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European Biophysics Journal: EBJ

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https://www.readbyqxmd.com/read/28639125/dlsanalysis-org-a-web-interface-for-analysis-of-dynamic-light-scattering-data
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28488019/on-the-role-of-external-force-of-actin-filaments-in-the-formation-of-tubular-protrusions-of-closed-membrane-shapes-with-anisotropic-membrane-components
#10
Luka Mesarec, Wojciech Góźdź, Samo Kralj, Miha Fošnarič, Samo Penič, Veronika Kralj-Iglič, Aleš Iglič
Biological membranes are composed of different components and there is no a priori reason to assume that all components are isotropic. It was previously shown that the anisotropic properties of membrane components may explain the stability of membrane tubular protrusions even without the application of external force. Our theoretical study focuses on the role of anisotropic membrane components in the stability of membrane tubular structures generated or stabilized by actin filaments. We show that the growth of the actin cytoskeleton inside the vesicle can induce the partial lateral segregation of different membrane components...
May 9, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28478484/one-pathogen-two-stones-are-australian-tree-frog-antimicrobial-peptides-synergistic-against-human-pathogens
#11
Marc-Antoine Sani, Siobhan Carne, Sarah A Overall, Alexandre Poulhazan, Frances Separovic
Antimicrobial peptides (AMPs) may act by targeting the lipid membranes and disrupting the bilayer structure. In this study, three AMPs from the skin of Australian tree frogs, aurein 1.2, maculatin 1.1 and caerin 1.1, were investigated against Gram-negative Escherichia coli, Gram-positive Staphylococcus aureus, and vesicles that mimic their lipid compositions. Furthermore, equimolar mixtures of the peptides were tested to identify any synergistic interactions in antimicrobial activity. Minimum inhibition concentration and minimum bactericidal concentration assays showed significant activity against S...
May 6, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28478483/co-chaperoning-by-amyloid-forming-proteins-cystatins-vs-crystallins
#12
Eva Žerovnik
Cystatins and crystallins are both neuroprotective proteins. Except for their function as cysteine cathepsins inhibitors, cystatins are Aβ binding proteins and presumably protect neurons from intracellular Aβ and extracellular Aβ plaques. Pathological mutations of cystatin C cause amyloid angiopathy. Crystallins, known as small heat shock proteins, bind not only Aβ peptide but also other crystallins in the eye lens and prevent their aggregation. Mutations in crystallins cause cataracts and myopathies. Cross-interactions between amyloidogenic proteins, intrinsically disordered and folded proteins, can also occur...
May 6, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28477084/one-stage-immobilization-of-the-microalga-porphyridium-purpureum-using-a-biocompatible-silica-precursor-and-study-of-the-fluorescence-of-its-pigments
#13
S S Voznesenskiy, A Yu Popik, E L Gamayunov, T Yu Orlova, Zh V Markina, I V Postnova, Yu A Shchipunov
The biocompatible silica precursor tetrakis(2-hydroxyethyl)orthosilicate with ethylene glycol residues was used instead of the common alcohol-containing tetraethoxysilane for the first time to prepare a biorecognition element by entrapping the marine microalga Porphyridium purpureum into a silica matrix by a one-stage sol-gel procedure at conditions (pH, ionic strength, and temperature) appropriate for living cells. We show that the microalga immobilized in this way fully maintains its viability and functionality...
May 5, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28474199/some-factors-affecting-the-process-of-photoinduced-hydroxylaminolysis-in-different-bacteriorhodopsin-based-media
#14
REVIEW
Anna B Druzhko, Tatyana V Dyukova, Sergey K Pirutin
This review presents the results of studies concerning some factors that affect the process of photoinduced hydroxylaminolysis (PHA) in bacteriorhodopsin (BR) and different BR-based media. We consider the peculiar properties of the PHA reaction in water suspensions of BR and BR-based media depending on variation in PHA ingredients, and in particular the use of O-substituted hydroxylamines instead of hydroxylamine hydrochloride. In addition, we discuss how such factors as preliminary ultra-sonication affect the reaction of PHA in the course of BR bleaching and following the reconstitution of bacterioopsin...
May 4, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28466098/lone-pair-%C3%AF-interactions-in-biological-systems-occurrence-function-and-physical-origin
#15
REVIEW
Jiří Kozelka
Lone pair-π interactions are now recognized as a supramolecular bond whose existence in biological systems is documented by a growing number of examples. They are commonly attributed to electrostatic forces. This review attempts to highlight some recent discoveries evidencing the important role which lone pair-π interactions, and anion-π interactions in particular, play in stabilizing the structure and affecting the function of biomolecules. Special attention is paid to studies exploring the physical origin of these at first glance counterintuitive interactions between a lone pair of electrons of one residue and the π-cloud of another...
May 2, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28424847/characterization-of-microtubule-buckling-in-living-cells
#16
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
https://www.readbyqxmd.com/read/28409219/carbonylation-of-atrial-myosin-prolongs-its-interaction-with-actin
#17
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
https://www.readbyqxmd.com/read/28409218/transmembrane-helices-containing-a-charged-arginine-are-thermodynamically-stable
#18
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
https://www.readbyqxmd.com/read/28401261/angiotensin-ii-induces-the-aggregation-of-native-and-oxidized-low-density-lipoprotein
#19
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
https://www.readbyqxmd.com/read/28374045/pdb2cd-visualises-dynamics-within-protein-structures
#20
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
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