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European Biophysics Journal: EBJ

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https://www.readbyqxmd.com/read/29785510/measuring-translational-diffusion-of-15-n-enriched-biomolecules-in-complex-solutions-with-a-simplified-1-h-15-n-hmqc-filtered-best-sequence
#1
Shenggen Yao, Thomas G Meikle, Ashish Sethi, Frances Separovic, Jeffrey J Babon, David W Keizer
Pulsed-field gradient nuclear magnetic resonance has seen an increase in applications spanning a broad range of disciplines where molecular translational diffusion properties are of interest. The current study introduces and experimentally evaluates the measurement of translational diffusion coefficients of 15 N-enriched biomolecules using a 1 H-15 N HMQC-filtered band-selective excitation short transient (BEST) sequence as an alternative to the previously described SOFAST-XSTE sequence. The results demonstrate that accurate translational diffusion coefficients of 15 N-labelled peptides and proteins can be obtained using this alternative 1 H-15 N HMQC-filtered BEST sequence which is implementable on NMR spectrometers equipped with probes fitted with a single-axis field gradient, including most cryoprobes dedicated to bio-NMR...
May 21, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29785509/why-so-far-have-epidemics-always-eventually-petered-out-quasispecies-theory-suggests-a-testable-answer
#2
Andreas Dress
In this paper, it is argued that the fact that, so far, even the worst and most far-reaching epidemics-from the Plague of Athens in 430 BC and the Plague of Justinian in 541/542 AD to the Hong Kong Flu from 1968/69-always finally petered out can be explained using Manfred Eigen's quasispecies concept: Indeed, as the infectious agents, while duplicating themselves in the infected organisms, mutate all the time, these infected organisms carry along quite a multitude of mutational variants or-in Manfred Eigen's terms-a whole quasispecies of infectious agents implying that, within that quasispecies, those variants that differ from the wild type may actually serve as some kind of vaccination program when infecting some previously uninfected persons...
May 21, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29777290/two-dimensional-grid-optimization-for-sedimentation-velocity-analysis-in-the-analytical-ultracentrifuge
#3
Haram Kim, Emre Brookes, Weiming Cao, Borries Demeler
Sedimentation velocity experiments performed in the analytical ultracentrifuge are modeled using finite-element solutions of the Lamm equation. During modeling, three fundamental parameters are optimized: the sedimentation coefficients, the diffusion coefficients, and the partial concentrations of all solutes present in a mixture. A general modeling approach consists of fitting the partial concentrations of solutes defined in a two-dimensional grid of sedimentation and diffusion coefficient combinations that cover the range of possible solutes for a given mixture...
May 17, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29774374/manfred-eigen-from-relaxation-kinetics-to-evolution
#4
(no author information available yet)
No abstract text is available yet for this article.
May 17, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29748855/multi-speed-sedimentation-velocity-simulations-with-ultrascan-iii
#5
Tayler L Williams, Gary E Gorbet, Borries Demeler
Recent developments in the UltraScan-III software make it possible to model multi-speed analytical ultracentrifugation sedimentation velocity experiments using finite-element solutions of the Lamm equation. Using simulated data, we demonstrate here how these innovations can be used to enhance the resolution of sedimentation velocity experiments when compared to single-speed experiments. Using heterogeneous systems covering as much as five orders of magnitude in molar mass and fivefold in anisotropy, we compare results from runs performed at multiple speeds to those obtained from single-speed experiments, fitted individually and analyzed globally over multiple speeds, and quantify resolution for sample heterogeneous in size and anisotropy...
May 10, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29737373/membrane-electroporation-chemical-thermodynamics-and-flux-kinetics-revisited-and-refined
#6
Eberhard Neumann, Sergej Kakorin
The chemical thermodynamic concept for membrane electroporation is critically revisited. The hysteresis in the electric field dependence of the rapid in-field electroporation events (on the in-field hysteresis branch) and the slower post-field pore resealing process (zero-field hysteresis branch) is a typical ensemble property involving rapid single-pore opening-closing events that are temporally and spatially distributed. In the case of spherical membrane shells in homogeneous external fields, the acting local field is dependent on the polar-angular position...
May 8, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29704025/effect-of-glycerol-on-photobleaching-of-cytochrome-raman-lines-in-frozen-yeast-cells
#7
Konstantin A Okotrub, Nikolay V Surovtsev
We applied a Raman spectroscopy approach to investigate the effect of a cryoprotectant on the redox state of cytochromes on freezing yeast cells. The redox activity of cytochromes was studied using time-resolved photobleaching of the resonance Raman lines. It is found that ice formation causes a drastic change in the redox state of cytochromes in cells frozen without cryoprotectant, whereas in the presence of glycerol the effects of ice formation are more gradual. The photobleaching rate of cells frozen in glycerol solution shows a gradual slowing with temperature decrease and an abrupt slowdown below - 48 °C...
