1,721,040 research outputs found
Some ligands enhance the efflux of other ligands by the escherichia coli multidrug pump AcrB
No full textBy measuring quantitatively the active efflux of cephalosporins by the RND (resistance-nodulation-division) family efflux pump AcrB in intact cells of Escherichia coli, we found that the simultaneous presence of another substrate, such as chloramphenicol, benzene, cyclohexane, or Arg beta-naphthilamide, significantly enhanced the extrusion of cephalosporins. The stimulation occurred also in a strain expressing the covalently linked trimer of AcrB, and thus cannot be ascribed to the enhanced assembly of the trimer from AcrB monomers. When Va1139 of AcrB was changed into Phe, the stimulation by benzene was found to occur at much lower concentration of the solvent. A plausible explanation of these observations is that the AcrB pump is constructed to pump out very rapidly the solvent or chloramphenicol molecules, and thus the efflux of cephalosporins, which presumably bind to a different subsite within the large binding pocket of AcrB, can become facilitated. Computer simulations of ligand binding to AcrB, both by docking and by molecular dynamics simulations, produced results supporting and extending this hypothesis. Benzene and the cephalosporin nitrocefin can bind simultaneously to the distal binding pocket of AcrB, both in the wild type and in the V139F variant. Interestingly, while the binding position and strength of benzene are almost unaffected by the presence of nitrocefin, this latter substrate is significantly displaced toward the exit gate in both wild type and mutant transporter in the presence of benzene. Additionally, the cephalosporin efflux may be enhanced by the binding of solvents (sometimes to the cephalosporin-free protomer), which could accelerate AcrB conformational changes necessary for substrate extrusion
Molecular simulations of drugs targeting the DNA: Insight into Mechanism, Thermodynamics and Kinetics of Molecular Recognition
No full textIn Silico Prediction of Peptide Self-assembly into Nanostructures
No full textSelf-assembling peptides bear tremendous potential in the fields of material sciences, nanoscience, and medicine. In contrary to the popular building blocks used in supramolecular chemistry, which exploit rigid molecular structures with defined geometry, peptides are highly flexible. This feature renders the prediction of their most stable conformations and self-assembly ability, as well as an understanding of the mechanism behind aggregation, more challenging for experimental techniques. In this context, in silico techniques have progressed at a fast pace to provide highly valuable tools to study, predict, and visualize peptides’ behavior and their dynamics to assist with their design. In this chapter, we will provide an overview of popular computational techniques used to investigate the self-assembly of peptides and peptide-containing molecules. Together with the applications, we will briefly discuss the pros and cons of these methodologies and conclude with a perspective on the future directions that this exciting field can lead to
A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins
No full textMany relevant biological processes take place on time scales not reachable by standard all-atom computer simulations. The translocation of antibiotics through non-specific bacterial porins is an example. Microscopic effects compete to determine penetration routes and, consequently, free energy barriers to be overcome. Since bacteria can develop resistance to treatment also by reducing their antibiotic permeability, to understand the microscopic aspects of antibiotic translocation is an important step to rationalize drug design. Here, to investigate the translocation we propose a complete numerical model that combines the diffusion-controlled rate theory and a kinetic Monte Carlo scheme based on both experimental data and microscopically well-founded all-atom simulations. Within our model, an antibiotic translocating through an hour-glass-shaped channel can be described as a molecule moving on a potential of mean force featuring several affinity sites and a high central barrier. The implications of our results for the characterization of antibiotic translocation at invivo concentrations are discussed. The presence of an affinity site close to the mouth of the channel seems to favor the translocation of antibiotics, the affinity site acting as a particle reservoir. Possible connections between results and the appearance of mutations in clinical strains are also outlined
Molecular Recognition Routes Of DNA By Anticancer Ligands: Mechanisms and Free Energies Explored Via Molecular Dynamics Simulations
No full textMolecular recognition of the DNA minor groove is a multi-route process which can involve many steps before the formation of the most stable adduct. In particular, many studies have pointed out the importance of events like sliding along the groove and dissociation (which is a relevant step in the translocation among different sequences) for the affinity and the specificity of minor groove binders.
