Bacteria use small molecules called siderophores to scavenge iron. Siderophore-Fe³⁺complexes are recognised by outer-membrane transporters and imported into the periplasm in a process dependent on the inner-membrane protein TonB. The siderophore enterobactin is secreted by members of the family Enterobacteriaceae, but many other bacteria includingPseudomonasspecies can use it. Here, we show that thePseudomonastransporter PfeA recognises enterobactin using extracellular loops distant from the pore. The relevance of this site is supported by in vivo and in vitro analyses. We suggest there is a second binding site deeper inside the structure and propose that correlated changes in hydrogen bonds link binding-induced structural re-arrangements to the structural adjustment of the periplasmic TonB-binding motif.

Developing effective antibiotics against Gram-negative bacteria remains challenging due to their protective outer membrane. With this study, we investigated the relationship between antibiotic permeation through the OmpF porin of Escherichia coli and antimicrobial efficacy. We measured the relative permeability coefficients (RPCs) through the bacterial porin by liposome swelling assays, including non-antibacterial molecules, and the minimum inhibitory concentrations (MICs) against E. coli. We developed a machine learning (ML) approach by combining classification and regression models to correlate these data sets. Our strategy allowed us to quantify the negative correlation between RPC and MIC values, clearly indicating that increased permeability through OmpF generally leads to improved antimicrobial activity. Moreover, the correlation was remarkable only for compounds with significant permeability coefficients. Conversely, when permeation ability is low, other factors play the most significant role in antimicrobial potency. Importantly, the proposed ML-based approach was set by exploiting the available seminal information from previous investigations in order to keep the number of molecular descriptors to the minimum for greater interpretability. This provided valuable insights into the complex interplay between different molecular properties in defining the overall outer membrane permeation and, consequently, the antimicrobial efficacy. From a practical perspective, the presented approach does not aim at identifying the “golden rule” for boosting antibiotic potency. The automated protocol presented here could be used to inspect, in silico, many alternatives of a given molecular structure, with the output being the list of the best candidates to be then synthesized and tested. This could be a valuable in silico tool for researchers in both academia and industry to rapidly evaluate novel potential compounds and reduce costs and time during the early drug discovery stage.

The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) stands out as a pivotal structural component. We used cryo-electron microscopy to reveal unique features, such as an unconventional protein belt (DR_1364) around the main secretin (GspD), and a cap (DR_0940) found to be a separated subunit rather than integrated with GspD. Furthermore, a novel region at the N-terminus of the GspD constitutes an additional second gate, supplementing the one typically found in the outer membrane region. This T2SS was found to contribute to envelope integrity, while also playing a role in nucleic acid and nutrient trafficking. Studies on intact cell envelopes show a consistent T2SS structure repetition, highlighting its significance within the cellular framework.

We investigated, by using all‐atom molecular dynamics simulations, the effect of the outer membrane of Gram‐negative bacteria, composed in the outer leaflet by polar/charged lipopolysaccharides (LPS), on the electrostatic properties of general porins from the Enterobacteriaceae family. General porins constitute the main path for the facilitated diffusion of polar antibiotics through the outer membrane. As model system we selected OmpK36 from Klebsiella pneumoniae, the ortholog of OmpC from Escherichia coli. This species presents high variability of amino acid composition of porins, with the effect to increase its resistance to the penetration of antibiotics. The various properties we analyzed seem to indicate that LPS acts as an independent layer without affecting the internal electrostatic properties of OmpK36. The only apparent effect on the microsecond time scale we sampled is the appearance of calcium ions, when present at moderate concentration in solution, inside the pore. However, we noticed increased fluctuations of the polarization density and only minor changes on its average value.

The possibility of using fullerenes as containers for toxic beryllium atoms is studied by a multi‐scale approach in which first‐principles and classical molecular dynamics simulations are combined. By studying the energetics, electronic and spectroscopic properties of Be‐fullerene systems and by simulating their interaction at finite temperature in vacuo and in representative biological environments it is concluded that: i) Be endohedral complexes can be obtained by implanting Be atoms at energies >2.3 eV that is consistent with laser implantation technologies; ii) it is in principle possible to distinguish stable endohedral complexes from metastable exohedral ones by optical absorption, suggesting that optical spectroscopy can be a valuable a non‐destructive technique to assist the synthesis and the control of implanted films iii) the Be‐endohedral complexes are long‐lived and thermodynamically stable and can confine beryllium both in vacuo and in aqueous solution; iv) Be@C60 complexes are likely unable to penetrate the selectivity filters of a prototypical protein showing that fullerene prevents undesired interactions with biomolecules and toxicity effects of Be²⁺ related to replacement of the Ca²⁺. Overall, these results provide an assessment on the possibility to encapsulate Be atoms into fullerenes by ion implantation to synthesize inert and highly stable and safe molecular containers for toxic beryllium radionuclides. Great opportunities are expected for the realization and application of Be‐C60 complexes to nanotechnology and nanomedicine with particularly appealing perspectives in the field of neutron capture therapy of cancer.