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European Biophysics Journal: EBJ

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https://www.readbyqxmd.com/read/28725998/membrane-phase-transition-during-heating-and-cooling-molecular-insight-into-reversible-melting
#1
Liping Sun, Rainer A Böckmann
With increasing temperature, lipid bilayers undergo a gel-fluid phase transition, which plays an essential role in many physiological phenomena. In the present work, this first-order phase transition was investigated for variable heating and cooling rates for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer by means of atomistic molecular dynamics simulations. Alternative methods to track the melting temperature [Formula: see text] are compared. The resulting [Formula: see text] is shown to be independent of the scan rate for small heating rates (0...
July 19, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28725997/mitotic-spindle-kinetochore-fibers-hold-on-tight-to-interpolar-bundles
#2
REVIEW
Iva M Tolić
When a cell starts to divide, it forms a spindle, a micro-machine made of microtubules, which separates the duplicated chromosomes. The attachment of microtubules to chromosomes is mediated by kinetochores, protein complexes on the chromosome. Spindle microtubules can be divided into three major classes: kinetochore microtubules, which form k-fibers ending at the kinetochore; interpolar microtubules, which extend from the opposite sides of the spindle and interact in the middle; and astral microtubules, which extend towards the cell cortex...
July 19, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28712066/effect-of-ph-and-ionic-strength-on-the-binding-strength-of-anti-pf4-polyanion-antibodies
#3
Thi-Huong Nguyen, Andreas Greinacher
Antibodies against the chemokine platelet factor 4 (PF4) in complex with heparin cause the prothrombotic adverse drug reaction heparin-induced thrombocytopenia (HIT). The current dilemma for laboratory diagnosis of HIT is that only about 50% of these antibodies are pathogenic, but the widely available enzyme immunosorbent assays (EIA), used for diagnosis in the clinical laboratory cannot differentiate between non-pathogenic- and pathogenic (platelet activating) antibodies. It would be highly desirable to improve diagnosis for HIT...
July 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28712065/erratum-to-stochastic-phenotypic-interconversion-in-tumors-can-generate-heterogeneity
#4
Giuseppina Simone
No abstract text is available yet for this article.
July 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28710521/efflux-drug-transporters-at-the-forefront-of-antimicrobial-resistance
#5
REVIEW
Tahmina Rahman, Benjamin Yarnall, Declan A Doyle
Bacterial antibiotic resistance is rapidly becoming a major world health consideration. To combat antibiotics, microorganisms employ their pre-existing defence mechanisms that existed long before man's discovery of antibiotics. Bacteria utilise levels of protection that range from gene upregulation, mutations, adaptive resistance, and production of resistant phenotypes (persisters) to communal behaviour, as in swarming and the ultimate defence of a biofilm. A major part of all of these responses involves the use of antibiotic efflux transporters...
July 14, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28698919/unperturbed-hydrocarbon-chains-and-liquid-phase-bilayer-lipid-chains-a-computer-simulation-study
#6
Alexander L Rabinovich, Alexander P Lyubartsev, Dmitrii V Zhurkin
In this work, the properties of saturated and unsaturated fatty acid acyl chains 16:0, 18:0, 18:1(n-9)cis, 18:2(n-6)cis, 18:3(n-3)cis, 18:4(n-3)cis, 18:5(n-3)cis, 20:4(n-6)cis, 20:5(n-3)cis and 22:6(n-3)cis in a bilayer liquid crystalline state and similar hydrocarbon chains (with CH[Formula: see text] terminal groups instead of C=O groups) in the unperturbed state characterised by a lack of long-range interaction were investigated. The unperturbed hydrocarbon chains were modelled by Monte Carlo simulations at temperature [Formula: see text] K; sixteen fully hydrated homogeneous liquid crystalline phosphatidylcholine bilayers containing these chains were studied by molecular dynamics simulations at the same temperature...
July 11, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28695249/first-study-on-iron-complexes-in-blood-and-organ-samples-from-thalassaemic-and-normal-laboratory-mice-using-m%C3%A3-ssbauer-spectroscopy
#7
George Charitou, Vlassis Petousis, Charalambos Tsertos, Yannis Parpottas, Marina Kleanthous, Marios Phylactides, Soteroula Christou
Measurements of iron complexes and iron stores in the body are crucial for evaluation and management of chelation therapy targeted against iron accumulation or overload in blood and organs. In this work, blood and tissue samples from one normal and one thalassaemic laboratory mouse were studied using (57)Fe Mössbauer spectroscopy at 78 K for the first time. In contrast to human patients, these laboratory mice did not receive any medical treatment, thus the iron components present in the samples are not altered from their natural state...
