European Biophysics Journal

http://link.springer.com/journal/249

List of Papers (Total 166)

Viruses: incredible nanomachines. New advances with filamentous phages

During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could ...

Viral membrane proteins

This special issue on ‘Viral membrane proteins’ incorporates a series of research articles that were presented at the ‘Conference on Viral Membrane Proteins’, held at the University of Heidelberg, Germany, on 12–14 December 2008. The aim of the symposium was to involve all areas of research in this emerging field focusing on biophysical and clinically relevant approaches as well as ...

Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification

The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 × ...

An ultrasoft X-ray multi-microbeam irradiation system for studies of DNA damage responses by fixed- and live-cell fluorescence microscopy

Localized induction of DNA damage is a valuable tool for studying cellular DNA damage responses. In recent decades, methods have been developed to generate DNA damage using radiation of various types, including photons and charged particles. Here we describe a simple ultrasoft X-ray multi-microbeam system for high dose-rate, localized induction of DNA strand breaks in cells at ...

XIX meeting of the Italian Society of Pure and Applied Biophysics

This special issue of the European Biophysics Journal contains papers presented as invited lectures or oral contributions at the XIX meeting of the Italian Society of Pure and Applied Biophysics, also known as SIBPA. The conference was held in Rome, 17–20 September 2008 at the “Sacro Cuore” Catholic University. For the second time, the first was in 2006, the articles presented at ...

Probing complexes with single fluorophores: factors contributing to dispersion of FRET in DNA/RNA duplexes

Single molecule fluorescent microscopy is a method for the analysis of the dynamics of biological macromolecules by detecting the fluorescence signal produced by fluorophores associated with the macromolecule. Two fluorophores located in a close proximity may result in Förster resonance energy transfer (FRET), which can be detected at the single molecule level and the efficiency of ...

Inter-subunit disulfide cross-linking in homomeric and heteromeric P2X receptors

P2X receptors are ATP-gated cation channels and assembled as homotrimers or heterotrimers from seven cloned subunits. Each subunit contains two transmembrane domains connected by a large extracellular loop. We have previously shown that replacement of two conserved residues, K68 and F291, by cysteine residues leads to disulfide cross-linking between neighbouring P2X1 subunits. ...

Orthosteric and allosteric binding sites of P2X receptors

P2X receptors for ATP comprise a distinct family of ligand gated ion channels with a range of properties. They have been shown to be involved in a variety of physiological processes including blood clotting, sensory perception, pain sensation, bone formation as well as inflammation and may provide a number of novel drug targets. In addition to the orthosteric site for ATP binding ...

The voltage dependence of hEag currents is not determined solely by membrane-spanning domains

The ether-à-go-go potassium channels hEag1 and hEag2 are highly homologous. Even though both possess identical voltage-sensing domain S4, the channels act differently in response to voltage. Therefore we asked whether transmembrane domains other than the voltage sensor could contribute to the voltage-dependent behaviour of these potassium channels. For this chimaeras were created, ...

Proteolysis of prion protein by cathepsin S generates a soluble β-structured intermediate oligomeric form, with potential implications for neurotoxic mechanisms

Formation of PrP aggregates is considered to be a characteristic event in the pathogenesis of TSE diseases, accompanied by brain inflammation and neurodegeneration. Factors identified as contributing to aggregate formation are of interest as potential therapeutic targets. We report that in vitro proteolysis of ovine PrP94–233 (at neutral pH and in the absence of denaturants) by the ...

Photogeneration of membrane potential hyperpolarization and depolarization in non-excitable cells

We monitored femtosecond laser induced membrane potential changes in non-excitable cells using patchclamp analysis. Membrane potential hyperpolarization of HeLa cells was evoked by 780 nm, 80 fs laser pulses focused in the cellular cytoplasm at average powers of 30–60 mW. Simultaneous detection of intracellular Ca2+ concentration and membrane potential revealed coincident ...

satFRET: estimation of Förster resonance energy transfer by acceptor saturation

We demonstrate theoretically and experimentally the quantification of Förster resonance energy transfer (FRET) by direct and systematic saturation of the excited state of acceptor molecules. This version of acceptor depletion methods for FRET estimation, denoted as “satFRET” is reversible and suitable for time-resolved measurements. The technique was investigated theoretically ...

