1
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Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
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Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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2
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Bellotto O, Scarel E, Pierri G, Rozhin P, Kralj S, Polentarutti M, Bandiera A, Rossi B, Vargiu AV, Tedesco C, Marchesan S. Supramolecular Hydrogels and Water Channels of Differing Diameters from Dipeptide Isomers. Biomacromolecules 2024; 25:2476-2485. [PMID: 38551400 DOI: 10.1021/acs.biomac.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Dipeptides stereoisomers and regioisomers composed of norleucine (Nle) and phenylalanine (Phe) self-assemble into hydrogels under physiological conditions that are suitable for cell culture. The supramolecular behavior, however, differs as the packing modes comprise amphipathic layers or water channels, whose diameter is defined by either four or six dipeptide molecules. A variety of spectroscopy, microscopy, and synchrotron-radiation-based techniques unveil fine details of intermolecular interactions that pinpoint the relationship between the chemical structure and ability to form supramolecular architectures that define soft biomaterials.
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Affiliation(s)
- Ottavia Bellotto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Erica Scarel
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Giovanni Pierri
- Department Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Petr Rozhin
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Slavko Kralj
- Department Materials Synthesis, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Department Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | | | - Antonella Bandiera
- Department Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy
| | - Attilio V Vargiu
- Department Physics, University of Cagliari, Cittadella Universitaria S.P. 8 km. 0.7, 09042 Monserrato, CA Italy
| | - Consiglia Tedesco
- Department Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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3
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Adorinni S, Gentile S, Bellotto O, Kralj S, Parisi E, Cringoli MC, Deganutti C, Malloci G, Piccirilli F, Pengo P, Vaccari L, Geremia S, Vargiu AV, De Zorzi R, Marchesan S. Peptide Stereochemistry Effects from p Ka-Shift to Gold Nanoparticle Templating in a Supramolecular Hydrogel. ACS Nano 2024; 18:3011-3022. [PMID: 38235673 DOI: 10.1021/acsnano.3c08004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The divergent supramolecular behavior of a series of tripeptide stereoisomers was elucidated through spectroscopic, microscopic, crystallographic, and computational techniques. Only two epimers were able to effectively self-organize into amphipathic structures, leading to supramolecular hydrogels or crystals, respectively. Despite the similarity between the two peptides' turn conformations, stereoconfiguration led to different abilities to engage in intramolecular hydrogen bonding. Self-assembly further shifted the pKa value of the C-terminal side chain. As a result, across the pH range 4-6, only one epimer predominated sufficiently as a zwitterion to reach the critical molar fraction, allowing gelation. By contrast, the differing pKa values and higher dipole moment of the other epimer favored crystallization. The four stereoisomers were further tested for gold nanoparticle (AuNP) formation, with the supramolecular hydrogel being the key to control and stabilize AuNPs, yielding a nanocomposite that catalyzed the photodegradation of a dye. Importantly, the AuNP formation occurred without the use of reductants other than the peptide, and the redox chemistry was investigated by LC-MS, NMR, and infrared scattering-type near field optical microscopy (IR s-SNOM). This study provides important insights for the rational design of simple peptides as minimalistic and green building blocks for functional nanocomposites.
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Affiliation(s)
- Simone Adorinni
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Serena Gentile
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Ottavia Bellotto
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Evelina Parisi
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Maria C Cringoli
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Caterina Deganutti
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Giuliano Malloci
- Physics Department, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Federica Piccirilli
- Elettra Sincrotrone Trieste, 34149 Basovizza, Italy
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Paolo Pengo
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Lisa Vaccari
- Elettra Sincrotrone Trieste, 34149 Basovizza, Italy
| | - Silvano Geremia
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Attilio V Vargiu
- Physics Department, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Rita De Zorzi
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Silvia Marchesan
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
- Unit of Trieste, INSTM, 34127 Trieste, Italy
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4
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Gervasoni S, Mehla J, Bergen CR, Leus IV, Margiotta E, Malloci G, Bosin A, Vargiu AV, Lomovskaya O, Rybenkov VV, Ruggerone P, Zgurskaya HI. Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump. mBio 2023; 14:e0140323. [PMID: 37493633 PMCID: PMC10470492 DOI: 10.1128/mbio.01403-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/27/2023] Open
Abstract
Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump of Pseudomonas aeruginosa is MexAB-OprM, in which the inner membrane transporter MexB is responsible for the recognition and binding of compounds. The high importance of this pump in clinical antibiotic resistance made it a subject of intense investigations and a promising target for the discovery of efflux pump inhibitors. This study is focused on a series of peptidomimetic compounds developed as effective inhibitors of MexAB-OprM. We performed multi-copy molecular dynamics simulations, machine-learning (ML) analyses, and site-directed mutagenesis of MexB to investigate interactions of MexB with representatives of efflux avoiders, substrates, and inhibitors. The analysis of both direct and water-mediated protein-ligand interactions revealed characteristic patterns for each class, highlighting significant differences between them. We found that efflux avoiders poorly interact with the access binding site of MexB, and inhibition engages amino acid residues that are not directly involved in binding and transport of substrates. In agreement, machine-learning models selected different residues predictive of MexB substrates and inhibitors. The differences in interactions were further validated by site-directed mutagenesis. We conclude that the substrate translocation and inhibition pathways of MexB split at the interface (between the main putative binding sites) and at the deep binding pocket and that interactions outside of the hydrophobic patch contribute to the inhibition of MexB. This molecular-level information could help in the rational design of new inhibitors and antibiotics less susceptible to the efflux mechanism. IMPORTANCE Multidrug transporters recognize and expel from cells a broad range of ligands including their own inhibitors. The difference between the substrate translocation and inhibition routes remains unclear. In this study, machine learning and computational and experimental approaches were used to understand dynamics of MexB interactions with its ligands. Our results show that some ligands engage a certain combination of polar and charged residues in MexB binding sites to be effectively expelled into the exit funnel, whereas others engage aromatic and hydrophobic residues that slow down or hinder the next step in the transporter cycle. These findings suggest that all MexB ligands fit into this substrate-inhibitor spectrum depending on their physico-chemical structures and properties.
