1,720,980 research outputs found
The Effect of Lipopolysaccharides on the Electrostatic Properties of Gram-Negative General Porins from Enterobacteriaceae
Full text linkWe 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.We analyzed structural and electrostatic properties of the porin OmpK36 within various membrane environments, including the lipopolysaccharide from Klebsiella pneumoniae and Escherichia coli, and a POPC bilayer. Our results reveal distinct influences of the different environments: while the average value of the transversal electric field remains relatively constant, the environments modulate its fluctuations, suggesting a subtle role of the surrounding. imag
Diffusion of molecules through nanopores under confinement: Time-scale bridging and crowding effects via Markov state model
Full text linkPassive 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
Diffusion of large particles through small pores: From entropic to enthalpic transport
Full text linkWe present a statistical model for solving and predicting the transport of large molecules through small flexible channels. The average radius of the channel and the average radius of the molecule are the only two quantities determining the steric part of the potential of mean force for the translocation, in the case of a small rigid particle and a large rigid channel: the barrier is completely entropic and is described by the Fick-Jacobs model. However, the flexibility of the channel's cross section and that of the molecule's size have a significant effect on transport, especially when a large molecule goes through a narrow channel. In this case, the steric barrier changes its statistical nature becoming enthalpic, and we predict a strong temperature enhancement of the diffusion current through the channel. The flexibility is described in terms of the equilibrium fluctuations of the channel and of the molecule. The model is compared with the all-atom MD simulations of the transport of hard spheres of various radii and of drug molecules through a biological nanochannel. For the case of Gaussian fluctuations, we derived a simple analytical expression for the steric barrier, which can be quantified using average size and fluctuations of the channel and of the molecule
The key role of the central cavity in sodium transport through ligand-gated two-pore channels
Full text linkSubcellular 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
The influence of permeability through bacterial porins in whole-cell compound accumulation
Full text linkThe 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
The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway
Full text linkWe 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
Analysis of fast channel blockage: revealing substrate binding in the microsecond range
No full textFor an antibiotic to be effective, it needs to cross the outer membrane barrier and reach the target inside
the cell. Hydrophilic antibiotics, e.g. β-lactams, use porin channels to cross the outer membrane and
accumulate in the periplasm. Experimental determination of antibiotic interactions with porin is performed
by using electrophysiology on a single channel level by noise analysis or single event analysis methods.
We report a novel framework for analyzing the ion-current noise, taking into account the corrections
due to the analogous filter and the sampling procedure, with the goal of extending the time resolution
to a range previously inaccessible by event analysis or by conventional noise analysis. The new method
allows one to analyse fast binding events and/or the case when the single channel is not completely
blocked by the substrate. We demonstrate the power of this approach by using as an example the interactions
of meropenem, an antibiotic of the carbapenem family, with the OmpF porin that is considered
to be one of the main pathways for antibiotics to enter Escherichia coli. The presence of meropenem in
OmpF is detected by ion current blockages, and the on and off rates are estimated from the concentration
dependence of the average ion current and of its power spectral density. The obtained average
residence time of the antibiotic inside the channel is in the range of a few microseconds, i.e. more than
50 times smaller than the inverse cut-off frequency of the analogous filter
Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria
Full text linkModern 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
Machine Learning Prediction of Small Molecule Accumulation in Escherichia Coli Enhanced with Descriptor Statistics
No full textAntibiotic resistance, particularly among Gram-negative bacteria, poses a significant healthcare challenge due to their ability to evade antibiotic action through various mechanisms. In this study, we explore the prediction of small molecule accumulation in Gram-negative bacteria by using machine learning techniques enhanced with statistical descriptors derived from molecular dynamics simulations. We begin by identifying a minimal set of molecular descriptors that maximize the model's predictive power while preserving human interpretability. We optimize model accuracy, precision, and the area under the receiver operating characteristic curve through an iterative process. We demonstrate that the inclusion of statistical descriptors significantly improves model performance across various prediction metrics. Particularly, the addition of statistical descriptors related to dipole moment and minimum projection radius enhances the model's predictive capabilities, shedding light on the physicochemical properties crucial for small molecule accumulation. Our findings highlight the importance of considering statistical moments beyond mean values in predictive modeling and suggest avenues for future research. Overall, our study provides insights into the complex dynamics of antibiotic accumulation in Escherichia coli bacterial cells, generalizable to other Gram-negative species, offering a promising approach for the discovery of effective antibacterial agents, identifying new hits, and improving them to define effective lead agents
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