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Biophysical Chemistry

Damien Hall
A different approach is described for analyzing sedimentation equilibrium experiments of indefinitely self-associating systems. The procedure involves application of conservation of mass criteria, along with local evaluation of the weight average molar mass, to generate a polynomial based on a composite pseudo-independent variable. The outlined method does not depend upon non-linear regression to generate a solution, but instead requires evaluation of the roots of a high-order polynomial.
June 10, 2017: Biophysical Chemistry
José L Neira, Francisco J Florencio, M Isabel Muro-Pastor
Glutamine synthetase (GS) catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. The activity of Synechocystis sp. PCC 6803 GS type I is regulated by protein-protein interactions with a 65-residue-long protein (IF7). IF7 binds initially to GS through residues at its N terminus. In this work, we studied the conformational preferences of the N-terminal region of IF7 (IF7pep, residues Ala7-Ala29), its binding to GS and its functional properties. Isolated IF7pep populated a nascent helix in aqueous solution...
June 1, 2017: Biophysical Chemistry
Nico König, Michael Paulus, Karin Julius, Julian Schulze, Matthias Voetz, Metin Tolan
In the present work two subclasses of the human antibody Immunoglobulin G (IgG) have been investigated by Small-Angle X-ray Scattering under high hydrostatic pressures up to 5kbar. It is shown that IgG adopts a symmetric T-shape in solution which differs significantly from available crystal structures. Moreover, high-pressure experiments verify the high stability of the IgG molecule. It is not unfolded by hydrostatic pressures of up to 5kbar but a slight increase of the radius of gyration was observed at elevated pressures...
May 26, 2017: Biophysical Chemistry
L Petecchia, F Viti, F Sbrana, M Vassalli, P Gavazzo
The stroma of human bone marrow contains a population of skeletal stem cells (hBM-MSC) which are common ancestors, among the others, of osteoblasts and adipocytes. It has been proposed that the imbalance between hBM-MSC osteogenesis and adipogenesis, which naturally accompanies bone marrow senescence, may contribute to the development of bone-associated diseases, like osteoporosis. The possibility to reproduce this mechanism in vitro has been demonstrated, providing a good model to disclose the details of the complex bone-fat generation homeostasis...
May 26, 2017: Biophysical Chemistry
Antonella Battisti, Paola Morici, Francesco Ghetti, Antonella Sgarbossa
Conventional antimicrobial strategies have become increasingly ineffective due to the rapid emergence of antibiotic resistance among pathogenic bacteria. In order to overcome this problem, antimicrobial PhotoDynamic Therapy (PDT) is considered a promising alternative therapy. PDT has a broad spectrum of action and low mutagenic potential. It is particularly effective when microorganisms present endogenous photosensitizing pigments. Helicobacter pylori (Hp), a pathogen notoriously responsible of severe gastric infections (chronic gastritis, peptic ulcer, MALT lymphoma and gastric adenocarcinoma), produces and accumulates the photosensitizers protoporphyrin IX and coproporphyrin, thus it might be a suitable target of antimicrobial PDT...
May 26, 2017: Biophysical Chemistry
Kazuki Nomura, Yuki Kuwabara, Wataru Kuwabara, Hiroyuki Takahashi, Kanako Nakajima, Mayumi Hayashi, Akinori Iguchi, Toru Shigematsu
We previously obtained a pressure-tolerant (piezotolerant) and a pressure sensitive (piezosensitive) mutant strain, under ambient temperature, from Saccharomyces cerevisiae strain KA31a. The inactivation kinetics of these mutants were analyzed at 150 to 250MPa with 4 to 40°C. By a multiple regression analysis, the pressure and temperature dependency of the inactivation rate constants k values of both mutants, as well as the parent strain KA31a, were well approximated with high correlation coefficients (0.92 to 0...
May 24, 2017: Biophysical Chemistry
Barbara Storti, Giovanni Checcucci, Francesco Ghetti, Riccardo Nifosi, Ranieri Bizzarri
Oxyblepharismin is the photo-oxidized form of blepharismin, the chromophore responsible for the photophobic response of heterotrich ciliate Blepharisma japonicum, and represents a nice model for the study of photo-transduction. In this work, we focused on the photophysical characterization of OxyBP, in view of highlighting the main features related to excitation and emission. By a combined experimental and computational approach we identified the main features of absorption and fluorescence emission of the molecule in solvents of different properties, identifying the nature of transitions as well as the possible heterogeneity at ground/excited state...