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Affiliation(s)
- Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Charles R. Bergen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Enrico Margiotta
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Andrea Bosin
- Department of Physics, University of Cagliari, Monserrato, Italy
| | | | | | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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5
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Trampari E, Prischi F, Vargiu AV, Abi-Assaf J, Bavro VN, Webber MA. Functionally distinct mutations within AcrB underpin antibiotic resistance in different lifestyles. NPJ Antimicrob Resist 2023; 1:2. [PMID: 38686215 PMCID: PMC11057200 DOI: 10.1038/s44259-023-00001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2024]
Abstract
Antibiotic resistance is a pressing healthcare challenge and is mediated by various mechanisms, including the active export of drugs via multidrug efflux systems, which prevent drug accumulation within the cell. Here, we studied how Salmonella evolved resistance to two key antibiotics, cefotaxime and azithromycin, when grown planktonically or as a biofilm. Resistance to both drugs emerged in both conditions and was associated with different substitutions within the efflux-associated transporter, AcrB. Azithromycin exposure selected for an R717L substitution, while cefotaxime for Q176K. Additional mutations in ramR or envZ accumulated concurrently with the R717L or Q176K substitutions respectively, resulting in clinical resistance to the selective antibiotics and cross-resistance to other drugs. Structural, genetic, and phenotypic analysis showed the two AcrB substitutions confer their benefits in profoundly different ways. R717L reduces steric barriers associated with transit through the substrate channel 2 of AcrB. Q176K increases binding energy for cefotaxime, improving recognition in the distal binding pocket, resulting in increased efflux efficiency. Finally, we show the R717 substitution is present in isolates recovered around the world.
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Affiliation(s)
- Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, S. P. 8, km. 0.700, 09042 Monserrato, Italy
| | - Justin Abi-Assaf
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
- Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7UA UK
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6
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Gervasoni S, Malloci G, Bosin A, Vargiu AV, Zgurskaya HI, Ruggerone P. Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of Pseudomonas aeruginosa. Phys Chem Chem Phys 2022; 24:16566-16575. [PMID: 35766032 PMCID: PMC9278589 DOI: 10.1039/d2cp00951j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The drug/proton antiporter MexB is the engine of the major efflux pump MexAB-OprM in Pseudomonas aeruginosa. This protein is known to transport a large variety of compounds, including antibiotics, thus conferring a multi-drug resistance phenotype. Due to the difficulty of producing co-crystals, only two X-ray structures of MexB in a complex with ligands are available to date, and mechanistic aspects are largely hypothesized based on the body of data collected for the homologous protein AcrB of Escherichia coli. In particular, a recent study (Ornik-Cha, Wilhelm, Kobylka et al., Nat. Commun., 2021, 12, 6919) reported a co-crystal structure of AcrB in a complex with levofloxacin, an antibiotic belonging to the important class of (fluoro)-quinolones. In this work, we performed a systematic ensemble docking campaign coupled to the cluster analysis and molecular-mechanics optimization of docking poses to study the interaction between 36 quinolone antibiotics and MexB. We additionally investigated surface complementarity between each molecule and the transporter and thoroughly assessed the computational protocol adopted against the known experimental data. Our study reveals different binding preferences of the investigated compounds towards the sub-sites of the large deep binding pocket of MexB, supporting the hypothesis that MexB substrates oscillate between different binding modes with similar affinity. Interestingly, small changes in the molecular structure translate into significant differences in MexB–quinolone interactions. All the predicted binding modes are available for download and visualization at the following link: https://www.dsf.unica.it/dock/mexb/quinolones. Putative binding modes (BMs) of quinolones to the bacterial efflux transporter MexB were identified. Multiple interaction patterns are possible, supporting the hypothesis that substrates oscillate between different BMs with similar affinity.![]()
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Affiliation(s)
- Silvia Gervasoni
- Department of Physics, University of Cagliari, Citt. Universitaria, I-09042 Monserrato (Cagliari), Italy.
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Citt. Universitaria, I-09042 Monserrato (Cagliari), Italy.
| | - Andrea Bosin
- Department of Physics, University of Cagliari, Citt. Universitaria, I-09042 Monserrato (Cagliari), Italy.
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Citt. Universitaria, I-09042 Monserrato (Cagliari), Italy.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Citt. Universitaria, I-09042 Monserrato (Cagliari), Italy.
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7
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Gervasoni S, Malloci G, Bosin A, Vargiu AV, Zgurskaya HI, Ruggerone P. AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials. Sci Data 2022; 9:148. [PMID: 35365662 PMCID: PMC8976083 DOI: 10.1038/s41597-022-01261-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is a major threat to public health. The development of chemo-informatic tools to guide medicinal chemistry campaigns in the efficint design of antibacterial libraries is urgently needed. We present AB-DB, an open database of all-atom force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and curated physico-chemical descriptors of antimicrobial compounds. We considered more than 300 molecules belonging to 25 families that include the most relevant antibiotic classes in clinical use, such as β-lactams and (fluoro)quinolones, as well as inhibitors of key bacterial proteins. We provide traditional descriptors together with properties obtained with Density Functional Theory calculations. Noteworthy, AB-DB contains less conventional descriptors extracted from μs-long molecular dynamics simulations in explicit solvent. In addition, for each compound we make available force-field parameters for the major micro-species at physiological pH. With the rise of multi-drug-resistant pathogens and the consequent need for novel antibiotics, inhibitors, and drug re-purposing strategies, curated databases containing reliable and not straightforward properties facilitate the integration of data mining and statistics into the discovery of new antimicrobials. Measurement(s) | molecular physical property analysis objective | Technology Type(s) | Computer Modeling |
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Affiliation(s)
- Silvia Gervasoni
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
| | - Giuliano Malloci
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy.
| | - Andrea Bosin
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
| | - Attilio V Vargiu
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, OK, 73072, United States
| | - Paolo Ruggerone
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
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8
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Scarel E, Bellotto O, Rozhin P, Kralj S, Tortora M, Vargiu AV, De Zorzi R, Rossi B, Marchesan S. Single-atom substitution enables supramolecular diversity from dipeptide building blocks. Soft Matter 2022; 18:2129-2136. [PMID: 35179536 DOI: 10.1039/d1sm01824h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dipeptides are popular building blocks for supramolecular gels that do not persist in the environment and may find various applications. In this work, we show that a simple substitution on the aromatic side-chain of phenylalanine with either fluorine or iodine enables supramolecular diversity upon self-assembly at neutral pH, leading to hydrogels or crystals. Each building block is characterized by 1H- and 13C-NMR spectroscopy, LC-MS, circular dichroism, and molecular models. The supramolecular behaviour is monitored with a variety of techniques, including circular dichroism, oscillatory rheology, transmission electron microscopy, attenuated total reflectance Fourier-transformed infrared spectroscopy, visible Raman spectroscopy, synchrotron-radiation single-crystal X-ray diffraction and UV Resonance Raman spectroscopy, allowing key differences to be pinpointed amongst the halogenated analogues.
