Matteo Ceccarelli

Altered Antibiotic Transport in Ompc Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. Coli.

Antibiotic-resistant bacteria, particularly Gram negative species, present significant health care challenges. The permeation of antibiotics through the outer membrane is largely effected by the porin superfamily, changes in which contribute to antibiotic resistance. A series of antibiotic resistant E. coli isolates were obtained from a patient during serial treatment with various antibiotics. The sequence of OmpC changed at three positions during treatment giving rise to a total of four OmpC variants (denoted OmpC20, OmpC26, OmpC28 and OmpC33, in which OmpC20 was derived from the first clinical isolate). We demonstrate that expression of the OmpC K12 porin in the clinical isolates lowers the MIC, consistent with modified porin function contributing to drug resistance. By a range of assays we have established that the three mutations that occur between OmpC20 and OmpC33 modify transport of both small molecules and antibiotics across the outer membrane. This results in the modulation of resistance to antibiotics, particularly cefotaxime. Small ion unitary conductance measurements of the isolated porins do not show significant differences between isolates. Thus, resistance does not appear to arise from major changes in pore size. Crystal structures of all four OmpC clinical mutants and molecular dynamics simulations also show that the pore size is essentially unchanged. Molecular dynamics simulations suggest that perturbation of the transverse electrostatic field at the constriction zone reduces cefotaxime passage through the pore, consistent with laboratory and clinical data. This subtle modification of the transverse electric field is a very different source of resistance than occlusion of the pore or wholesale destruction of the transverse field and points to a new mechanism by which porins may modulate antibiotic passage through the outer membrane.

Molecular basis of enrofloxacin translocation through OmpF, an outer membrane channel of Escherichia coli--when binding does not imply translocation.

The molecular pathway of enrofloxacin, a fluoroquinolone antibiotic, through the outer membrane channel OmpF of Escherichia coli is investigated. High-resolution ion current fluctuation analysis reveals a strong affinity for enrofloxacin to OmpF, the highest value ever recorded for an antibiotic-channel interaction. A single point mutation in the constriction zone of OmpF, replacing aspartic acid at the 113 position with asparagine (D113N), lowers the affinity to a level comparable to other antibiotics. All-atom molecular dynamics simulations allow rationalizing the translocation pathways: wild-type OmpF has two symmetric binding sites for enrofloxacin located at each channel entry separated by a large energy barrier in the center, which inhibits antibiotic translocation. In this particular case, our simulations suggest that the ion current blockages are caused by molecules occupying either one of these peripheral binding sites. Removal of the negative charge on position 113 removes the central barrier and shifts the two peripheral binding sites to a unique central site, which facilitates translocation. Fluorescence steady-state measurements agree with the different location of binding sites for wild-type OmpF and the mutant. Our results demonstrate how a single-point mutation of the porin, and the resulting intrachannel shift of the affinity site, may substantially modify translocation.

A concerted variational strategy for investigating rare events

A strategy for finding transition paths connecting two stable basins is presented. The starting point is the Hamilton principle of stationary action; we show how it can be transformed into a minimum principle through the addition of suitable constraints like energy conservation. Methods for improving the quality of the paths are presented: for example, the Maupertuis principle can be used for determining the transition time of the trajectory and for coming closer to the desired dynamic path. A saddle point algorithm (conjugate residual method) is shown to be efficient for reaching a “true” solution of the original variational problem.

CO escape from myoglobin with metadynamics simulations

The relatively small size of myoglobin makes it suitable for the investigation of the ligand escape process in respiratory proteins and, in general, an ideal model system for the study of the more general structure‐function paradigm. In this work, we use Molecular Dynamics simulations combined with an accelerated algorithm, the metadynamics, to probe the escape of CO from myoglobin. Our approach permits to quantitatively describe the escape process via the reconstruction of the associated free energy surface. Additionally, hints on the involvement of a larger numbers of residues than hitherto assumed in the gating process are extracted from our data. Proteins 2008.

Molecular Simulations Reveal the Mechanism and the Determinants for Ampicillin Translocation through OmpF

We use a multiscale approach, combining molecular dynamics simulations with metadynamics, to simulate the translocation of ampicillin through OmpF from Escherichia coli (E. coli). In-depth analysis has allowed us to reveal the complete picture of the translocation process in terms of both energetics and physicochemical properties. We have demonstrated the existence of a unique affinity site at the constriction region, accessible from both sides and defined by specific pore-antibiotic interactions. By providing optimal binding, the constriction region works like an enzyme toward the permeation of ampicillin. We find reduction in entropy to be compensated by enthalpic contributions from a favorable network of interactions (hydrogen bonds and hydrophobic contacts) which is also mediated by two slow water molecules bridging the antibiotic-pore interactions. Finally, as ampicillin assumes a preferential value for a torsional angle when at the constriction region, we investigated the consequence of the conformational preorganization of ampicillin toward its translocation. As a whole, our analysis opens the way to chemical modifications of antibiotics to allow improving uptake through porins contributing to combat bacterial resistance.