Detailed state model of CaMKII activation and autophosphorylation

By combining biochemical experiments with computer modelling of biochemical reactions we elucidated some of the currently unresolved aspects of calcium–calmodulin-dependent protein kinase II (CaMKII) activation and autophosphorylation that might be relevant for its physiological function and provided a model that incorporates in detail the mechanism of CaMKII activation and ...

HIV-1–cellular interactions analyzed by single virus tracing

Single virus tracing (SVT) allows the direct investigation of the entry pathway of viruses into living cells. Using fluorescently labeled virus-like particles (VLPs) and SVT, we have studied the interaction between human immunodeficiency virus type 1 (HIV-1) and the plasma membrane of living cells. From the trajectories of freely diffusing VLPs in solution, we established that the ...

Non-Gaussian curvature distribution of actin-propelled biomimetic colloid trajectories

We analyze the motion of colloids propelled by a comet-like tail of polymerizing actin filaments. The curvature of the particle trajectories deviates strongly from a Gaussian distribution, implying that the underlying microscopic processes are fluctuating in a non-independent manner. Trajectories for beads of different size all showed the same non-Gaussian behavior, while the mean ...

Push-me-pull-you: how microtubules organize the cell interior

Dynamic organization of the cell interior, which is crucial for cell function, largely depends on the microtubule cytoskeleton. Microtubules move and position organelles by pushing, pulling, or sliding. Pushing forces can be generated by microtubule polymerization, whereas pulling typically involves microtubule depolymerization or molecular motors, or both. Sliding between a ...

Dynamics of C-phycocyanin in various deuterated trehalose/water environments measured by quasielastic and elastic neutron scattering

The molecular understanding of protein stabilization by the disaccharide trehalose in extreme temperature or hydration conditions is still debated. In the present study, we investigated the role of trehalose on the dynamics of the protein C-phycocyanin (C-PC) by neutron scattering. To single out the motions of C-PC hydrogen (H) atoms in various trehalose/water environments, ...

Modulation of the conductance of a 2,2′-bipyridine-functionalized peptidic ion channel by Ni2+

An α-helical amphipathic peptide with the sequence H2N-(LSSLLSL)3-CONH2 was obtained by solid phase synthesis and a 2,2′-bipyridine was coupled to its N-terminus, which allows complexation of Ni2+. Complexation of the 2,2′-bipyridine residues was proven by UV/Vis spectroscopy. The peptide helices were inserted into lipid bilayers (nano black lipid membranes, nano-BLMs) that suspend ...

Dynamics of hydration water in deuterated purple membranes explored by neutron scattering

The function and dynamics of proteins depend on their direct environment, and much evidence has pointed to a strong coupling between water and protein motions. Recently however, neutron scattering measurements on deuterated and natural-abundance purple membrane (PM), hydrated in H2O and D2O, respectively, revealed that membrane and water motions on the ns–ps time scale are not ...

ANNINE-6plus, a voltage-sensitive dye with good solubility, strong membrane binding and high sensitivity

We present a novel voltage-sensitive hemicyanine dye ANNINE-6plus and describe its synthesis, its properties and its voltage-sensitivity in neurons. The dye ANNINE-6plus is a salt with a double positively charged chromophore and two bromide counterions. It is derived from the zwitterionic dye ANNINE-6. While ANNINE-6 is insoluble in water, ANNINE-6plus exhibits a high solubility of ...

Protection of liposomes against fusion during drying by oligosaccharides is not predicted by the calorimetric glass transition temperatures of the dry sugars

Sugars play an important role in the desiccation tolerance of most anhydrobiotic organisms. It has been shown in previous studies that different structural families of oligosaccharides have different efficacies to interact with phospholipid headgroups and protect membranes from solute leakage during drying. Here, we have compared three families of linear oligosaccharides (fructans ...