In this contribution we present our recent work on the subject. Umbrella sampling and metadynamics were used to characterize mechanisms and free energy profiles of molecular recognition routes by the antitumoral agents anthramycin, duocarmycin and distamycin. Our results are in very good agreement with the available experimental data, and provide insights on the influence of factors like size, charge and flexibility on the molecular recognition process
Meropenem vs. Imipenem interacting with MexB: structural and dynamical determinants of the efflux action on two substrates
No full textActive extrusion of drugs through efflux pumps constitutes
one of the main mechanisms of multidrug resistance in cells.
In recent years, large efforts have been devoted to the biochemical
and structural characterization of RND efflux
pumps in Gram-negative bacteria, in particular the AcrB/ATolC
system of E.Coli. Specific attention has been addressed
to the active part of the efflux system, constituted by the AcrB
unit. Despite the presence of several data, crucial questions
concerning its functioning are still open. The understanding
of the structure-dynamics-function relationship of MexB, the
analogous transporter in P. Aeruginosa, encounters even
more difficulties, because of the lack of structural data of the
transporter in complex with substrates. To shade some light
on the activity of MexB, we performed computational studies
on MexB interacting with two compounds, meropenem and
imipenem, the first known to be a good substrate, and the
second a modest one. Several techniques were used in the
present work, ranging from flexible docking [1] to standard
and targeted molecular dynamics (MD) simulations. Starting
from the published crystal structure [2] we identified the most
probable poses of the two compounds in both the original
experimental and in the MD-equilibrated structures. We used
information from AcrB binding pocket in order to find relevant
binding sites of the two compounds in the analogous binding
pocket of MexB.
Meropenem frequently lies with appropriate orientation in a
pocket similar to the one identified for doxorubicin in AcrB [3],
while the occurrence of imipenem poses in the same pocket
is very scarce. Additionally, when present in the pocket,
imipenem is located in a position that renders very unlikely its
extrusion toward the OprM docking domain during the simulation
of the functional peristalsis. The analysis of the
trajectories has provided a complete inventory of the
transporter and antibiotic hot spots, which is key information
in terms of screening and design of antibiotics and inhibitors.
[1] Zacharias M., Protein Sci 2003, 12, 1271-82.
[2] Sennhauser G., et al., J Mol Biol 2009, 389, 134-145.
[3] Murakami S., et al., Nature 2006, 443, 173-9
Computational study of correlated domain motions in the AcrB efflux transporter
Full text linkAs active part of the major efflux system in E. coli bacteria, AcrB is responsible
for the uptake and pumping of toxic substrates from the periplasm toward the extra-
cellular space. In combination with the channel protein TolC and membrane fusion protein AcrA, this efflux pump is able to help the bacterium to survive different kinds of noxious compounds. With the present study we intend to enhance the understanding of the interactions between the domains and monomers, e.g., the transduction of
mechanical energy from the transmembrane domain into the porter domain, correlated
motions of different subdomains within monomers and cooperative effects between monomers. To this end, targeted molecular dynamics simulations have been employed either steering the whole protein complex or specific parts thereof. By forcing only parts of the complex towards specific conformational states, the risk for transient ar-
tificial conformations during the simulations is reduced. Distinct cooperative effects
between the monomers in AcrB have been observed. Possible allosteric couplings have
been identified providing microscopic insights that might be exploited to design more efficient inhibitors of efflux systems
Erratum: Role of water during the extrusion of substrates by the efflux transporter AcrB (Journal of Physical Chemistry B (2011) 115 (8278-8287) DOI: 10.1021/jp200996x)
No full textRND efflux pumps: structural information translated into function and inhibition mechanisms
No full textEfflux pumps of the Resistance Nodulation Division (RND) superfamily play a major role in the intrinsic and acquired resistance of Gram-negative pathogens to antibiotics. Moreover, they are largely responsible for multi-drug resistance (MDR) phenomena in these bacteria. The last decade has seen a sharp increase in the number of experimental and computational studies aimed at understanding their functional mechanisms. Most of these studies focused on the RND drug/proton antiporter AcrB, part of the AcrAB-TolC efflux pump actively recognizing and expelling noxious agents from the interior of bacteria. These studies have been focused on the dynamical interactions between AcrB and its substrates and inhibitors, on the details of the proton translocation mechanisms, and on the way AcrB assembles with protein partners to build up a functional pump. In this review we summarize these advances focusing on the role of AcrB
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