April 27, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29691610/novel-approaches-to-probe-the-binding-of-recoverin-to-membranes
#8
Kim Potvin-Fournier, Geneviève Valois-Paillard, Marie-Claude Gagnon, Thierry Lefèvre, Pierre Audet, Line Cantin, Jean-François Paquin, Christian Salesse, Michèle Auger
Recoverin is a protein involved in the phototransduction cascade by regulating the activity of rhodopsin kinase through a calcium-dependent binding process at the surface of rod outer segment disk membranes. We have investigated the interaction of recoverin with zwitterionic phosphatidylcholine bilayers, the major lipid component of the rod outer segment disk membranes, using both 31 P and 19 F solid-state nuclear magnetic resonance (NMR) and infrared spectroscopy. In particular, several novel approaches have been used, such as the centerband-only detection of exchange (CODEX) technique to investigate lipid lateral diffusion and 19 F NMR to probe the environment of the recoverin myristoyl group...
April 24, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29687344/spatiotemporal-relationships-defining-the-adaptive-gating-of-the-bacterial-mechanosensitive-channel-mscs
#9
Uğur Çetiner, Andriy Anishkin, Sergei Sukharev
Adaptive desensitization and inactivation are common properties of most ion channels and receptors. The mechanosensitive channel of small conductance MscS, which serves as a low-threshold osmolyte release valve in most bacteria, inactivates not from the open, but from the resting state under moderate tensions. This mechanism enables the channel to respond differently to slow tension ramps versus abruptly applied stimuli. In this work, we present a reconstruction of the energy landscape for MscS transitions based on patch current kinetics recorded under special pressure protocols...
April 23, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29675648/multi-wavelength-analytical-ultracentrifugation-of-human-serum-albumin-complexed-with-porphyrin
#10
Courtney N Johnson, Gary E Gorbet, Heidi Ramsower, Julio Urquidi, Lorenzo Brancaleon, Borries Demeler
The new Beckman Coulter Optima AUC instrument, which features multi-wavelength detection that couples the hydrodynamic separation of colloidal mixtures to spectral deconvolution of interacting and non-interacting solutes present in a mixture, was used to analyze the composition of human serum albumin (HSA) bound to metallo-protoporphyrin. We present new methods implemented in UltraScan that permit Optima AUC-derived multi-wavelength data to be spectrally decomposed in the same fashion as has been made possible for the Cölfen detector earlier...
April 19, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29666888/precise-determination-of-protein-extinction-coefficients-under-native-and-denaturing-conditions-using-sv-auc
#11
Andreas Hoffmann, Kerstin Grassl, Janine Gommert, Christian Schlesak, Alexander Bepperling
The accurate determination of protein concentration is an important though non-trivial task during the development of a biopharmaceutical. The fundamental prerequisite for this is the availability of an accurate extinction coefficient. Common approaches for the determination of an extinction coefficient for a given protein are either based on the theoretical prediction utilizing the amino acid sequence or the photometric determination combined with a measurement of absolute protein concentration. Here, we report on an improved SV-AUC based method utilizing an analytical ultracentrifuge equipped with absorbance and Rayleigh interference optics...
April 17, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29663020/the-self-association-and-thermal-denaturation-of-caprine-and-bovine-%C3%AE-lactoglobulin
#12
Jennifer M Crowther, Jane R Allison, Grant A Smolenski, Alison J Hodgkinson, Geoffrey B Jameson, Renwick C J Dobson
Milk components, such as proteins and lipids, have different physicochemical properties depending upon the mammalian species from which they come. Understanding the different responses of these milks to digestion, processing, and differences in their immunogenicity requires detailed knowledge of these physicochemical properties. Here we report on the oligomeric state of β-lactoglobulin from caprine milk, the most abundant protein present in the whey fraction. At pH 2.5 caprine β-lactoglobulin is predominantly monomeric, whereas bovine β-lactoglobulin exists in a monomer-dimer equilibrium at the same protein concentrations...
April 16, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29654475/nmr-comparison-of-hyphal-and-yeast-candida-albicans-serotype-b-mannans
#13
Peter Bystrický, Eva Machová, Slavomír Bystrický
A change from a globular to a filamentous hyphal form is an important feature in the pathogenicity of yeasts. Such a dimorphism while infecting a host organism is thought to be also accompanied in the case of Candida albicans spp. by a structural rearrangement of surface mannan antigen. The presented work brings new insights into the molecular structural changes of mannan C. albicans serotype B based on NMR experimental data. 1 H and 13 C signal identification of the anomeric region and the assignment of their linkage type is presented here...
