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European Biophysics Journal: EBJ

Adedayo A Fodeke
To study the effect of non-specific interactions arising from proteins being in a crowded environment on physiological processes, the self-interaction of concentrated Dextran T70 and Ficoll 70 and the interactions between a dilute protein and these polymeric macromolecules were quantified using non-ideal tracer sedimentation equilibrium. Sedimentation equilibria of each polymer were measured between 5 and 37 °C, and sedimentation equilibria of 2 mg cm-3 superoxide dismutase (SOD) in 0-0.1 g cm-3 of each polymer was also measured...
January 11, 2019: European Biophysics Journal: EBJ
Adalberto Brunetti, Marcella Arciuli, Leonardo Triggiani, Fabio Sallustio, Anna Gallone, Raffaele Tommasi
After light absorption, melanin converts very rapidly the energy gained into heat. The time scale of this process ranges from tens of femtoseconds to a few nanoseconds. Femtosecond transient absorption allows for exploration of such photo-induced carrier dynamics to observe the de-excitation pathways of the biological complex. Here, we report on the ultrafast relaxation of suspensions of Sepia melanin in DMSO at room temperature using a femtosecond broadband pump and probe technique by photoexciting in the UV and probing in the entire visible range...
January 11, 2019: European Biophysics Journal: EBJ
Darci M S Esquivel, Eliane Wajnberg, Leonel Cardozo de Menezes E Souza, Daniel Acosta-Avalos, Márcia Barbosa Pinho, Ana Yoshi Harada
How geomagnetic field information is collected and processed by insects for orientation and navigation remains elusive. In social insects, magnetic particles are well accepted as magnetic sensors. Ants have the ability to home and hunt, and some migratory and nomadic species can migrate or move over long distances for which magnetoreception is an important mechanism. It was shown previously that ferromagnetic resonance (FMR) spectral parameters of one migratory and one nomadic ant could be distinguished from Brazilian Solenopsis ant species and that these parameters correlate to the local geomagnetic field...
January 3, 2019: European Biophysics Journal: EBJ
Daniela Meleleo, Gabriella Notarachille, Vincenzo Mangini, Fabio Arnesano
Mercury (Hg) and lead (Pb) are known to be toxic non-radioactive elements, with well-described neurotoxicology. Much evidence supports the implication of metals as potential risk cofactors in Alzheimer's disease (AD). Although the action mechanism of the two metals remains unclear, Hg and Pb toxicity in AD could depend on their ability to favour misfolding and aggregation of amyloid beta proteins (Aβs) that seem to have toxic properties, particularly in their aggregated state. In our study, we evaluated the effect of Hg and Pb both on the Aβ42 ion channel incorporated in a planar lipid membrane made up of phosphatidylcholine containing 30% cholesterol and on the secondary structure of Aβ42 in an aqueous environment...
January 2, 2019: European Biophysics Journal: EBJ
Anatoliy I Dragan, Christopher M Read, Colyn Crane-Robinson
The nature of water on the surface of a macromolecule is reflected in the temperature dependence of the heat effect, i.e., the heat capacity change, ΔCp, that accompanies its removal on forming a complex. The relationship between ΔCp and the nature of the surface dehydrated cannot be modeled for DNA by the use of small molecules, as previously done for proteins, since the contiguous surfaces of the grooves cannot be treated as the sum of small component molecules such as nucleotides. An alternative approach is used here in which ΔCp is measured for the formation of several protein/DNA complexes and the calculated contribution from protein dehydration subtracted to yield the heat capacity change attributable to dehydration of the DNA...
December 14, 2018: European Biophysics Journal: EBJ
Vaida Paketurytė, Vaida Linkuvienė, Georg Krainer, Wen-Yih Chen, Daumantas Matulis
In rational drug design, it is important to determine accurately and with high precision the binding constant (the affinity or the change in Gibbs energy, ∆G), the change in enthalpy (ΔH), and the entropy change upon small molecule drug binding to a disease-related target protein. These thermodynamic parameters of the protein-ligand association reaction are usually determined by isothermal titration calorimetry (ITC). Here, the repeatability, precision, and accuracy of the measurement of the affinity and the change in enthalpy upon acetazolamide (AZM) interaction with human carbonic anhydrase II (CA II) are discussed based on the measurements using several ITC instruments...
