European Biophysics Journal最新文献

In the quantitative characterization of experimental systems the observation of a time-independent response can signify the attainment of thermodynamic equilibrium. However, there are also situations where the time-independence of experimental response merely reflects the attainment of a kinetic steady state. Although quantitative expressions derived on the basis of kinetic steady-state attainment retain validity for a system at thermodynamic equilibrium, those based on attainment of thermodynamic equilibrium do not apply to systems merely reflecting the attainment of a kinetic steady state. This survey of experimental procedures encountered during research endeavours over the past six decades has revealed many situations where the source of the time-independent instrumental response was correctly identified, but also a number where the responses were misinterpreted.

Red fluorescent protein mRuby is an important labelling tool for super-resolution imaging. With the addition of thioacetate, it was found here that the red colour of the protein aqueous solution changed, although still clear and transparent. Light spectrophotometry exhibited that, with the increase of thioacetate concentration, the absorption spectra changed abruptly. Crystallography showed the binding of thioacetate at the chromophore of mRuby. Atomic-resolution serial structures of mRuby single crystal showed snapshots of step-by-step reduction of thioacetate upon light irradiation. This observation suggests new insights for FP-compound interaction research and light energy harvesting for green chemistry.

The article presents a study on the disruption of the bacterial membrane by celandine (CME) and dandelion (TOE) extracts containing bioactive compounds responsible for their antibacterial activity. The in vitro microbiological tests showed antibacterial effect both on Gram-positive (Staphylococcus aureus and Streptococcus pyogenes) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) pathogenic bacteria species. However, in the case of celandine herb extract, the effect was stronger, especially for Gram-positive bacteria. For a deeper understanding of the mechanism of antibacterial action, both studied extracts were subjected to biophysical studies on artificial bacterial lipid membranes, modeled with the Langmuir monolayers technique. The monolayer investigations were performed using two approaches: (i) monitoring the penetration of extracts injected into the aqueous subphase beneath a compressed lipid film, and (ii) comparing surface pressure–area isotherms recorded on a subphase with and without addition of extracts. These experiments confirmed the activity of TOE and CME at the membrane level, demonstrating the penetration of extract components into the membranes and their fluidizing effect. AFM analysis of the domain structures of the films transferred onto solid supports (Langmuir-Blodgett) revealed differences in film topography induced by the extracts and are in a good agreement with the results of biological tests and analytical analyses of the tested extracts. These findings confirm that the stronger antibacterial effect of CME, associated with a higher content of bioactive compounds, exerts a more destructive effect on the bacterial lipid membranes compared to TOE.

Advances in artificial intelligence, particularly in deep learning, are transforming the field of protein structure prediction. AlphaFold has emerged as a benchmark tool due to its remarkable ability to model protein folding based solely on amino acid sequences. Nevertheless, despite these impressive achievements, several prediction failures still occur. In this study, we focus on two multidomain proteins, LicT from Bacillus subtilis and P1 from the Rice Yellow Mottle Virus, that have long resisted structural characterization. Both proteins exhibit inter-domain flexibility, dimerization, and dynamic behavior in response to phosphorylation (for LicT) or zinc binding (for P1). Here, we screen the performances of AlphaFold versions against these two proteins endowed with a complex conformational landscape and show the present impossibility to correctly predict all domains simultaneously.

Bitter taste type 2 G protein-coupled receptors (TAS2R GPCRs) detect bitter substances on the tongue, but they are also prevalent in tissues throughout the human body that play a role in cancer and other diseases, making them targets for pharmacological research. However, structural information on G protein (GP)-bound TAS2R complexes resolved by cryogenic electron microscopy (cryo-EM) is available for only 4 of the 25 TAS2Rs. Herein, we show that AlphaFold (AF) predictions of GP-bound TAS2R14 and TAS2R46 agree well with cryo-EM structure determinations, thus suggesting that the AF2 predicted structures for all 25 TAS2Rs could be used as starting points for drug development. Although useful starting points, we show that Molecular Dynamics (MD) studies are needed to refine the AF2 structures to get sufficient accuracy for drug design. We find that the MD simulations agree well with the cryo-EM structures at 85 K, but significant changes occur in the MD structures at 310 K that arise from thermal fluctuations frozen-out in the cryo-EM structure, making them far less pronounced at 85 K. We conclude that for TAS2Rs for which cryo-EM structures are not available, AF2 predicted structures followed by MD at 310 K provide a basis for TAS2R drug discovery.