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Affiliation(s)
- Erica Scarel
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Petr Rozhin
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Slavko Kralj
- Jožef Stefan Institute, Materials Synthesis Dept., Jamova 39, 1000 Ljubljana, Slovenia
- University of Ljubljana, Pharmaceutical Technology Dept., Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Mariagrazia Tortora
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy.
| | - Attilio V Vargiu
- University of Cagliari, Physics Dept., 09042 Monserrato, Cagliari, Italy
| | - Rita De Zorzi
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy.
| | - Silvia Marchesan
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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9
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Garofalo B, Bonvin AM, Bosin A, Di Giorgio FP, Ombrato R, Vargiu AV. Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine. Front Mol Biosci 2022; 9:839249. [PMID: 35309507 PMCID: PMC8927717 DOI: 10.3389/fmolb.2022.839249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/11/2022] [Indexed: 01/29/2023] Open
Abstract
Voltage-gated potassium channels of the Kv7.x family are involved in a plethora of biological processes across many tissues in animals, and their misfunctioning could lead to several pathologies ranging from diseases caused by neuronal hyperexcitability, such as epilepsy, or traumatic injuries and painful diabetic neuropathy to autoimmune disorders. Among the members of this family, the Kv7.2 channel can form hetero-tetramers together with Kv7.3, forming the so-called M-channels, which are primary regulators of intrinsic electrical properties of neurons and of their responsiveness to synaptic inputs. Here, prompted by the similarity between the M-current and that in Kv7.2 alone, we perform a computational-based characterization of this channel in its different conformational states and in complex with the modulator retigabine. After validation of the structural models of the channel by comparison with experimental data, we investigate the effect of retigabine binding on the two extreme states of Kv7.2 (resting-closed and activated-open). Our results suggest that binding, so far structurally characterized only in the intermediate activated-closed state, is possible also in the other two functional states. Moreover, we show that some effects of this binding, such as increased flexibility of voltage sensing domains and propensity of the pore for open conformations, are virtually independent on the conformational state of the protein. Overall, our results provide new structural and dynamic insights into the functioning and the modulation of Kv7.2 and related channels.
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Affiliation(s)
| | - Alexandre M.J.J. Bonvin
- Faculty of Science—Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Andrea Bosin
- Department of Physics, University of Cagliari, Cagliari, Italy
| | | | - Rosella Ombrato
- Angelini Pharma S.p.A., Rome, Italy
- *Correspondence: Rosella Ombrato, ; Attilio V. Vargiu,
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, Cagliari, Italy
- *Correspondence: Rosella Ombrato, ; Attilio V. Vargiu,
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10
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Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Comput Struct Biotechnol J 2022; 20:252-260. [PMID: 35024097 PMCID: PMC8717590 DOI: 10.1016/j.csbj.2021.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Efflux pumps of the Resistance-Nodulation-cell Division (RND) superfamily contribute to intrinsic and acquired resistance in Gram-negative pathogens by expelling chemically unrelated antibiotics with high efficiency. They are tripartite systems constituted by an inner-membrane-anchored transporter, an outer membrane factor protein, and a membrane fusion protein. Multimerization of the membrane fusion protein is an essential prerequisite for full functionality of these efflux pumps. In this work, we employed complementary computational techniques to investigate the stability of a dimeric unit of MexA (the membrane fusion protein of the MexAB-OprM RND efflux pump of Pseudomonas aeruginosa), and to provide a molecular rationale for the effect of the G72S substitution, which affects MexAB-OprM functionality by impairing the assembly of MexA. Our findings indicate that: i) dimers of this protein are stable in multiple µs-long molecular dynamics simulations; ii) the mutation drastically alters the conformational equilibrium of MexA, favouring a collapsed conformation that is unlikely to form dimers or higher order assemblies. Unveiling the mechanistic aspects underlying large conformational distortions induced by minor sequence changes is informative to efforts at interfering with the activity of this elusive bacterial weapon. In this respect, our work further confirms how molecular simulations can give important contribution and useful insights to characterize the mechanism of highly complex biological systems.
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Affiliation(s)
- Pierpaolo Cacciotto
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Andrea Basciu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesco Oliva
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Martin Zacharias
- Physics Department, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
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11
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. Virtual Screening and Drug Docking 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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D’Cunha N, Moniruzzaman M, Haynes K, Malloci G, Cooper CJ, Margiotta E, Vargiu AV, Uddin MR, Leus IV, Cao F, Parks JM, Rybenkov VV, Ruggerone P, Zgurskaya HI, Walker JK. Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides. ACS Infect Dis 2021; 7:2650-2665. [PMID: 34379382 DOI: 10.1021/acsinfecdis.1c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB-TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.
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Affiliation(s)
- Napoleon D’Cunha
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Keith Haynes
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Enrico Margiotta
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Muhammad R. Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Feng Cao
- John Cochran Division, Department of Veteran Affairs Medical Center, St. Louis, Missouri 63106, United States
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - John K. Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
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13
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Zgurskaya HI, Malloci G, Chandar B, Vargiu AV, Ruggerone P. Bacterial efflux transporters' polyspecificity - a gift and a curse? Curr Opin Microbiol 2021; 61:115-123. [PMID: 33940284 DOI: 10.1016/j.mib.2021.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/24/2022]
Abstract
All mechanisms of clinical antibiotic resistance benefit from activities of polyspecific efflux pumps acting to reduce intracellular accumulation of toxins and antibiotics. In Gram-negative bacteria, the major polyspecific efflux transporters belong to the Resistance-Nodulation-cell Division (RND) superfamily of proteins, which are capable of expelling thousands of structurally diverse compounds. Recent structural and functional advances generated novel insights into mechanisms underlying the biochemical versatility of RND transporters. This opinion article reviews these mechanisms and discusses implications of the polyspecificity of RND transporters for bacterial survival and for the development of efflux pump inhibitors effective in clinics.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, United States.
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042 Monserrato (Cagliari), Italy
| | - Brinda Chandar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, United States
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, 09042 Monserrato (Cagliari), Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042 Monserrato (Cagliari), Italy
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14
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Garcia AM, Melchionna M, Bellotto O, Kralj S, Semeraro S, Parisi E, Iglesias D, D’Andrea P, De Zorzi R, Vargiu AV, Marchesan S. Nanoscale Assembly of Functional Peptides with Divergent Programming Elements. ACS Nano 2021; 15:3015-3025. [PMID: 33576622 PMCID: PMC8023796 DOI: 10.1021/acsnano.0c09386] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Self-assembling peptides are being applied both in the biomedical area and as building blocks in nanotechnology. Their applications are closely linked to their modes of self-assembly, which determine the functional nanostructures that they form. This work brings together two structural elements that direct nanoscale self-association in divergent directions: proline as a β-breaker and the β-structure-associated diphenylalanine motif, into a single tripeptide sequence. Amino acid chirality was found to resolve the tension inherent to these conflicting self-assembly instructions. Stereoconfiguration determined the ability of each of the eight possible Pro-Phe-Phe stereoisomers to self-associate into diverse nanostructures, including nanoparticles, nanotapes, or fibrils, which yielded hydrogels with gel-to-sol transition at a physiologically relevant temperature. Three single-crystal structures and all-atom molecular dynamics simulations elucidated the ability of each peptide to establish key interactions to form long-range assemblies (i,e., stacks leading to gelling fibrils), medium-range assemblies (i.e., stacks yielding nanotapes), or short-range assemblies (i.e., dimers or trimers that further associated into nanoparticles). Importantly, diphenylalanine is known to serve as a binding site for pathological amyloids, potentially allowing these heterochiral systems to influence the fibrillization of other biologically relevant peptides. To probe this hypothesis, all eight Pro-Phe-Phe stereoisomers were tested in vitro on the Alzheimer's disease-associated Aβ(1-42) peptide. Indeed, one nonfibril-forming stereoisomer effectively inhibited Aβ fibrillization through multivalent binding between diphenylalanine motifs. This work thus defined heterochirality as a useful feature to strategically develop future therapeutics to interfere with pathological processes, with the additional value of resistance to protease-mediated degradation and biocompatibility.
