The influence of permeability through bacterial porins in whole-cell compound accumulation

The lack of new drugs for Gram-negative pathogens is a global threat to modern medicine. The complexity of their cell envelope, with an additional outer membrane, hinders internal accumulation and thus, the access of molecules to their targets. Our limited understanding of the molecular basis for compound influx and efflux from these pathogens is a major bottleneck for the discovery of effective antibacterial compounds. Here we analyse the correlation between the whole-cell compound accumulation of ~200 molecules and their predicted porin permeability coefficient (influx), using a recently developed scoring function. We found a strong linear relationship (74%) between the two, confirming porins key in compound uptake in Gram-negative bacteria. The analysis of this unique dataset aids to better understand the molecular descriptors behind whole-cell accumulation and molecular uptake in Gram-negative bacteria

Theoretical study of molecular electronic excitations and optical transitions of C60

We report results on ab initio calculations of excited states of the fullerene molecule by using configuration interaction (CI) approach with singly excited determinants (SCI). We have used both the experimental geometry and the one optimized by the density functional method and worked with basis sets at the cc-pVTZ and aug-cc-pVTZ level. Contrary to the early SCI semiempirical calculations, we find that two lowest $^1 T_{1u} \leftarrow {}^1 A_g$ electron optical lines are situated at relatively high energies of ~5.8 eV (214 nm) and ~6.3 eV (197 nm). These two lines originate from two $^1 T_{1u} \leftarrow {}^1 A_g$ transitions: from HOMO to (LUMO+1) ($6h_u \to 3t_{1g}$) and from (HOMO--1) to LUMO ($10h_g \to 7t_{1u}$). The lowest molecular excitation, which is the $1 ^3 T_{2g}$ level, is found at ~2.5 eV. Inclusion of doubly excited determinants (SDCI) leads only to minor corrections to this picture. We discuss possible assignment of absorption bands at energies smaller than 5.8 eV (or $\lambda$ larger than 214 nm).Comment: 6 pages, 1 figure, 9 Table

Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria

Modern medicine relies upon antibiotics, but we have arrived to the point where our inability to come up with new effective molecules against resistant pathogens, together with the declining private investment, is resulting in the number of untreatable infections increasing worldwide at worrying pace. Among other pathogens, widely recognized institutions have indicated Gram-negative bacteria as particularly challenging, due to the presence of the outer membrane. The very first step in the action of every antibiotic or adjuvant is the permeation through this membrane, with small hydrophilic drugs usually crossing through protein channels. Thus, a detailed understanding of their properties at a molecular level is crucial. By making use of Molecular Dynamics simulations, we compared the two main porins of four members of the Enterobacteriaceae family, and, in this paper, we show their shared geometrical and electrostatic characteristics. Then, we used metadynamics simulations to reconstruct the free energy for permeation of selected diazobicyclooctans through OmpF. We demonstrate how porins features are coupled to those of the translocating species, modulating their passive permeation. In particular, we show that the minimal projection area of a molecule is a better descriptor than its molecular mass or the volume. Together with the magnitude and orientation of the electric dipole moment, these are the crucial parameters to gain an efficient compensation between the entropic and enthalpic contributions to the free energy barrier required for permeation. Our results confirm the possibility to predict the permeability of molecules through porins by using a few molecular parameters and bolster the general model according to which the free energy increase is mostly due to the decrease of conformational entropy, and this can be compensated by a favorable alignment of the electric dipole with respect to the channel intrinsic electric field

Electronic and transport properties of rectangular graphene macromolecules and zigzag carbon nanotubes of finite length

We study one dimensional (1D) carbon ribbons with the armchair edges and the zigzag carbon nanotubes and their counterparts with finite length (0D) in the framework of the H\"{u}ckel model. We prove that a 1D carbon ribbon is metallic if its width (the number of carbon rings) is equal to $2+3n$. We show that the dispersion law (electron band energy) of a 1D metallic ribbon or a 1D metallic carbon nanotube has a universal {\it sin-}like dependence at the Fermi energy which is independent of its width. We find that in case of metallic graphene ribbons of finite length (rectangular graphene macromolecules) or nanotubes of finite length the discrete energy spectrum in the vicinity of $\varepsilon=0$ (Fermi energy) can be obtained exactly by selecting levels from the same dispersion law. In case of a semiconducting graphene macromolecule or a semiconducting nanotube of finite length the positions of energy levels around the energy gap can be approximated with a good accuracy. The electron spectrum of 0D carbon structures often include additional states at energy $\varepsilon=0$, which are localized on zigzag edges and do not contribute to the volume conductivity.Comment: 6 pages, 5 figure

