one hand, mechanisms under cardiovascular drug effects will be investigated in a comprehensive way by the simultaneous recording of electrophysiological and mechanical activities. On the other hand, computational models of electromechanics provide a powerful tool for the research of cardiomyocytes...
December 23, 2016: European Biophysics Journal: EBJ
Vladimir P Zhdanov
The exocytotic pathway of secretion of molecules from cells includes transport by vesicles, tether-mediated fusion of vesicles with the plasma membrane accompanied by pore formation, and diffusion-mediated release of their contents via a pore to the outside. In related basic biophysical studies, vesicle-content release is tracked by measuring corresponding amperometric spikes. Although experiments of this type have a long history, the understanding of the underlying physics is still elusive. The present study elucidates the likely contribution of line energy, membrane tension and bending, osmotic pressure, hydration forces, and tethers to the potential energy for fusion-related pore formation and evolution...
December 10, 2016: European Biophysics Journal: EBJ
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Ilya Ioshikhes, Amutha Ramaswamy
Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level...
December 8, 2016: European Biophysics Journal: EBJ
Leila Karami, Ali Akbar Saboury, Elham Rezaee, Sayyed Abbas Tabatabai
The soluble epoxide hydrolase (sEH) enzyme plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. Inhibition of sEH provides a new approach to the treatment of inflammation, hypertension and atherosclerosis. In this study, the binding modes and inhibition mechanisms of the new oxadiazole-based amide inhibitors of the human soluble epoxide hydrolase were investigated by molecular docking and molecular dynamics (MD) simulation followed by the MM-GBSA method to calculate the binding free energy of each inhibitor to sEH...
December 7, 2016: European Biophysics Journal: EBJ
Vratislav Cmiel, Josef Skopalik, Katerina Polakova, Jan Solar, Marketa Havrdova, David Milde, Ivan Justan, Massimiliano Magro, Zenon Starcuk, Ivo Provaznik
In the last few years, magnetically labeled cells have been intensively explored, and non-invasive cell tracking and magnetic manipulation methods have been tested in preclinical studies focused on cell transplantation. For clinical applications, it is desirable to know the intracellular pathway of nanoparticles, which can predict their biocompatibility with cells and the long-term imaging properties of labeled cells. Here, we quantified labeling efficiency, localization, and fluorescence properties of Rhodamine derivatized superparamagnetic maghemite nanoparticles (SAMN-R) in mesenchymal stromal cells (MSC)...
November 26, 2016: European Biophysics Journal: EBJ
Manuela Maffei, Emanuela Longa, Antonio Sabatini, Alberto Vacca, Stefano Iotti
In vitro motility assay (IVMA) experiments were performed to analyze the movement of actin filaments sliding on a pavement of myosin molecules at different [ATP] and [ADP]. In standard experimental conditions at [ATP] = 2 mM, about 80% of the actin filaments move in unloaded conditions with a constant velocity. However, a fraction of at least 20% static actin filaments is always present. The accepted explanation is the occurrence of damaged "rigor"-like myosin heads that do not undergo the normal ATP-dependent cycling motion...
March 2017: European Biophysics Journal: EBJ
Giuseppina Simone
Phenotype variations define heterogeneity in biological and molecular systems, and play a crucial mechanistic role, and heterogeneity has been demonstrated in tumor cells. In this work, cells from blood of patients affected by colon cancer were analyzed and sorted using a microfluidic assay based on galactose-active moieties and incubated for culturing in severe combined immunodeficiency (SCID) mice. Based on the results of these experiments, a model based on Markov theory is implemented and discussed to explain the equilibrium existing between phenotypes of cell subpopulations sorted using the microfluidic assay...
March 2017: European Biophysics Journal: EBJ
Umesh Kalathiya, Monikaben Padariya, Maciej Baginski
Shelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate the molecular basis of these interactions, we employed molecular dynamics (MD) simulations of TRF1TRFH-TIN2TBM and TRF2TRFH-TIN2TBM/ApolloTBM complexes and of the isolated proteins...
March 2017: European Biophysics Journal: EBJ
Ida Louise Jørgensen, Gerdi Christine Kemmer, Thomas Günther Pomorski
Studying membrane proteins at the molecular level represents a major challenge in biochemistry due to the complexity of the membrane in which they are embedded. As an important step towards a detailed understanding of their action and molecular functioning, current studies focus on membrane proteins reconstituted into artificial lipid environments. Such reconstituted systems allow for a more flexible choice of biochemical, biophysical, and microscopy techniques for characterizing the proteins. This review gives an overview of the methods currently available for reconstituting membrane proteins in a functional state into giant unilamellar vesicles, and discusses some key methods to verify successful reconstitution...
March 2017: European Biophysics Journal: EBJ
D Meshach Paul, R Rajasekaran
Natowicz syndrome (mucopolysaccharidoses type 9) is a lysosomal storage disorder caused by deficient or defective human hyaluronidase 1. The disorder is not well studied at the molecular level. Therefore, a new in silico approach was proposed to study the molecular basis on which one clinically observed mutation, Glu268Lys, results in a defective enzyme. The native and mutant structures were subjected to comparative analyses using a conformational sampling approach for geometrical variables viz, RMSF, RMSD, and Ramachandran plot...
March 2017: European Biophysics Journal: EBJ
Joanna Kotyńska, Izabela Dobrzyńska, Zbigniew A Figaszewski
Interactions of alkali metal cations (Li(+), Na(+), K(+), Cs(+)) with phosphatidylcholine (PC) liposomal membranes were investigated through experimental studies and theoretical considerations. Using a microelectrophoresis technique, charge densities of experimental membrane surfaces were measured as a function of the pH of electrolyte solutions. Equilibria between the PC liposomal membranes and monovalent ions were mathematically analyzed and described quantitatively through a previously proposed theoretical model...
March 2017: European Biophysics Journal: EBJ
Petar Eftimov, Norihiko Yokoi, Vesselin Tonchev, Yana Nencheva, Georgi As Georgiev
The surface properties of meibomian secretion (MGS), the major constituent of the tear film (TF) lipid layer, are of key importance for TF stability. The interfacial properties of canine, cMGS, and feline, fMGS, meibum films were studied using a Langmuir surface balance. These species were selected because they have blinking frequency and TF stability similar to those of humans. The sample's performance during dynamic area changes was evaluated by surface pressure (π)-area (A) isocycles and the layer structure was monitored with Brewster angle microscopy...
March 2017: European Biophysics Journal: EBJ
Richards Grzhibovskis, Elisabeth Krämer, Ingolf Bernhardt, Björn Kemper, Carl Zanden, Nikolay V Repin, Bogdan V Tkachuk, Marina V Voinova
The phenomenon of physical contact between red blood cells and artificial surfaces is considered. A fully three-dimensional mathematical model of a bilayer membrane in contact with an artificial surface is presented. Numerical results for the different geometries and adhesion intensities are found to be in agreement with experimentally observed geometries obtained by means of digital holographic microscopy.
March 2017: European Biophysics Journal: EBJ
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