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Affiliation(s)
- Ana M. Garcia
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Michele Melchionna
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- INSTM, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Ottavia Bellotto
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Slavko Kralj
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- Materials
Synthesis Department, Jožef Stefan
Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sabrina Semeraro
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Evelina Parisi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Daniel Iglesias
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Paola D’Andrea
- Life
Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Attilio V. Vargiu
- Physics
Department, University of Cagliari, S.P. 8, km. 0.700, 09042 Monserrato, Italy
| | - Silvia Marchesan
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- INSTM, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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15
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Basciu A, Vargiu AV, Malloci G, Ruggerone P, Bonvin AM. In Silico Generation of Holo-Like Conformations of Very Flexible Allosteric Proteins Bearing Multiple Binding Sites. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Kralj S, Bellotto O, Parisi E, Garcia AM, Iglesias D, Semeraro S, Deganutti C, D’Andrea P, Vargiu AV, Geremia S, De Zorzi R, Marchesan S. Heterochirality and Halogenation Control Phe-Phe Hierarchical Assembly. ACS Nano 2020; 14:16951-16961. [PMID: 33175503 PMCID: PMC7872421 DOI: 10.1021/acsnano.0c06041] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/30/2020] [Indexed: 05/05/2023]
Abstract
Diphenylalanine is an amyloidogenic building block that can form a versatile array of supramolecular materials. Its shortcomings, however, include the uncontrolled hierarchical assembly into microtubes of heterogeneous size distribution and well-known cytotoxicity. This study rationalized heterochirality as a successful strategy to address both of these pitfalls and it provided an unprotected heterochiral dipeptide that self-organized into a homogeneous and optically clear hydrogel with excellent ability to sustain fibroblast cell proliferation and viability. Substitution of one l-amino acid with its d-enantiomer preserved the ability of the dipeptide to self-organize into nanotubes, as shown by single-crystal XRD analysis, whereby the pattern of electrostatic and hydrogen bonding interactions of the backbone was unaltered. The effect of heterochirality was manifested in subtle changes in the positioning of the aromatic side chains, which resulted in weaker intermolecular interactions between nanotubes. As a result, d-Phe-l-Phe self-organized into homogeneous nanofibrils with a diameter of 4 nm, corresponding to two layers of peptides around a water channel, and yielded a transparent hydrogel. In contrast with homochiral Phe-Phe stereoisomer, it formed stable hydrogels thermoreversibly. d-Phe-l-Phe displayed no amyloid toxicity in cell cultures with fibroblast cells proliferating in high numbers and viability on this biomaterial, marking it as a preferred substrate over tissue-culture plastic. Halogenation also enabled the tailoring of d-Phe-l-Phe self-organization. Fluorination allowed analogous supramolecular packing as confirmed by XRD, thus nanotube formation, and gave intermediate levels of bundling. In contrast, iodination was the most effective strategy to augment the stability of the resulting hydrogel, although at the expense of optical transparency and biocompatibility. Interestingly, iodine presence hindered the supramolecular packing into nanotubes, resulting instead into amphipathic layers of stacked peptides without the occurrence of halogen bonding. By unravelling fine details to control these materials at the meso- and macro-scale, this study significantly advanced our understanding of these systems.
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Affiliation(s)
- Slavko Kralj
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- Materials
Synthesis Department, Jožef Stefan
Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Ottavia Bellotto
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Evelina Parisi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Ana M. Garcia
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Daniel Iglesias
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Sabrina Semeraro
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Caterina Deganutti
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Paola D’Andrea
- Life
Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Attilio V. Vargiu
- Physics
Department, University of Cagliari, s.p. 8, km. 0.700, 09042 Monserrato, Italy
| | - Silvano Geremia
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Silvia Marchesan
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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17
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Johnson RM, Fais C, Parmar M, Cheruvara H, Marshall RL, Hesketh SJ, Feasey MC, Ruggerone P, Vargiu AV, Postis VLG, Muench SP, Bavro VN. Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella. Microorganisms 2020; 8:E943. [PMID: 32585951 PMCID: PMC7355581 DOI: 10.3390/microorganisms8060943] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.
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Affiliation(s)
- Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Chiara Fais
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds LS1 3HE, UK; (M.P.); (V.L.G.P.)
| | - Harish Cheruvara
- Diamond Light Source, Membrane Protein Laboratory (MPL), Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK;
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Sophie J. Hesketh
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Matthew C. Feasey
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato, Italy; (C.F.); (P.R.); (A.V.V.)
| | - Vincent L. G. Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds LS1 3HE, UK; (M.P.); (V.L.G.P.)
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (R.M.J.); (S.J.H.); (M.C.F.)
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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18
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Basciu A, Malloci G, Koukos P, Pietrucci F, Bonvin AM, Vargiu AV. EDES: A Protocol to Generate Holo-Like and Druggable Protein Conformations Starting from the APO Structure. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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19
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Abstract
Minimalistic peptides composed of d- and l-amino acids are attractive building blocks for functional supramolecular materials, including catalysts. d-Amino acids have long been known to promote turn conformations in peptides, yet unexpected twists continue to emerge on their effects on self-assembly. The combination of single-crystal X-ray diffraction and full-atom molecular dynamics have finally unraveled fine details of how l-d-l-tripeptides visit different conformations in solution and establish key interactions in supramolecular structures.
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20
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Tam HK, Malviya VN, Foong WE, Herrmann A, Malloci G, Ruggerone P, Vargiu AV, Pos KM. Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB. J Mol Biol 2019; 432:861-877. [PMID: 31881208 DOI: 10.1016/j.jmb.2019.12.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022]
Abstract
AcrAB(Z)-TolC is the main drug efflux transporter complex in Escherichia coli. The extrusion of various toxic compounds depends on several drug binding sites within the trimeric AcrB transporter. Membrane-localized carboxylated substrates, such as fusidic acid and hydrophobic β-lactams, access the pump via a groove between the transmembrane helices TM1 and TM2. In this article, the transport route from the initial TM1/TM2 groove binding site toward the deep binding pocket located in the periplasmic part has been addressed via molecular modeling studies followed by functional and structural characterization of several AcrB variants. We propose that membrane-embedded drugs bind initially to the TM1/TM2 groove, are oriented by the AcrB PN2 subdomain, and are subsequently transported via a PN2/PC1 interface pathway directly toward the deep binding pocket. Our work emphasizes the exploitation of multiple transport pathways by AcrB tuned to substrate physicochemical properties related to the polyspecificity of the pump.