July 10, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28695248/divergent-effects-of-anesthetics-on-lipid-bilayer-properties-and-sodium-channel-function
#8
REVIEW
Karl F Herold, Olaf S Andersen, Hugh C Hemmings
General anesthetics revolutionized medicine by allowing surgeons to perform more complex and much longer procedures. This widely used class of drugs is essential to patient care, yet their exact molecular mechanism(s) are incompletely understood. One early hypothesis over a century ago proposed that nonspecific interactions of anesthetics with the lipid bilayer lead to changes in neuronal function via effects on membrane properties. This model was supported by the Meyer-Overton correlation between anesthetic potency and lipid solubility and despite more recent evidence for specific protein targets, in particular ion-channels, lipid bilayer-mediated effects of anesthetics is still under debate...
July 10, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28687859/impact-of-a-discordant-helix-on-%C3%AE-amyloid-structure-aggregation-ability-and-toxicity
#9
Yi-Cheng Chen
According to amyloid cascade hypothesis, the deposit of amyloid-β (Aβ) peptide is the main cause of Alzheimer's disease (AD). The aggregation ability and toxicity of Aβ peptides are highly associated with the sequence and conformation. A discordant helix is a helical segment with a tendency to form a β-strand conformation and has been found in many amyloid-like proteins or peptides. In this review, we summarize the current knowledge of the properties of a Aβ discordant helix and its impact on the Aβ structure, aggregation ability and cytotoxicity...
July 7, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28685171/the-biophysics-of-a-critical-phenomenon-colonization-and-sedimentation-of-the-photosynthetic-bacteria-rubrivivax-gelatinosus
#10
Mariann Kis, Gábor Sipka, Ferhan Ayaydin, Péter Maróti
In response to environmental changes, the photosynthetic bacterium Rubrivivax gelatinosus (Rvx.) can switch from a planktonic lifestyle to a phototrophic biofilm. Like in critical phenomena, the colonization and sedimentation of the cells is abrupt and hard to predict causally, and the underlying biophysics of the mechanisms involved is not known. Herein, we report basic experimental observations and quantitative explanations as keys to understanding microbial turnover of aggregates. (1) The moment of sedimentation can be controlled by the height of the tube of cultivation, by the concentrations of externally added Ficoll (a highly branched polymer) and/or of internally produced polysaccharides (constituents of the biofilm)...
July 6, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28656475/gravity-and-neuronal-adaptation-in-vitro-and-in-vivo-from-neuronal-cells-up-to-neuromuscular-responses-a-first-model
#11
REVIEW
Florian P M Kohn, Ramona Ritzmann
For decades it has been shown that acute changes in gravity have an effect on neuronal systems of human and animals on different levels, from the molecular level to the whole nervous system. The functional properties and gravity-dependent adaptations of these system levels have been investigated with no or barely any interconnection. This review summarizes the gravity-dependent adaptation processes in human and animal organisms from the in vitro cellular level with its biophysical properties to the in vivo motor responses and underlying sensorimotor functions of human subjects...
June 27, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28639125/dlsanalysis-org-a-web-interface-for-analysis-of-dynamic-light-scattering-data
#12
Steen Hansen
A web interface ( www.DLSanalysis.org ) for indirect Laplace transformation of dynamic light scattering data is presented. When experimental data are uploaded to the server they are processed in a few seconds, and the result is displayed on the screen in the form of a size distribution together with the experimental data and the fit to the data. No other user input than the experimental data is necessary, but various options for the analysis may be selected. No local installation of software or registration is necessary...
June 21, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28623388/lateral-diffusion-and-signaling-of-receptor-for-advanced-glycation-end-products-rage-a-receptor-involved-in-chronic-inflammation
#13
Aleem Syed, Qiaochu Zhu, Emily A Smith
Membrane diffusion is one of the key mechanisms in the cellular function of receptors. The signaling of receptors for advanced glycation end-products (RAGE) has been extensively studied in the context of several pathological conditions, however, very little is known about RAGE diffusion. To fill this gap, RAGE lateral diffusion is probed in native, cholesterol-depleted, and cytoskeleton-altered cellular conditions. In native GM07373 cellular conditions, RAGE has a 90% mobile fraction and an average diffusion coefficient of 0...