May 24, 2017: Biophysical Chemistry
Adriana Campos-Ramírez, Maripaz Márquez, Liliana Quintanar, Luis F Rojas-Ochoa
In this work we study the effect of solution ionic strength on the structural evolution of amidated amyloid beta peptide Aβ (1-40) oligomers at the early stages of fibril formation. By light scattering, we follow the time evolution of the structure and short-time dynamics of peptide structures at low ionic strengths. Our results allow identifying initial oligomer structures as the effective building blocks in the amyloid fibrils formation and indicate that the oligomers growth pathway, from compact structures to flexible chain-like structures, becomes faster as the solution ionic strength is increased...
May 19, 2017: Biophysical Chemistry
Marco Elio Tabacchi, Settimo Termini
Biophysics, just by looking at its name, indicates an interdisciplinary scientific activity, although the notion of interdisciplinarity, as such, seems to be not widely or specifically discussed by biophysicists. The same seems to have happened as well in the early stages of the development of cybernetics, notably in Norbert Wiener's writings. This situation seems to contrast with what has happened in subsequent developments of cybernetics ideas, notably in general system theory and cognitive sciences. After a few general reflections on the notion of interdisciplinarity, its sophisticated variants and the path leading to the birth of cognitive science, we shall refer to Wiener's thought to extracts aspects and indications that could be useful today, also for what concerns the social responsibility of scientists, which could be seen as stemming from a very general form of interdisciplinarity...
May 19, 2017: Biophysical Chemistry
Paolo Trost, Cristiana Picco, Joachim Scholz-Starke, Margherita Festa, Laura Lagostena, Alex Costa, Francesca Sparla, Armando Carpaneto
Living cells exploit the electrical properties of matter for a multitude of fundamental physiological processes, such as accumulation of nutrients, cellular homeostasis, signal transmission. While ion channels and transporters (able to couple ions to various substrates) have been extensively studied, direct measurements of electron currents mediated by specific proteins are just at the beginning. Here, we present the various electrophysiological approaches that have allowed recordings of electron currents and highlight the future potential of such experiments...
May 19, 2017: Biophysical Chemistry
F Stellato, Z Fusco, R Chiaraluce, V Consalvi, S Dinarelli, E Placidi, M Petrosino, G C Rossi, V Minicozzi, S Morante
Far-UV Circular Dichroism experiments and Atomic Force Microscopy tomography are employed to assess the impact of β-sheet breakers on the Aβ1-40 peptide aggregation process in the presence of Cu(2+) or Zn(2+) transition metals. In this work we focus on two specific 5-amino acids long β-sheet breakers, namely the LPFFD Soto peptide, already known in the literature, and the LPFFN peptide recently designed and studied by our team. We provide evidence that both β-sheet breakers are effective in reducing the Aβ1-40 aggregation propensity, even in the presence of metal ions...
May 15, 2017: Biophysical Chemistry
Aura M Jiménez Garduño, Leon J Juárez-Hernández, María J Polanco, Laura Tosatto, Daniela Michelatti, Daniele Arosio, Manuela Basso, Maria Pennuto, Carlo Musio
Spinal and bulbar muscular atrophy (SBMA), also known as Kennedy's disease, is a motor neuron disease caused by the expansion of a polymorphic CAG tandem repeat encoding a polyglutamine (polyQ) tract in the androgen receptor (AR) gene. SBMA is triggered by the binding of mutant AR to its natural ligands, testosterone and dihydrotestosterone (DHT). To investigate the neuronal alterations of motor neuron cell models of SBMA, we applied patch-clamp methods to verify how polyQ expansions in the AR alter cell ionic currents...
May 10, 2017: Biophysical Chemistry
Laura Colombo, Alessio Gamba, Laura Cantù, Mario Salmona, Fabrizio Tagliavini, Valeria Rondelli, Elena Del Favero, Paola Brocca
We investigated the effects of punctual A-to-V and A-to-T mutations in the amyloid precursor protein APP, corresponding to position 2 of Aβ1-42. Those mutations had opposite effects on the onset and progression of Alzheimer disease, the former inducing early AD pathology and the latter protecting against the onset of the disease. We applied Static and Dynamic Light Scattering and Circular Dichroism, to study the different mutants in the early stages of the aggregation process, essential for the disease. Comparative results showed that the aggregation pathways differ in the kinetics and extent of the process, in the size of the aggregates and in the evolution of the secondary structure, resulting in fibrils of different morphology, as seen by AFM...