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Affiliation(s)
- Heng-Keat Tam
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany
| | - Viveka N Malviya
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany
| | - Wuen-Ee Foong
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany
| | - Andrea Herrmann
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, S.P. 8 Km 0.700, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, S.P. 8 Km 0.700, 09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, S.P. 8 Km 0.700, 09042 Monserrato (CA), Italy.
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt Am Main, Germany.
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21
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Atzori A, Malloci G, Prajapati JD, Basciu A, Bosin A, Kleinekathöfer U, Dreier J, Vargiu AV, Ruggerone P. Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB. J Phys Chem B 2019; 123:4625-4635. [PMID: 31070373 PMCID: PMC6939625 DOI: 10.1021/acs.jpcb.9b01351] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The drug/proton antiporter AcrB, part of the major efflux pump AcrABZ-TolC in Escherichia coli, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multidrug resistance phenotype. However, the molecular features differentiating between good and poor substrates of the pump have yet to be identified. In this work, we combined molecular docking with molecular dynamics simulations to study the interactions between AcrB and two representative cephalosporins, cefepime and ceftazidime (a good and poor substrate of AcrB, respectively). Our analysis revealed different binding preferences of the two compounds toward the subsites of the large deep binding pocket of AcrB. Cefepime, although less hydrophobic than ceftazidime, showed a higher affinity than ceftazidime for the so-called hydrophobic trap, a region known for binding inhibitors and substrates. This supports the hypothesis that surface complementarity between the molecule and AcrB, more than the intrinsic hydrophobicity of the antibiotic, is a feature required for the interaction within this region. Oppositely, the preference of ceftazidime for binding outside the hydrophobic trap might not be optimal for triggering allosteric conformational changes needed to the transporter to accomplish its function. Altogether, our findings could provide valuable information for the design of new antibiotics less susceptible to the efflux mechanism.
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Affiliation(s)
- Alessio Atzori
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | | | - Andrea Basciu
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | - Andrea Bosin
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Jürg Dreier
- Basilea Pharmaceutica International Ltd., Grenzacherstrasse 487, 4058 Basel, Switzerland
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
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Basciu A, Malloci G, Pietrucci F, Bonvin AMJJ, Vargiu AV. Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. J Chem Inf Model 2019; 59:1515-1528. [PMID: 30883122 DOI: 10.1021/acs.jcim.8b00730] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Understanding molecular recognition of small molecules by proteins in atomistic detail is key for drug design. Molecular docking is a widely used computational method to mimic ligand-protein association in silico. However, predicting conformational changes occurring in proteins upon ligand binding is still a major challenge. Ensemble docking approaches address this issue by considering a set of different conformations of the protein obtained either experimentally or from computer simulations, e.g., molecular dynamics. However, holo structures prone to host (the correct) ligands are generally poorly sampled by standard molecular dynamics simulations of the apo protein. In order to address this limitation, we introduce a computational approach based on metadynamics simulations called ensemble docking with enhanced sampling of pocket shape (EDES) that allows holo-like conformations of proteins to be generated by exploiting only their apo structures. This is achieved by defining a set of collective variables that effectively sample different shapes of the binding site, ultimately mimicking the steric effect due to the ligand. We assessed the method on three challenging proteins undergoing different extents of conformational changes upon ligand binding. In all cases our protocol generates a significant fraction of structures featuring a low RMSD from the experimental holo geometry. Moreover, ensemble docking calculations using those conformations yielded in all cases native-like poses among the top-ranked ones.
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Affiliation(s)
- Andrea Basciu
- Dipartimento di Fisica , Università di Cagliari, Cittadella Universitaria , I- 09042 Monserrato (CA) , Italy
| | - Giuliano Malloci
- Dipartimento di Fisica , Università di Cagliari, Cittadella Universitaria , I- 09042 Monserrato (CA) , Italy
| | - Fabio Pietrucci
- Sorbonne Université , Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Attilio V Vargiu
- Dipartimento di Fisica , Università di Cagliari, Cittadella Universitaria , I- 09042 Monserrato (CA) , Italy.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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Di Palma F, Daino GL, Ramaswamy VK, Corona A, Frau A, Fanunza E, Vargiu AV, Tramontano E, Ruggerone P. Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition. Antivir Chem Chemother 2019; 27:2040206619889220. [PMID: 31744306 PMCID: PMC6883671 DOI: 10.1177/2040206619889220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023] Open
Abstract
Ebola virus high lethality relies on its ability to efficiently bypass the host innate antiviral response, which senses the viral dsRNA through the RIG-I receptor and induces type I interferon α/β production. In the bypassing action, the Ebola virus protein VP35 plays a pivotal role at multiple levels of the RIG-I cascade, masking the viral 5′-triphosphorylated dsRNA from RIG-I, and interacting with other cascade components. The VP35 type I interferon inhibition is exerted by the C-terminal domain, while the N-terminal domain, containing a coiled-coil region, is primarily required for oligomerization. However, mutations at key VP35 residues L90/93/107A (VP35-3m) in the coiled-coil region were reported to affect oligomerization and reduce type I interferon antagonism, indicating a possible but unclear role of homo-oligomerization on VP35 interaction with the RIG-I pathway components. In this work, we investigated the VP35 dimerization thermodynamics and its contribution to type I interferon antagonism by computational and biological methods. Focusing on the coiled-coil region, we combined coarse-grained and all-atom simulations on wild type VP35 and VP35-3m homo-dimerization. According to our results, wild type VP35 coiled-coil is able to self-assemble into dimers, while VP35-3m coiled-coil shows poor propensity to even dimerize. Free-energy calculations confirmed the key role of L90, L93 and L107 in stabilizing the coiled-coil homo-dimeric structure. In vitro type I interferon antagonism studies, using full-length wild type VP35 and VP35-3m, revealed that VP35 homo-dimerization is an essential preliminary step for dsRNA binding, which appears to be the main factor of the VP35 RIG-I cascade inhibition, while it is not essential to block the other steps.
