Mutations in the essential outer membrane protein BamA contribute to Escherichia coli resistance to the antimicrobial peptide TAT-RasGAP.

Antimicrobial peptides (AMPs) are promising alternatives to classical antibiotics against antibiotic-resistant pathogens. TAT-RasGAP is an AMP with broad range antibacterial activity, but its mechanism of action is unknown. In this study, we analyzed a strain of Escherichia coli with extensive resistance to TAT-RasGAP but not to other AMPs that we obtained after twenty passages during an in vitro resistance selection experiment.

Predicting multiple taste sensations with a multiobjective machine learning method.

Taste perception plays a pivotal role in guiding nutrient intake and aiding in the avoidance of potentially harmful substances through five basic tastes - sweet, bitter, umami, salty, and sour. Taste perception originates from molecular interactions in the oral cavity between taste receptors and chemical tastants. Hence, the recognition of taste receptors and the subsequent perception of taste heavily rely on the physicochemical properties of food ingredients.

Influence of dexamethasone on the interaction between glucocorticoid receptor and SOX9: A molecular dynamics study.

The glucocorticoid receptor (GR) is a nuclear receptor that controls critical biological processes by regulating the transcription of specific genes. GR transcriptional activity is modulated by a series of ligands and coenzymes, where a ligand can act as an agonist or antagonist. GR agonists, such as the glucocorticoids dexamethasone (DEX) and prednisolone, are widely prescribed to patients with inflammatory and autoimmune diseases.

Toward a general and interpretable umami taste predictor using a multi-objective machine learning approach.

The umami taste is one of the five basic taste modalities normally linked to the protein content in food. The implementation of fast and cost-effective tools for the prediction of the umami taste of a molecule remains extremely interesting to understand the molecular basis of this taste and to effectively rationalise the production and consumption of specific foods and ingredients. However, the only examples of umami predictors available in the literature rely on the amino acid sequence of the analysed peptides, limiting the applicability of the models.

Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study.

The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds of copolymers containing more than 50 repeating units, have until now rarely been simulated, due to a lack of computational power. Therefore, a flexible amphiphilic triblock copolymer (mPEG-α-PLL-PLA) containing a total of 80 repeating units, has been emulated and synthesized to embody compactified nanoconstructs of over 900 assembled copolymers, sized between 80 and 100 nm, for siRNA complexing purposes.

A survey on computational taste predictors.

Unlabelled: Taste is a sensory modality crucial for nutrition and survival, since it allows the discrimination between healthy foods and toxic substances thanks to five tastes, i.e., sweet, bitter, umami, salty, and sour, associated with distinct nutritional or physiological needs.

Highlighting the effect of amyloid beta assemblies on the mechanical properties and conformational stability of cell membrane.

Alzheimer disease (AD) is the most common cause of dementia, characterized by a progressive decline in cognitive function due to the abnormal aggregation and deposition of Amyloid beta (Aβ) fibrils in the brain of patients. In this context, the molecular mechanisms of protein misfolding and aggregation that are known to induce significant biophysical alterations in cells, including destabilization of plasma membranes, remain partially unclear. Physical interaction between the Aβ assemblies and the membrane leads to the disruption of the cell membrane in multiple ways including, surface carpeting, generation of transmembrane channels and detergent-like membrane dissolution.

The Impact of Natural Compounds on S-Shaped Aβ42 Fibril: From Molecular Docking to Biophysical Characterization.

The pursuit for effective strategies inhibiting the amyloidogenic process in neurodegenerative disorders, such as Alzheimer's disease (AD), remains one of the main unsolved issues, and only a few drugs have demonstrated to delay the degeneration of the cognitive system. Moreover, most therapies induce severe side effects and are not effective at all stages of the illness. The need to find novel and reliable drugs appears therefore of primary importance.

Molecular and Coarse-Grained Modeling to Characterize and Optimize Dendrimer-Based Nanocarriers for Short Interfering RNA Delivery.

Dendrimer nanocarriers are unique hyper-branched polymers with biomolecule-like properties, representing a promising prospect as a nucleic acid delivery system. The design of effective dendrimer-based gene carriers requires considering several parameters, such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity. In detail, the rational design of the dendrimer surface chemistry has been ascertained to play a crucial role on the efficiency of interaction with nucleic acids.