European Biophysics Journal最新文献

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.

The global outbreak of COVID-19 pandemic has been accompanied by the emergence of numerous mutated forms of the SARS-CoV-2 virus, exhibiting an increasingly refined capacity to adapt to the human host. The majority of mutations affect viral proteins, particularly the Spike glycoprotein (S), leading to alterations in their physicochemical properties, in secondary structures and biological functions. In the present work, we performed, to the best of our knowledge, the first infrared spectroscopic characterization of monomeric spike glycoprotein subunits 1 (S1) of SARS-CoV-2 Beta variant at pH 7.4, combining the experimental results with Molecular Dynamic simulations, Definition of Secondary Structure of Proteins (DSSP) assignments and hydrophobicity calculations. This integrated approach has yielded valuable insights into the protein secondary structure, hydrophobic behaviour, conformational dynamics, and functional attributes, factors essential for a comprehensive understanding of the viral protein domain. Our results reveal that the SARS-CoV-2 S1 Beta variant is characterized by a secondary structure enriched with antiparallel β-sheets, as consistently supported by both experimental data and computational models. Moreover, a comparative analysis of the experimental results with hydrophobicity calculations indicates that the Beta variant exhibits a slightly more hydrophilic nature relative to the SARS-CoV-2 S1 Wild Type.

The EuPRAXIA project is a European initiative aimed at developing groundbreaking, ultra-compact accelerator research infrastructures based on novel plasma acceleration concepts. The EuPRAXIA@SPARC_LAB facility, located in the Italian National Institute for Nuclear Physics-Frascati National Laboratory, will be the first operating Free Electron Laser facility of EuPRAXIA, based on an accelerator module driven by an electron bunch driver. The Free Electron Laser will produce ultra-short photon pulses in the soft X-ray region. The photons will be delivered to an endstation, called AQUA, to perform a wide range of experiments in atomic and molecular physics, chemistry, and life sciences for both academic and industrial users. Thanks to its wavelength, which falls within the so-called 'water window', AQUA will be particularly well-suited for coherent imaging and ion spectroscopy measurements on biological samples at room temperature in a fully hydrated environment. This unique capability opens up innovative experimental schemes for studying biological systems in states that closely resemble their physiological conditions. This paper presents numerical simulations of coherent diffraction imaging and Coulomb explosion imaging experiments, anticipating future studies at AQUA on biological samples.