European Biophysics Journal最新文献

The aqueous extract of Moringa oleifera leaves has been previously characterized for its polyphenolic composition, yet the behavior of its colloidal aggregates under dilution remains largely unexplored. In this study, we investigate the structural and chemical properties of these aggregates at room temperature, focusing on their stability and surface exposure upon dilution. Although the aggregates break up as dilution increases, they never fully dissolve within the conditions explored. Both multi-angle static light scattering and dynamic light scattering highlight aggregates fragmentation and size heterogeneity under dilution. UV-vis absorption spectroscopic data strongly suggest that the aggregates of different sizes present in the extract are homogeneously constituted, as their spectra are similar to those of the main polyphenol components. The Folin-Ciocâlteu assay reveals an increase in gallic acid equivalent values normalized for extract concentration, suggesting that fragmentation prompted by dilution enhances the exposure of reactive sites. A very basic model, considering only one kind of aggregate with uniform density, is employed to support this interpretation. Assuming this model, the Folin-Ciocâlteu assay data allow to grasp the law regulating the change of the aggregate average size under dilution, i.e., a power law. Additionally, in-liquid atomic force microscopy imaging confirms the presence of smaller but still aggregated particles at high dilution, enabling the calculation of a height distribution, that is consistent with the model prediction. These findings provide insights into the dynamic behavior of polyphenol-rich aggregates in aqueous systems and their potential implications for bioavailability and reactivity.

We characterized a DNA/gold interface designed for the detection of the SARS-CoV-2 RNA-dependent RNA polymerase/Helicase (RdRp/Hel) sequence. Using broadband spectroscopic ellipsometry (SE) and a difference spectra approach, we monitored molecular modifications at the interface, from probe sequence deposition to the insertion of a molecular spacer and subsequent hybridization with the target. The UV region revealed the characteristic DNA absorption peak around 260 nm, while changes in δΔ in the NIR correlated with increased optical thickness following each deposition step. The optical response was analyzed as a function of target concentration, and the binding affinity curve, derived from δΔ values at 800 nm, was fitted using a first-order Langmuir model, yielding a dissociation constant K_D = (70 ± 10) nM, consistent with literature values. Selectivity studies demonstrated that the interface effectively discriminates the SARS-CoV-2 sequence from the SARS-CoV HKU variant, even in a crowded environment. A complementary platform targeting the SARS-CoV HKU sequence confirmed selective detection of HKU over SARS-CoV-2. These findings highlight the potential for parallel detection of different viral sequences.

Open science is now established as an important paradigm for publicly funded research. The main principle being that to ensure best use of research data and integrity of the scientific process the information from experiments should be made widely and freely available. However, dedicated technical infrastructure to enable useful access to comprehensive experimental information in molecular biophysics is lacking, in particular in regard to repositories for raw measurement data. The Molecular Biophysics Database (MBDB) was created to fill this gap. The MBDB provides a common and extensible framework to store and access raw measurement data from a growing number of biophysical methods, currently including bio-layer interferometry, isothermal titration calorimetry, surface plasmon resonance, and microscale thermophoresis, with additional methods planned for the future. Alongside the raw measurement data from these methods, a rich set of metadata to enable data reuse is captured in accordance with the FAIR data management principles. An overview of the data models and technologies that were used to create the MBDB is presented here.

Ascorbate (ASC) is a key redox buffer in plant cells, whose antioxidant capacity depends on its balance with monodehydroascorbate (MDHA), its one-electron oxidation product. In the cytoplasm of Arabidopsis mesophyll cells, ASC is present at high concentrations and interacts with enzymes that oxidize it to MDHA, such as ascorbate peroxidases, as well as with enzymes that regenerate it, like NAD(P)H-dependent MDHA oxidoreductases (MDHAR) and glutathione-dependent dehydroascorbate reductases (DHAR). In vacuoles, ASC is found at lower concentrations and vacuoles lack these enzymes, but it can still undergo non-enzymatic oxidation by phenoxy radicals generated by class III peroxidases. It has been discovered that vacuoles isolated from Arabidopsis mesophyll cells contain an electron transport system that functionally connects the cytoplasmic and vacuolar ASC pools, acting as a transmembrane MDHA oxidoreductase dependent on Asc. Patch-clamp measurements have shown that electron currents across the tonoplast depend on the presence of ASC as an electron donor and MDHA or ferricyanide as electron acceptors on opposite sides of the membrane. These electron currents are catalyzed by cytochrome b561 isoform A (CYB561A), a tonoplast redox protein with ASC-binding sites in both the cytoplasm and the vacuole, electrically connected by two heme b groups. The recent functional characterization of other members of the cytochrome b561 family underscores how these proteins are essential for cellular redox balance and metabolism, facilitating electron transport across membranes and supporting processes such as iron homeostasis, stress defence, and cell wall modifications, highlighting their fundamental role in plant physiology.

Cytochrome C is a key protein involved in electron transport within the mitochondrial respiratory chain and in apoptosis mechanisms. In this work, we provide a detailed theoretical analysis of the binding mechanism between cytochrome-C and a cardiolipin-containing membrane. Molecular dynamics simulations, along with protein contact network and fractal dimension analyses were employed to investigate the structural changes in cytochrome-C during the binding process. Our results suggest that cytochrome-C follows a two-step binding mechanism, starting with a rapid initial interaction, followed by slower conformational rearrangements. We identified two different cytochrome-C conformations at the membrane: a compact, native-like structure and an extended form. The latter, stabilized by Lys72, exhibits a higher binding affinity (≈ 2 kcal/mol) compared to the former. Protein extension also correlates with increased protein-membrane contact and altered heme ring orientation, suggesting that the partial unfolding of cytochrome-C could be crucial for its peroxidase activity and its role in apoptosis. These findings enhance the understanding of the cytochrome-C's membrane interactions and its diverse functions.