No abstract

Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.

Homologous classes of Polycyclic Aromatic Hydrocarbons (PAHs) in their crystalline state are among the most promising materials for organic opto-electronics. Following previous works on oligoacenes we present a systematic comparative study of the electronic, optical, and transport properties of oligoacenes, phenacenes, circumacenes, and oligorylenes. Using density functional theory (DFT) and timedependent DFT we computed: (i) electron affinities and first ionization energies; (ii) quasiparticle correction to the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap; (iii) molecular reorganization energies; (iv) electronic absorption spectra of neutral and ±1 charged systems. The excitonic effects are estimated by comparing the optical gap and the quasiparticle corrected HOMO-LUMO energy gap. For each molecular property computed, general trends as a function of molecular size and charge state are discussed. Overall, we find that circumacenes have the best transport properties, displaying a steeper decrease of the molecular reorganization energy at increasing sizes, while oligorylenes are much more efficient in absorbing low-energy photons in comparison to the other classes.

Abstract. We computed the absolute photo-absorption cross-sections up to the vacuum ultaviolet (VUV) of a total of 20 Polycyclic Aromatic Hydrocarbons (PAHs) and their respective cations, ranging in size from naphthalene (C 10 H 8 ) to dicoronylene (C 48 H 20 ). We used an implementation in real time and real space of the Time-Dependent Density Functional Theory (TD-DFT), an approach which was proven to yield accurate results for conjugated molecules such as benzene. Concerning the low-lying excited states of π * ← π character occurring in the near-IR, visible and near-UV spectral range, the computed spectra are in good agreement with the available experimental data, predicting vertical excitation energies precise to within a few tenths of eV, and the corresponding oscillator strengths to within experimental errors, which are indeed the typical accuracies currently achievable by TD-DFT. We find that PAH cations, like their parent molecules, display strong π * ← π electronic transitions in the UV, a piece of information which is particularly useful since a limited amount of laboratory data is available concerning the absorption properties of PAH ions in this wavelength range. Moreover, a detailed discussion of the UV-VUV properties of both neutral and cation species is presented. Concerning neutrals, the agreement with existing laboratory data is very good, the specific TD-DFT implementation used in this work apparently being able to reproduce the overall far-UV behaviour, including the broad absorption peak dominated by σ * ← σ transitions, which matches well both in position and width. The implications of these results are discussed in conjunction with the contribution PAH-like molecules are expected to give to the interstellar extinction curve.

We present a systematic theoretical study of the five smallest oligoacenes (naphthalene, anthracene, tetracene, pentacene, and hexacene) in their anionic, neutral, cationic, and dicationic charge states. We used density functional theory (DFT) to obtain the ground-state optimised geometries, and time-dependent DFT (TD-DFT) to evaluate the electronic absorption spectra. Total-energy differences enabled us to evaluate the electron affinities and first and second ionisation energies, the quasiparticle correction to the HOMO-LUMO energy gap and an estimate of the excitonic effects in the neutral molecules. Electronic absorption spectra have been computed by combining two different implementations of TD-DFT: the frequency-space method to study general trends as a function of charge-state and molecular size for the lowest-lying in-plane long-polarised and short-polarised π → π ⋆ electronic transitions, and the real-time propagation scheme to obtain the whole photo-absorption cross-section up to the far-UV. Doubly-ionised PAHs are found to display strong electronic transitions of π → π ⋆ character in the near-IR, visible, and near-UV spectral ranges, like their singly-charged counterparts. While, as expected, the broad plasmon-like structure with its maximum at about 17-18 eV is relatively insensitive to the charge-state of the molecule, a systematic decrease with increasing positive charge of the absorption cross-section between ∼6 and ∼12 eV is observed for each member of the class.

Bacteria use small molecules called siderophores to scavenge iron. Siderophore-Fe 3+ 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 including Pseudomonas species can use it. Here, we show that the Pseudomonas transporter 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.

Context. In the framework of the interstellar PAH hypothesis, far-IR skeletal bands are expected to be a fingerprint of single species in this class. Aims. A detailed model of the photo-physics of interstellar PAHs is required for such single-molecule identification of their far-IR features in the presently available Infrared Space Observatory data and in those of the forthcoming Herschel Space Observatory mission. Methods. We modelled the detailed photophysics of a vast sample of species in different radiation fields, using a compendium of Monte-Carlo techniques and quantum-chemical calculations. This enabled us to validate the use of purely theoretical data and assess the expected accuracy and reliability of the resulting synthetic far-IR emission spectra. Results. We produce positions and intensities of the expected far-IR features that ought to be emitted by each species in the sample in the considered radiation fields. A composite emission spectrum for our sample is computed for one of the most favourable sources for detection, namely the Red Rectangle nebula. The resulting spectrum is compared with the estimated dust emission in the same source to assess the dependence of detectability on key molecular parameters. Conclusions. Identifying specific PAHs from their far-IR features is going to be a difficult feat in general; still, it may well be possible under favourable conditions.

Resistance-Nodulation-cell Division (RND) transporters AcrB and AcrD of Escherichia coli expel a wide range of substrates out of the cell in conjunction with AcrA and TolC, contributing to the onset of bacterial multidrug resistance. Despite sharing an overall sequence identity of ~66% (similarity ~80%), these RND transporters feature distinct substrate specificity patterns whose underlying basis remains elusive. We performed exhaustive comparative analyses of the putative substrate binding pockets considering crystal structures, homology models and conformations extracted from multi-copy μs-long molecular dynamics simulations of both AcrB and AcrD. The impact of physicochemical and topographical properties (volume, shape, lipophilicity, electrostatic potential, hydration and distribution of multi-functional sites) within the pockets on their substrate specificities was quantitatively assessed. Differences in the lipophilic and electrostatic potentials among the pockets were identified. In particular, the deep pocket of AcrB showed the largest lipophilicity convincingly pointing out its possible role as a lipophilicity-based selectivity filter. Furthermore, we identified dynamic features (not inferable from sequence analysis or static structures) such as different flexibilities of specific protein loops that could potentially influence the substrate recognition and transport profile. Our findings can be valuable for drawing structure (dynamics)-activity relationship to be employed in drug design.