December 8, 2018: European Biophysics Journal: EBJ
Michał Arabski, Ilona Stabrawa, Aldona Kubala-Kukuś, Katarzyna Gałczyńska, Dariusz Banaś, Łukasz Piskorz, Ewa Forma, Magdalena Bryś, Waldemar Różański, Marek Lipiński
The aim of this study was to analyze the correlation between past bacterial infections and the type and chemical composition of urinary stones experienced by human patients. Bacteria have been recognized to contribute to urinary stones; however, the role of uropathogens in the development of specific stones has not been extensively investigated. The detection of past bacterial infection (eleven different bacterial species) in urinary stones from 83 patients was made on a DNA level using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) and correlated with the chemical composition of urinary stones measured using X-ray powder diffraction (XPRD) technique and their elemental composition by total reflection X-ray fluorescence (TXRF)...
November 27, 2018: European Biophysics Journal: EBJ
S Mitra, D Ray, G Bhattacharya, R Gupta, D Sen, V K Aswal, S K Ghosh
The large number of potential applications of ionic liquids (ILs) requires an understanding of their environmental impacts including their adverse effects on microorganisms living in soil and water. The molecular mechanism of toxic activities of these liquids is yet to be understood in detail. Any foreign molecules, interacting with an organism, have to encounter first the cellular membrane, which is predominantly composed of the lipid bilayer. In this work, multilamellar vesicles (MLV) of phospholipids have been used to shed light on the effect of an IL on the structure of a cellular membrane...
November 24, 2018: European Biophysics Journal: EBJ
Wei Zhang, Jiahai Zhang, Christopher A MacRaild, Raymond S Norton, Robin F Anders, Xuecheng Zhang
The abundant Plasmodium falciparum merozoite surface protein MSP2, a potential malaria vaccine candidate, is an intrinsically disordered protein with some nascent secondary structure present in its conserved N-terminal region. This relatively ordered region has been implicated in both membrane interactions and amyloid-like aggregation of the protein, while the significance of the flanking-disordered region is unclear. In this study, we show that aggregation of the N-terminal conserved region of MSP2 is influenced in a length- and sequence-dependent fashion by the disordered central variable sequences...
November 15, 2018: European Biophysics Journal: EBJ
Marvin A Soriano-Ursúa, Martiniano Bello, Christian F Hernández-Martínez, Iván Santillán-Torres, Ruth Guerrero-Ramírez, José Correa-Basurto, José-Antonio Arias-Montaño, José G Trujillo-Ferrara
The design of beta2 adrenoceptor (β2 AR) agonists is attractive because of their wide-ranging applications in medicine, and the details of agonist interactions with β2 AR are interesting because it is considered a prototype for G-protein coupled receptors. Preclinical studies for agonist development have involved biological assays with guinea pigs due to a similar physiology to humans. Boron-containing Albuterol derivatives (BCADs) designed as bronchodilators have improved potency and efficacy compared with their boron-free precursor on guinea pig β2 ARs (gpβ2 ARs), and two of the BCADs (BR-AEA and boronterol) conserve these features on cells expressing human β2 ARs (hβ2 ARs)...
November 1, 2018: European Biophysics Journal: EBJ
Thomas Heimburg
No abstract text is available yet for this article.
December 2018: European Biophysics Journal: EBJ
Hirohisa Tamagawa, Kota Ikeda
According to standard membrane theory, the generation of membrane potential is attributed to transmembrane ion transport. However, there have been a number of reports of membrane behavior in conflict with the membrane theory of cellular potential. Putting aside the membrane theory, we scrutinized the generation mechanism of membrane potential from the view of the long-dismissed adsorption theory of Ling. Ling's adsorption theory attributes the membrane potential generation to mobile ion adsorption. Although Ling's adsorption theory conflicts with the broadly accepted membrane theory, we found that it well reproduces experimentally observed membrane potential behavior...
December 2018: European Biophysics Journal: EBJ
Khair Bux, Syed Abid Ali, Syed Tarique Moin
Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein...