April 13, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29610996/multi-speed-sedimentation-velocity-implementation-in-ultrascan-iii
#14
Gary E Gorbet, Subhashree Mohapatra, Borries Demeler
A framework for the global analysis of multi-speed analytical ultracentrifugation sedimentation velocity experiments is presented. We discuss extensions to the adaptive space-time finite element fitting methods implemented in UltraScan-III to model sedimentation velocity experiments where a single run is performed at multiple rotor speeds, and describe extensions in the optimization routines used for fitting experimental data collected at arbitrary multi-speed profiles. Our implementation considers factors such as speed dependent rotor stretching, the resulting radial shifting of the finite element solution's boundary conditions, and changes in the associated time-invariant noise...
April 2, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29600443/immuno-receptors-from-recognition-to-signaling-and-function
#15
REVIEW
Israel Pecht
The vertebrate adaptive immune response is initiated by specific recognition of antigens. This is carried out by molecules, soluble or cell surface receptors that are members of the Multichain Immune Recognition Receptors (MIRR) group of proteins. The soluble arm of the response is based on antibodies. Kinetic analysis of antibody-antigenic epitope interactions pioneered insights into the complexity underlying the capacity of relatively limited repertoires of antibodies to recognize an essentially unlimited range of epitopes by employing conformational diversity of a given single sequence...
March 29, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29594412/ferritin-from-the-haemolymph-of-adult-ants-an-extraction-method-for-characterization-and-a-ferromagnetic-study
#16
Eliane Wajnberg, Odivaldo C Alves, Jonas Perales, Surza Lucia G da Rocha, André Teixeira Ferreira, Luiz Cláudio Cameron, Darci M S Esquivel, Maria de Lourdes Barriviera
Ferritin has been studied in many animals, plants and bacteria. The main functions of ferritin in mammals are iron concentration and stabilization, protection against oxidants and iron storage for later developmental or iron-dependent activities. Although insect ferritin plays a key role in iron transport, only a few studies to date have examined its properties and function. Ferritin isolation from the haemolymph of adult Camponotus sericeiventris ants involved heating at 75 °C, followed by protein fractionation with 3...
March 28, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29594411/recent-advances-in-the-ultrascan-solution-modeller-us-somo-hydrodynamic-and-small-angle-scattering-data-analysis-and-simulation-suite
#17
Emre Brookes, Mattia Rocco
The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release...
March 28, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29569181/there-and-back-again-from-the-origin-of-life-to-single-molecules
#18
Petra Schwille
What is life? There is hardly a more fundamental question raised by aspiring researchers, and one less prone to ever be answered in a scientifically satisfying way. In the long, productive and highly influential period of research following his Nobel-recognised work on relaxation kinetics, Manfred Eigen made seminal contributions towards a quantifiable definition of life, with a strong focus on its evolutionary character. In the last years of his time as an active researcher, however, he devoted himself to another, purely experimental topic: the detection and analysis of single biomolecules in aqueous solution...
March 22, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29550902/controlled-depolymerisation-assessed-by-analytical-ultracentrifugation-of-low-molecular-weight-chitosan-for-use-in-archaeological-conservation
#19
Jennifer M K Wakefield, Richard B Gillis, Gary G Adams, Caitlin M A McQueen, Stephen E Harding
The heterogeneity and molecular weight of a chitosan of low molecular weight (molar mass) and low degree of acetylation (0.1) for potential use as a consolidant for decayed archaeological wood were examined by sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge before and after depolymerisation. Sedimentation velocity before depolymerisation revealed a uniform distribution of sedimentation coefficient with little concentration dependence. SEDFIT-MSTAR analysis revealed a weight average molecular weight Mw of (14...
March 17, 2018: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/29546436/effects-of-ph-and-aggregation-in-the-human-prion-conversion-into-scrapie-form-a-study-using-molecular-dynamics-with-excited-normal-modes
#20
Angelica Nakagawa Lima, Ronaldo Junio de Oliveira, Antônio Sérgio Kimus Braz, Maurício Garcia de Souza Costa, David Perahia, Luis Paulo Barbour Scott
There are two different prion conformations: (1) the cellular natural (PrPC ) and (2) the scrapie (PrPSc ), an infectious form that tends to aggregate under specific conditions. PrPC and PrPSc are widely different regarding secondary and tertiary structures. PrPSc contains more and longer β-strands compared to PrPC . The lack of solved PrPSc structures precludes a proper understanding of the mechanisms related to the transition between cellular and scrapie forms, as well as the aggregation process. In order to investigate the conformational transition between PrPC and PrPSc , we applied MDeNM (molecular dynamics with excited normal modes), an enhanced sampling simulation technique that has been recently developed to probe large structural changes...
March 15, 2018: European Biophysics Journal: EBJ
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