May 6, 2017: Biophysical Chemistry
Toru Shigematsu, Naho Furukawa, Ryo Takaoka, Mayumi Hayashi, Shoji Sasao, Shigeaki Ueno, Kanako Nakajima, Miyuki Kido, Kazuki Nomura, Akinori Iguchi
We analyzed the effect of high hydrostatic pressure (HHP) treatment on reducing sugar production in the tuberous root of sweet potato (Ipomoea batatas), based on pressure-gelatinization of starch and subsequent saccharification by internal amylases. HHP treatment at up to 600MPa at ambient temperature for 10min did not apparently affect the reducing sugar concentration in tuberous root. However, HHP treatment at 100 to 500MPa and 60°C or 70°C for 10min increased reducing sugar concentration as both the pressure and temperature increased...
May 1, 2017: Biophysical Chemistry
J Somkuti, Z Török, F Pfalzgraf, L Smeller
The concentration of macromolecules inside a cell is very high, which can affect the behavior of the enzymes, and consequently influence vital biological processes. This is called macromolecular crowding. Since the most important effect of macromolecular crowding is the excluded volume, we performed pressure experiments, where the volume (as conjugate parameter to the pressure) is the crucial factor. We measured the temperature and pressure stability of bovine serum albumin and lysozyme with various concentrations of crowding agents, dextran, Ficoll™ and lysozyme itself...
May 1, 2017: Biophysical Chemistry
Valeria Rondelli, Paola Brocca, Nicola Tranquilli, Giovanna Fragneto, Elena Del Favero, Laura Cantù
The preparation and investigation of model membranes is deserving growing interest both for the physics of complex systems, and for biology. The need of simplified models should preserve mimicking the qualifying characteristics of biological membranes, and keep non-invasive and detailed description. As a main feature, biological membranes are non-homogeneous in the disposition of components, both in the lateral and in the transverse direction. We prepared asymmetric supported membranes containing GM1 ganglioside in biomimetic proportion according to different protocols...
April 29, 2017: Biophysical Chemistry
Alessandro Roncador, Aura Matilde Jimenez-Garduño, Laura Pasquardini, Giovanni Giusti, Nicola Cornella, Lorenzo Lunelli, Cristina Potrich, Ruben Bartali, Lucrezia Aversa, Roberto Verucchi, Mauro Dalla Serra, Silvia Caponi, Salvatore Iannotta, Paolo Macchi, Carlo Musio
We report a comprehensive study of the biocompatibility and neurocompatibility of titanium dioxide films (TiO2) prepared by Pulsed Microplasma Cluster Source (PMCS). This technique uses supersonic pulsed beams seeded by clusters of the metal oxide synthesized in a plasma discharge. The final stoichiometry of the TiO2 thin films is tuned changing the gas mixture, achieving stoichiometric or oxygen overstoichiometric films. All the films showed consistent biocompatibility and a spontaneous absorption of poly-d-lysine (PDL) that favors the adhesion and growth of murine cortical neurons...
April 26, 2017: Biophysical Chemistry
G C Santini, C Potrich, L Lunelli, L Vanzetti, S L Marasso, M Cocuzza, F C Pirri, C Pederzolli
A reliable clinical assay based on circulating microRNAs (miRNAs) as biomarkers is highly required. Microdevices offer an attractive solution as a fast and inexpensive way of concentrating these biomarkers from a low sample volume. A previously developed polydimethylsiloxane (PDMS) microdevice able to purify and detect circulating miRNAs was here optimized. The optimization of the morphological and chemical surface properties by nanopatterning and functionalization is presented. Surfaces were firstly characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), fluorescamine assay and s-SDTB (sulphosuccinimidyl-4-o-(4,4-dimethoxytrityl) butyrate) assay and subsequently tested for their capacity to adsorb a fluorescent miRNA...
April 26, 2017: Biophysical Chemistry
Elizabeth A Ploetz, Paul E Smith
Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method...
April 25, 2017: Biophysical Chemistry
Kazuyuki Akasaka, Akihiro Maeno, Akira Yamazaki
A bacterial spore protects itself with an unusually high concentration (~10% in dry weight of spore) of dipicolinic acid (DPA), the release of which is considered the crucial step for inactivating it under mild pressure and temperature conditions. However, the process of how the spore releases DPA in response to pressure remains obscure. Here we apply (1)H high-resolution high-pressure NMR spectroscopy, for the first time, to the spore suspension of Bacillus subtilis natto and monitor directly and in real-time the leaking process of DPA in response to pressure of 200MPa at 20°C...
April 19, 2017: Biophysical Chemistry
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