June 16, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28620743/understanding-the-interactions-of-human-follicle-stimulating-hormone-with-single-walled-carbon-nanotubes-by-molecular-dynamics-simulation-and-free-energy-analysis
#14
Yasaman Mahmoodi, Faramarz Mehrnejad, Khosrow Khalifeh
Interactions of carbon nanotubes (CNTs) and blood proteins are of interest for nanotoxicology and nanomedicine. It is believed that the interactions of blood proteins and glycoproteins with CNTs may have important biological effects. In spite of many experimental studies of single-walled carbon nanotubes (SWCNT) and glycoproteins with different methods, little is known about the atomistic details of their association process or of structural alterations occurring in adsorbed glycoproteins. In this study, we have applied molecular dynamics simulation to investigate the interaction of follicle stimulating hormone (hFSH) with SWCNT...
June 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28620742/multireflection-propagation-of-conformational-kinks-in-a-two-component-model-of-dna-as-the-transfer-mode-of-the-transcriptional-replication-fork
#15
E S Shikhovtseva, V N Nazarov
The propagation, or movement, of a conformational kink along a linear structure can occur in capture, transfer, or multireflection modes. Here we use a model for two-component bistable polymer molecules with energetically non-equivalent stable states to model the propagation of the DNA transcription bubble via movement of a non-linear longitudinal stretching region along the DNA chain. We show that under certain conditions the longitudinal excitation can act as a reflector for a conformational kink and, furthermore, that conformational switching may propagate in a multireflection mode alongside conformational kink transition and conformational kink trapping...
June 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28620741/a-potential-new-stable-state-of-the-e-cadherin-strand-swapped-dimer-in-solution
#16
Alexandra Schumann-Gillett, Alan E Mark, Evelyne Deplazes, Megan L O'Mara
E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other...
June 15, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28612124/distribution-of-dipeptides-in-different-protein-structural-classes-an-effort-to-find-new-similarities
#17
Mahin Ghadimi, Emran Heshmati, Khosrow Khalifeh
Finding any regularity in the sequences of proteins and determining their correlation with structural features are of great interest for an understanding of molecular biology. We statistically analyzed the relative frequencies of all 400 possible dipeptides in a data set containing randomly selected proteins of different defined structural classes including all-alpha, all-beta, alpha + beta and alpha/beta families. We found that the distribution of dipeptides is not the same for different structural classes, and some of them are significantly far from a random distribution...
June 13, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28585042/characterizing-the-interactions-of-two-lipid-modifications-with-lipid-rafts-farnesyl-anchors-vs-palmitoyl-anchors
#18
Tao Zhang, Qichao Luo, Linlin Yang, Hualiang Jiang, Huaiyu Yang
Farnesyl (Far) and palmitoyl (Pal) anchors play important roles in the traffic of many lipidated proteins. Herein, we show the distinctive interactions and influences of the two lipid modifications on lipid rafts (LRs) and non-raft-like membranes using molecular dynamics simulations. Palmitoyl anchors behave in a more ordered fashion, pack tighter with the lipids of LRs and diffuse at a slower rate than farnesyl anchors in LRs. When interacting with non-raft-like membranes these two types of anchors become less ordered, pack more loosely with lipids, and diffuse at a higher rate...
June 5, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28567605/erratum-to-one-stage-immobilization-of-the-microalga-porphyridium-purpureum-using-a-biocompatible-silica-precursor-and-study-of-the-fluorescence-of-its-pigments
#19
S S Voznesenskiy, A Yu Popik, E L Gamayunov, T Yu Orlova, Zh V Markina, I V Postnova, Yu A Shchipunov
No abstract text is available yet for this article.
May 31, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28516266/constitutive-calcium-entry-and-cancer-updated-views-and-insights
#20
REVIEW
Olivier Mignen, Bruno Constantin, Marie Potier-Cartereau, Aubin Penna, Mathieu Gautier, Maxime Guéguinou, Yves Renaudineau, Kenji F Shoji, Romain Félix, Elsa Bayet, Paul Buscaglia, Marjolaine Debant, Aurélie Chantôme, Christophe Vandier
Tight control of basal cytosolic Ca(2+) concentration is essential for cell survival and to fine-tune Ca(2+)-dependent cell functions. A way to control this basal cytosolic Ca(2+) concentration is to regulate membrane Ca(2+) channels including store-operated Ca(2+) channels and secondary messenger-operated channels linked to G-protein-coupled or tyrosine kinase receptor activation. Orai, with or without its reticular STIM partner and Transient Receptor Potential (TRP) proteins, were considered to be the main Ca(2+) channels involved...
May 17, 2017: European Biophysics Journal: EBJ
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