Toward Screening for Antibiotics with Enhanced Permeation Properties through Bacterial Porins

Gram-negative bacteria are protected by an outer membrane barrier, and to reach their periplasmic target, penicillins have to diffuse through outer membrane porins such as OmpF. Here we propose a structure-dynamics-based strategy for improving such antibiotic uptake. Using a variety of experiments (high-resolution single channel recording, Minimum Inhibitory Concentration (MIC), liposome swelling assay) and accelerated molecular simulations, we decipher the subtle balance of interactions governing ampicillin diffusion through the porin OmpF. This suggests mutagenesis of a hot spot residue of OmpF for which additional simulations reveal drastic changes in the molecular and energetic pathway of ampicillins diffusion. Inverting the problem, we predict and describe how benzylpenicillin diffuses with a lower effective energy barrier by interacting differently with OmpF. The thorough comparison between the theoretical predictions and the three independent experiments, which were set up to measure the kinetics of transport and biological activity, gives insights on how to combine such different investigation techniques with the aim of providing complementary validation. Our study illustrates the importance of microscopic interactions at the constriction region of the biological channel to control the antibiotic flux through it. We conclude by providing a complete inventory of the channel and antibiotic hot spots and discuss the implications in terms of antibacterial screening and design.

Antibiotic Permeation across the OmpF Channel: Modulation of the Affinity Site in the Presence of Magnesium

We characterize the rate-limiting interaction of the antibiotic enrofloxacin with OmpF, a channel from the outer cell wall of Escherichia coli . Reconstitution of a single OmpF trimer into planar lipid membranes allows measurement of the ion current through the channel. Penetration of antibiotics causes ion current blockages, and their frequency allows a conclusion on the kinetics of channel entry and exit. In contrast to other antibiotics, enrofloxacin is able to block the OmpF channel for several milliseconds, reflecting high affinities comparable to substrate-specific channels such as the maltodextrin-specific maltoporin. Surprisingly, the presence of a divalent ion such as Mg(2+) leads to fast flickering with an increase in the rates of association and dissociation. All-atom computer modeling provides the most probable pathway able to identify the relevant rate-limiting interaction during antibiotic permeation. Mg(2+) has a high affinity for the aspartic acid at the 113 position (D113) in the center of the OmpF intracellular binding site. Therefore, the presence of Mg(2+) reverses the charge and enrofloxacin may cross the constriction region in its favorable orientation with the carboxylic group first.

Implication of Porins in β-Lactam Resistance of Providencia stuartii

An integrative approach combining biophysical and microbiological methods was used to characterize the antibiotic translocation through the outer membrane of Providencia stuartii. Two novel members of the General Bacterial Porin family of Enterobacteriaceae, named OmpPst1 and OmpPst2, were identified in P. stuartii. In the presence of ertapenem (ERT), cefepime (FEP), and cefoxitin (FOX) in growth media, several resistant derivatives of P. stuartii ATCC 29914 showed OmpPst1-deficiency. These porin-deficient strains showed significant decrease of susceptibility to β-lactam antibiotics. OmpPst1 and OmpPst2 were purified to homogeneity and reconstituted into planar lipid bilayers to study their biophysical characteristics and their interactions with β-lactam molecules. Determination of β-lactam translocation through OmpPst1 and OmpPst2 indicated that the strength of interaction decreased in the order of ertapenem ≫ cefepime > cefoxitin. Moreover, the translocation of these antibiotics through OmpPst1 was more efficient than through OmpPst2. Heterologous expression of OmpPst1 in the porin-deficient E. coli strain BL21(DE3)omp8 was associated with a higher antibiotic susceptibility of the E. coli cells to β-lactams compared with expression of OmpPst2. All our data enlighten the involvement of porins in the resistance of P. stuartii to β-lactam antibiotics.

Physical insights into permeation of and resistance to antibiotics in bacteria.

Bacteria can resist antibiotics simply by hindering physical access to the interior, where in general antibiotic targets are located. Gram-negative bacteria, protected by the outer membrane, possess in the latter several porins that act as a gate for the exchange of small hydrophilic molecules. These porins are water-filled membrane-protein channels that are considered to be the main pathway for different class of antibiotics, such as beta-lactams and fluoroquinolones. Bacterial strains resistant to antibiotics can either decrease the density of porins expressed in the outer membrane or decrease the porin internal size by mutating a few amino acids. In both cases, understanding how antibiotics diffuse through bacterial porins can help the design of new antibiotics that have better penetrating power. A considerable contribution can be offered by molecular dynamics simulations since reliability of force fields, computer power, and algorithms have considerably increased the predictive power thereof. Large systems, as pores inserted in a membrane, and long simulation runs are now feasible, and the time scale can be even extended via the use of accelerated techniques, such as metadynamics, and combined strategies. The details of interactions and processes, extracted from the simulations, complement experimental findings and also deepen aspects not accessible to experiments. In this paper we will review the results obtained by our group on this topic with a particular focus on possible general criteria that can guide the rational design of new antibacterial compounds.

The Gating Mechanism of the Human Aquaporin 5 Revealed by Molecular Dynamics Simulations

Aquaporins are protein channels located across the cell membrane with the role of conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high-resolution X-ray structure of the human aquaporin 5 (HsAQP5) shows that HsAQP5, as all the other known aquaporins, exhibits tetrameric structure. By means of molecular dynamics simulations we analyzed the role of spontaneous fluctuations on the structural behavior of the human AQP5. We found that different conformations within the tetramer lead to a distribution of monomeric channel structures, which can be characterized as open or closed. The switch between the two states of a channel is a tap-like mechanism at the cytoplasmic end which regulates the water passage through the pore. The channel is closed by a translation of the His67 residue inside the pore. Moreover, water permeation rate calculations revealed that the selectivity filter, located at the other end of the channel, regulates the flow rate of water molecules when the channel is open, by locally modifying the orientation of His173. Furthermore, the calculated permeation rates of a fully open channel are in good agreement with the reported experimental value.