December 2018: European Biophysics Journal: EBJ
Abbas Yousefpour, Sepideh Amjad-Iranagh, Fatemeh Goharpey, Hamid Modarress
In this work, the effects of the anti-hypertensive drug amlodipine in native and PEGylated forms on the malfunctioning of negatively charged lipid bilayer cell membranes constructed from DMPS or DMPS + DMPC were studied by molecular dynamics simulation. The obtained results indicate that amlodipine alone aggregates and as a result its diffusion into the membrane is retarded. In addition, due to their large size aggregates of the drug can damage the cell, rupturing the cell membrane. It is shown that PEGylation of amlodipine prevents this aggregation and facilitates its diffusion into the lipid membrane...
December 2018: European Biophysics Journal: EBJ
S V Efimov, Yu O Zgadzay, N B Tarasova, V V Klochkov
The protein hormone insulin exists in several forms in nature, and a large number of modified sequences are used in pharmacy. They differ by physicochemical properties and efficiency of biological action. Pancreatic bovine insulin was studied in an acidic solution by nuclear magnetic resonance spectroscopy. [Formula: see text]H and [Formula: see text]C NMR signal assignment of backbone and side chains was made by analysis of a set of 2D spectra obtained on a sample with natural isotope abundance. The presence of certain secondary structure elements was revealed on a qualitative level based on nuclear Overhauser effect spectroscopy, which are similar to those observed in the crystal structure...
December 2018: European Biophysics Journal: EBJ
Oleksii Zdorevskyi, Sergey N Volkov
Single-molecule experiments on DNA unzipping are analyzed on the basis of the mobility of nucleic bases in complementary pairs. Two possible scenarios of DNA double-helix unzipping are proposed and studied, using the atom-atom potential function method. According to the first scenario, the base pairs transit into a 'preopened' metastable state and then fully open along the 'stretch' pathway. In this case, the DNA unzipping takes place slowly and as an equilibrium process, with the opening energies being similar to the energies obtained in thermodynamic experiments on DNA melting...
December 2018: European Biophysics Journal: EBJ
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...
December 2018: European Biophysics Journal: EBJ
Guy Channell, Vlad Dinu, Gary G Adams, Stephen E Harding
In establishing the sources of data variability within sedimentation velocity analysis in the analytical ultracentrifuge and their relative importance, recent studies have demonstrated that alignment of the sample cells to the centre of rotation is the most significant contributing factor to overall variability, particularly for the characterisation of low levels of protein aggregation. Accurate mechanical and optical alignment tools have been recently designed. In this study, we (1) confirm the effect of misalignment observed by others on the estimated amounts of bovine serum albumin (BSA) monomer and dimer, and the sedimentation coefficient value for the BSA dimer; and (2) demonstrate the high performance of a mechanical alignment tool and the usefulness of a simple and complementary enhanced manual alignment protocol which should be useful for situations where these tools are not available...
October 2018: European Biophysics Journal: EBJ
Aalishaa A Azam, Jean M Kinder, G Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R Ault, Peter J F Henderson, Babur Z Chowdhry, Bruce D Alexander, Stephen E Harding, Mary K Phillips-Jones
Despite the importance of membrane proteins in cellular processes, studies of these hydrophobic proteins present major technical challenges, including expression and purification for structural and biophysical studies. A modified strategy of that proposed previously by Saidijam et al. (2005) and others, for the routine expression of bacterial membrane proteins involved in environmental sensing and antimicrobial resistance (AMR), is proposed which results in purification of sufficient proteins for biophysical experiments...
October 2018: European Biophysics Journal: EBJ
Stephen E Harding
The analytical ultracentrifuge (AUC) invented by T. Svedberg has now become an extremely versatile and diverse tool in Biochemistry and Polymer Science for the characterisation of the sizes, shapes and interactions of particles ranging in size from a few nanometres to tens of microns, or in molecular weight, M (molar mass) terms from a few hundred daltons to hundreds of megadaltons. We illustrate this diversity by reviewing recent work on (1) small lignin-like isoeugenols of M ~ 0.4-0.9 kDa for archaeological wood conservation, (2) protein-like association of a functional amino-cellulose M = 3...
October 2018: European Biophysics Journal: EBJ
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