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Affiliation(s)
- Francesco Di Palma
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Gian Luca Daino
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | | | - Angela Corona
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Aldo Frau
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Elisa Fanunza
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale
delle Ricerche (CNR), Monserrato, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
- Istituto Officina dei Materiali (CNR-IOM), UOS Cagliari SLACS,
Monserrato, Italy
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24
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Atzori A, Malviya VN, Malloci G, Dreier J, Pos KM, Vargiu AV, Ruggerone P. Identification and characterization of carbapenem binding sites within the RND-transporter AcrB. Biochim Biophys Acta Biomembr 2018; 1861:62-74. [PMID: 30416087 DOI: 10.1016/j.bbamem.2018.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022]
Abstract
Understanding the molecular determinants for recognition, binding and transport of antibiotics by multidrug efflux systems is important for basic research and useful for the design of more effective antimicrobial compounds. Imipenem and meropenem are two carbapenems whose antibacterial activity is known to be poorly and strongly affected by MexAB-OprM, the major efflux pump transporter in Pseudomonas aeruginosa. However, not much is known regarding recognition and transport of these compounds by AcrAB-TolC, which is the MexAB-OprM homologue in Escherichia coli and by definition the paradigm model for structural studies on efflux pumps. Prompted by this motivation, we unveiled the molecular details of the interaction of imipenem and meropenem with the transporter AcrB by combining computer simulations with biophysical experiments. Regarding the interaction with the two main substrate binding regions of AcrB, the so-called access and deep binding pockets, molecular dynamics simulations revealed imipenem to be more mobile than meropenem in the former, while comparable mobilities were observed in the latter. This result is in line with isothermal titration calorimetry, differential scanning experiments, and binding free energy calculations, indicating a higher affinity for meropenem than imipenem at the deep binding pocket, while both sharing similar affinities at the access pocket. Our findings rationalize how different physico-chemical properties of compounds reflect on their interactions with AcrB. As such, they constitute precious information to be exploited for the rational design of antibiotics able to evade efflux pumps.
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Affiliation(s)
- Alessio Atzori
- Department of Physics, University of Cagliari, 09042 Monserrato, CA, Italy
| | - Viveka N Malviya
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042 Monserrato, CA, Italy
| | - Jürg Dreier
- Basilea Pharmaceutica International Ltd., Grenzacherstrasse 487, 4058 Basel, Switzerland
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, 09042 Monserrato, CA, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042 Monserrato, CA, Italy,.
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25
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Garcia AM, Iglesias D, Parisi E, Styan KE, Waddington LJ, Deganutti C, De Zorzi R, Grassi M, Melchionna M, Vargiu AV, Marchesan S. Chirality Effects on Peptide Self-Assembly Unraveled from Molecules to Materials. Chem 2018. [DOI: 10.1016/j.chempr.2018.05.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ramaswamy VK, Vargiu AV, Malloci G, Dreier J, Ruggerone P. Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa. Front Microbiol 2018; 9:1144. [PMID: 29910784 PMCID: PMC5992780 DOI: 10.3389/fmicb.2018.01144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/14/2018] [Indexed: 12/14/2022] Open
Abstract
Secondary multidrug transporters of the resistance-nodulation-cell division (RND) superfamily contribute crucially to antibiotic resistance in Gram-negative bacteria. Compared to the most studied transporter AcrB of Escherichia coli, little is known about the molecular determinants of distinct polyspecificities of the most important RND transporters MexB and MexY of Pseudomonas aeruginosa. In an effort to add knowledge on this topic, we performed an exhaustive atomic-level comparison of the main putative recognition sites (access and deep binding pockets) in these two Mex transporters. We identified an underlying link between some structural, chemical and dynamical features of the binding pockets and the physicochemical nature of the corresponding substrates recognized by either one or both pumps. In particular, mosaic-like lipophilic and electrostatic surfaces of the binding pockets provide for both proteins several multifunctional sites for diffuse binding of diverse substrates. Specific lipophilicity signatures of the weakly conserved deep pocket suggest a key role of this site as a selectivity filter as in Acr transporters. Finally, the different dynamics of the bottom-loop in MexB and MexY support its possible role in binding of large substrates. Our work represents the first comparative study of the major RND transporters in P. aeruginosa and also the first structure-based study of MexY, for which no experimental structure is available yet.
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Affiliation(s)
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Jürg Dreier
- Basilea Pharmaceutica International Ltd., Basel, Switzerland
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Italy
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Cacciotto P, Ramaswamy VK, Malloci G, Ruggerone P, Vargiu AV. Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters. Methods Mol Biol 2018; 1700:179-219. [PMID: 29177832 DOI: 10.1007/978-1-4939-7454-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Efflux pumps of the resistance nodulation division (RND) superfamily are among the major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural information on AcrAB-TolC and MexAB-OprM, major efflux pumps of Escherichia coli and Pseudomonas aeruginosa respectively, boosted intensive research aimed at understanding the molecular mechanisms ruling the active extrusion processes. In particular, several studies were devoted to the understanding of the determinants behind the extraordinary broad specificity of the RND transporters AcrB and MexB. In this chapter, we discuss the ever-growing role computational methods have been playing in deciphering key structural and dynamical features of these transporters and of their interaction with substrates and inhibitors. We further discuss and illustrate examples from our lab of how molecular docking, homology modeling, all-atom molecular dynamics simulations and in silico free energy estimations can all together give precious insights into the processes of recognition and extrusion of substrates, as well as on the possible inhibition strategies.
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Affiliation(s)
- Pierpaolo Cacciotto
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Venkata K Ramaswamy
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy.
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28
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Ramaswamy VK, Vargiu AV, Malloci G, Dreier J, Ruggerone P. Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters. Sci Rep 2017; 7:8075. [PMID: 28808284 PMCID: PMC5556075 DOI: 10.1038/s41598-017-08747-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/18/2017] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Venkata Krishnan Ramaswamy
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, CA, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, CA, Italy
| | - Jürg Dreier
- Basilea Pharmaceutica International Ltd., Grenzacherstrasse 487, 4058, Basel, Switzerland
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, CA, Italy.
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29
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Vargiu AV, Krishnan VR, Malloci G, Ruggerone P. Transport Mechanism in the RND Transporter AcrD of E. coli. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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30
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Kinana AD, Vargiu AV, Nikaido H. Effect of site-directed mutations in multidrug efflux pump AcrB examined by quantitative efflux assays. Biochem Biophys Res Commun 2016; 480:552-557. [PMID: 27789287 DOI: 10.1016/j.bbrc.2016.10.083] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/23/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The Resistance-Nodulation-Division (RND) family transporter AcrB plays a major role in the intrinsic and increased resistance of Escherichia coli to a large number of antibiotics. The distal binding pocket within this multidrug efflux transporter is very large, but the effort to define the roles of various residues facing this pocket through site-directed mutagenesis so far involved only the determination of minimal inhibitory concentrations of drugs in mutants. METHODS We measured in intact E. coli cells the kinetics of efflux of two substrates, nitrocefin (a cephalosporin) that is predicted mainly to bind to the upper, "groove" domain of the pocket, and L-alanyl-β-naphthylamide (Ala-Naph) that is likely to bind to the lower, "cave" domain, in a number of site-directed mutants of AcrB, where a hydrophobic or aromatic residue was changed into alanine. RESULTS The efflux of nitrocefin became attenuated by some mutations in the groove domain, such as I278A and F178A, but in some experiments a mutation in the cave domain, F628A produced a similar result. In some cases an increased value of KM was detected. The efflux of Ala-Naph was increased by mutations in the cave domain, such as F136A and I626A, but also by those in the groove domain (I277A, I278A, F178A). In most cases the increased Vmax values appeared to be responsible. F610A mutation had a profound effect on the efflux of both substrates, as reported earlier. CONCLUSIONS Our data show for the first time effects of various substrate-binding pocket mutations on the kinetics of efflux of two substrates by the AcrB pump. They also confirm interactions between substrates and drugs predicted by MD simulation studies, and also reveal areas that need future research.