Structural analysis of the architecture and in situ localization of the main S-layer complex in Deinococcus radiodurans

Bacterial surface layers are paracrystalline assemblies of proteins that provide the first line of defense against environmental shocks. Here, we report the 3D structure, in situ localization, and orientation of the S-layer deinoxanthin-binding complex (SDBC), a hetero-oligomeric assembly of proteins that in Deinococcus radiodurans represents the main S-layer unit. The SDBC is resolved at 11-Å resolution by single-particle analysis, while its in situ localization is determined by cryo-electron crystallography on intact cell-wall fragments leading to a projection map at 4.5-Å resolution. The SDBC exhibits a triangular base with three comma-shaped pores, and a stalk departing orthogonally from the center of the base and oriented toward the intracellular space. Combining state-of-the-art techniques, results show the organization of this S-layer and its connection within the underlying membranes, demonstrating the potential for applications from nanotechnologies to medicine

Diffusion of molecules through nanopores under confinement: Time-scale bridging and crowding effects via Markov state model

Passive transport of molecules through nanopores is characterized by the interaction of molecules with pore internal walls and by a general crowding effect due to the constricted size of the nanopore itself, which limits the presence of molecules in its interior. The molecule-pore interaction is treated within the diffusion approximation by introducing the potential of mean force and the local diffusion coefficient for a correct statistical description. The crowding effect can be handled within the Markov state model approximation. By combining the two methods, one can deal with complex free energy surfaces taking into account crowding effects. We recapitulate the equations bridging the two models to calculate passive currents assuming a limited occupancy of the nanopore in a wide range of molecular concentrations. Several simple models are analyzed to clarify the consequences of the model. Eventually, a biologically relevant case of transport of an antibiotic molecule through a bacterial porin is used to draw conclusions (i) on the effects of crowding on transport of small molecules through biological channels, and (ii) to demonstrate its importance for modelling of cellular transport

The key role of the central cavity in sodium transport through ligand-gated two-pore channels

none4noSubcellular and organellar mechanisms have manifested a prominent importance for a broad variety of processes that maintain cellular life at its most basic level. Mammalian two-pore channels (TPCs) appear to be cornerstones of these processes in endo-lysosomes by controlling delicate ion-concentrations in their interiors. With evolutionary remarkable architecture and one-of-a-kind selectivity filter, TPCs are an extremely attractive topic per se. In the light of the current COVID-19 pandemic, hTPC2 emerges to be more than attractive. As a key regulator of the endocytosis pathway, it is potentially essential for diverse viral infections in humans, as demonstrated. Here, by means of multiscale molecular simulations, we propose a model of sodium transport from the lumen to the cytosol where the central cavity works as a reservoir. Since the inhibition of hTPC2 is proven to stop SARS-CoV2 in vitro, shedding light on the hTPC2 function and mechanism is the first step towards the selection of potential inhibiting candidates. This journal ismixedMilenkovic S.; Bodrenko I.V.; Carpaneto A.; Ceccarelli M.Milenkovic, S.; Bodrenko, I. V.; Carpaneto, A.; Ceccarelli, M

The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway

We investigated the diffusion of three cyclic boronates formulated as beta-lactamase inhibitors through the porin OmpF to evaluate their potential to cross OM via the porin pathway. The three nonbeta-lactam molecules diffuse through the porin eyelet region with the same mechanism observed for beta-lactam molecules and diazobicyclooctan derivatives, with the electric dipole moment aligned with the transversal electric field. In particular, the BOH group can interact with both the basic ladder and the acidic loop L3, which is characteristic of the size-constricted region of this class of porins. On one hand, we confirm that the transport of small molecules through enterobacter porins has a common general mechanism; on the other, the class of cyclic boronate molecules does not seem to have particular difficulties in diffusing through enterobacter porins, thus representing a good scaffold for new anti-infectives targeting Gram-negative bacteria research