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Affiliation(s)
- Alfred D Kinana
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, 09042, Monserrato, Italy
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.
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31
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Vargiu AV, Pos KM, Poole K, Nikaido H. Editorial: Bad Bugs in the XXIst Century: Resistance Mediated by Multi-Drug Efflux Pumps in Gram-Negative Bacteria. Front Microbiol 2016; 7:833. [PMID: 27303401 PMCID: PMC4885826 DOI: 10.3389/fmicb.2016.00833] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/17/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt am Main, Germany
| | - Keith Poole
- Department of Biomedical and Molecular Sciences, Queen's University Kingston, ON, Canada
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
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Abstract
Since its discovery, the Phe-Phe motif has gained in popularity as a minimalist building block to drive the self-assembly of short peptides and their analogues into nanostructures and hydrogels. Molecules based on the Phe-Phe motif have found a range of applications in nanomedicine, from drug delivery and biomaterials to new therapeutic paradigms. Here we discuss the various production methods for this class of compounds, and the characterization, nanomorphologies, and application of their self-assembled nanostructures. We include the most recent findings on their remarkable properties, which hold substantial promise for the creation of the next generation nanomedicines.
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Affiliation(s)
- Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km. 0.700, Monserrato 09042, Italy.
| | - Katie E Styan
- CSIRO Manufacturing, Bayview Ave Clayton, VIC 3168, Australia.
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Asthana S, Zucca P, Vargiu AV, Sanjust E, Ruggerone P, Rescigno A. Structure-Activity Relationship Study of Hydroxycoumarins and Mushroom Tyrosinase. J Agric Food Chem 2015; 63:7236-7244. [PMID: 26263396 DOI: 10.1021/acs.jafc.5b02636] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The structure-activity relationships of four hydroxycoumarins, two with the hydroxyl group on the aromatic ring of the molecule and two with the hydroxyl group replacing hydrogen of the pyrone ring, and their interactions with mushroom tyrosinase were studied. These compounds displayed different behaviors upon action of the enzyme. The two compounds, ar-hydroxylated 6-hydroxycoumarin and 7-hydroxycoumarin, were both weak substrates of the enzyme. Interestingly, in both cases, the product of the catalysis was the 6,7-hydroxycoumarin, although 5,6- and 7,8-isomers could also theoretically be formed. Additionally, both were able to reduce the formation of dopachrome when tyrosinase acted on its typical substrate, L-tyrosine. Although none of the compounds that contained a hydroxyl group on the pyrone ring were substrates of tyrosinase, the 3-hydroxycoumarin was a potent inhibitor of the enzyme, and the 4-hydroxycoumarin was not an inhibitor. These results were compared with those obtained by in silico molecular docking predictions to obtain potentially useful information for the synthesis of new coumarin-based inhibitors that resemble the structure of the 3-hydroxycoumarin.
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Affiliation(s)
- Shailendra Asthana
- †Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon Expressway, Haryana 121001, India
| | - Paolo Zucca
- §Dipartimento di Scienze Biomediche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, Cagliari, Italy
- #Consorzio UNO Università Oristano, 09170 Oristano, Italy
| | - Attilio V Vargiu
- ⊥Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, Cagliari, Italy
| | - Enrico Sanjust
- §Dipartimento di Scienze Biomediche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, Cagliari, Italy
| | - Paolo Ruggerone
- ⊥Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, Cagliari, Italy
| | - Antonio Rescigno
- §Dipartimento di Scienze Biomediche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, Cagliari, Italy
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Asthana S, Shukla S, Ruggerone P, Vargiu AV. Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations. Biochemistry 2014; 53:6941-53. [DOI: 10.1021/bi500490z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shailendra Asthana
- Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, CA, Italy
| | - Saumya Shukla
- Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, CA, Italy
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, CA, Italy
| | - Attilio V. Vargiu
- Dipartimento di Fisica, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato, CA, Italy
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Ruggerone P, Murakami S, Pos KM, Vargiu AV. RND efflux pumps: structural information translated into function and inhibition mechanisms. Curr Top Med Chem 2014; 13:3079-100. [PMID: 24200360 DOI: 10.2174/15680266113136660220] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/08/2013] [Accepted: 09/15/2013] [Indexed: 11/22/2022]
Abstract
Efflux 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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Affiliation(s)
| | | | | | - Attilio V Vargiu
- Department of Physics, University of Cagliari, S.P. 8, km 0.700, 09042 Monserrato (CA), Italy.
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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37
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Franco D, Vargiu AV, Magistrato A. Ru[(bpy)2(dppz)]2+ and Rh[(bpy)2(chrysi)]3+ Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation. Inorg Chem 2014; 53:7999-8008. [DOI: 10.1021/ic5008523] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Duvan Franco
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
| | - Attilio V. Vargiu
- Dipartimento
di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.700, I-09042 Monserrato, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
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Abstract
By 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 β-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 Val139 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.
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Affiliation(s)
- Alfred D Kinana
- Department of Molecular and Cell Biology, University of California , Berkeley California 94720, United States
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Asthana S, Shukla S, Vargiu AV, Ceccarelli M, Ruggerone P, Paglietti G, Marongiu ME, Blois S, Giliberti G, La Colla P. Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole. Biochemistry 2013; 52:3752-64. [DOI: 10.1021/bi400107h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shailendra Asthana
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Saumya Shukla
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | | | - Matteo Ceccarelli
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Giuseppe Paglietti
- Dipartimento di Scienze del
Farmaco, Università degli Studi di Sassari, Via Muroni 23/a, 07100 Sassari, Italy
| | - Maria E. Marongiu
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Sylvain Blois
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Gabriele Giliberti
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Paolo La Colla
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
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40
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Walther TH, Gottselig C, Grage SL, Wolf M, Vargiu AV, Klein MJ, Vollmer S, Prock S, Hartmann M, Afonin S, Stockwald E, Heinzmann H, Nolandt OV, Wenzel W, Ruggerone P, Ulrich AS. Folding and self-assembly of the TatA translocation pore based on a charge zipper mechanism. Cell 2013; 152:316-26. [PMID: 23332763 DOI: 10.1016/j.cell.2012.12.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 08/20/2012] [Accepted: 12/13/2012] [Indexed: 12/11/2022]
Abstract
We propose a concept for the folding and self-assembly of the pore-forming TatA complex from the Twin-arginine translocase and of other membrane proteins based on electrostatic "charge zippers." Each subunit of TatA consists of a transmembrane segment, an amphiphilic helix (APH), and a C-terminal densely charged region (DCR). The sequence of charges in the DCR is complementary to the charge pattern on the APH, suggesting that the protein can be "zipped up" by a ladder of seven salt bridges. The length of the resulting hairpin matches the lipid bilayer thickness, hence a transmembrane pore could self-assemble via intra- and intermolecular salt bridges. The steric feasibility was rationalized by molecular dynamics simulations, and experimental evidence was obtained by monitoring the monomer-oligomer equilibrium of specific charge mutants. Similar "charge zippers" are proposed for other membrane-associated proteins, e.g., the biofilm-inducing peptide TisB, the human antimicrobial peptide dermcidin, and the pestiviral E(RNS) protein.
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Affiliation(s)
- Torsten H Walther
- Karlsruhe Institute of Technology, Institute of Biological Interfaces, Institute of Organic Chemistry and CFN, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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41
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Ruggerone P, Vargiu AV, Collu F, Fischer N, Kandt C. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps. Comput Struct Biotechnol J 2013; 5:e201302008. [PMID: 24688701 PMCID: PMC3962194 DOI: 10.5936/csbj.201302008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 01/13/2023] Open
Abstract
Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
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Affiliation(s)
- Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700, 09042 Monserrato (CA), Cagliari, Italy ; CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700, 09042 Monserrato (CA), Cagliari, Italy ; CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesca Collu
- Departement fu r Chemie und Biochemie, Universita t Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Nadine Fischer
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
| | - Christian Kandt
- Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany
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Collu F, Vargiu AV, Dreier J, Cascella M, Ruggerone P. Recognition of imipenem and meropenem by the RND-transporter MexB studied by computer simulations. J Am Chem Soc 2012; 134:19146-58. [PMID: 23146101 DOI: 10.1021/ja307803m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Basic understanding of the means by which multidrug efflux systems can efficiently recognize and transport drugs constitutes a fundamental step toward development of compounds able to tackle the continuous outbreak of new bacterial strains resistant to traditional antibiotics. We applied a series of computational techniques, from molecular docking to molecular dynamics simulations and free energy estimate methods, to determine the differences in the binding properties of imipenem and meropenem, two potent antibiotics of the carbapenem family, to MexB, the RND transporter of the major efflux system of Pseudomonas aeruginosa. We identified and characterized two affinity sites in the periplasmic domain of the transporter, sharing strong similarities with the distal and proximal binding pockets identified in AcrB, the homologue of MexB in Escherichia coli. According to our results, meropenem has a higher affinity to the distal binding pocket than imipenem while both compounds are weakly bound to the proximal pocket. This different behavior is mainly due to the hydration properties of the nonpharmacophore part of the two compounds, being that of imipenem less bulky and hydrophobic. Our data provide for the first time a rationale at molecular level for the experimental evidence indicating meropenem as a compound strongly affected by MexB contrary to imipenem, which is apparently poorly transported by the same pump.
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Affiliation(s)
- Francesca Collu
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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43
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Ceccarelli M, Vargiu AV, Ruggerone P. A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins. J Phys Condens Matter 2012; 24:104012. [PMID: 22353387 DOI: 10.1088/0953-8984/24/10/104012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many 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 in vivo 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.
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Affiliation(s)
- Matteo Ceccarelli
- Dipartimento di Fisica, Università degli Studi di Cagliari, Campus Monserrato, I-09042 Monserrato, Italy.
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44
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Scorciapino MA, Pirri G, Vargiu AV, Ruggerone P, Giuliani A, Casu M, Buerck J, Wadhwani P, Ulrich AS, Rinaldi AC. A novel dendrimeric peptide with antimicrobial properties: structure-function analysis of SB056. Biophys J 2012; 102:1039-48. [PMID: 22404926 DOI: 10.1016/j.bpj.2012.01.048] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 01/17/2012] [Accepted: 01/30/2012] [Indexed: 01/15/2023] Open
Abstract
The novel antimicrobial peptide with a dimeric dendrimer scaffold, SB056, was empirically optimized by high-throughput screening. This procedure produced an intriguing primary sequence whose structure-function analysis is described here. The alternating pattern of hydrophilic and hydrophobic amino acids suggests the possibility that SB056 is a membrane-active peptide that forms amphiphilic β-strands in a lipid environment. Circular dichroism confirmed that the cationic SB056 folds as β-sheets in the presence of anionic vesicles. Lipid monolayer surface pressure experiments revealed unusual kinetics of monolayer penetration, which suggest lipid-induced aggregation as a membranolytic mechanism. NMR analyses of the linear monomer and the dendrimeric SB056 in water and in 30% trifluoroethanol, on the other hand, yielded essentially unstructured conformations, supporting the excellent solubility and storage properties of this compound. However, simulated annealing showed that many residues lie in the β-region of the Ramachandran plot, and molecular-dynamics simulations confirmed the propensity of this peptide to fold as a β-type conformation. The excellent solubility in water and the lipid-induced oligomerization characteristics of this peptide thus shed light on its mechanism of antimicrobial action, which may also be relevant for systems that can form toxic β-amyloid fibrils when in contact with cellular membranes. Functionally, SB056 showed high activity against Gram-negative bacteria and some limited activity against Gram-positive bacteria. Its potency against Gram-negative strains was comparable (on a molar basis) to that of colistin and polymyxin B, with an even broader spectrum of activity than numerous other reference compounds.
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Affiliation(s)
- Mariano A Scorciapino
- Department of Chemical Sciences, Istituto Officina dei Materiali del Consiglio Nazionale delle Ricerche, UOS SLACS, Italy
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45
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Affiliation(s)
- Attilio V. Vargiu
- CNR-IOM, Unità Operativa
di Supporto SLACS, c/o Dipartimento di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.7, I-09042 Monserrato,
Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos,
National
Simulation Center, c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste,
Italy
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46
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Ruggerone P, Vargiu AV, Collu F. Effects of Point Mutations on the Activity of AcrB. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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47
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Schulz R, Vargiu AV, Ruggerone P, Kleinekathöfer U. Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB. J Phys Chem B 2011. [DOI: 10.1021/jp2062282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Vargiu AV, Collu F, Schulz R, Pos KM, Zacharias M, Kleinekathöfer U, Ruggerone P. Effect of the F610A mutation on substrate extrusion in the AcrB transporter: explanation and rationale by molecular dynamics simulations. J Am Chem Soc 2011; 133:10704-7. [PMID: 21707050 DOI: 10.1021/ja202666x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The tripartite efflux pump AcrAB-TolC is responsible for the intrinsic and acquired multidrug resistance in Escherichia coli. Its active part, the homotrimeric transporter AcrB, is in charge of the selective binding of substrates and energy transduction. The mutation F610A has been shown to significantly reduce the minimum inhibitory concentration of doxorubicin and many other substrates, although F610 does not appear to interact strongly with them. Biochemical study of transport kinetics in AcrB is not yet possible, except for some β-lactams, and other techniques should supply this important information. Therefore, in this work, we assess the impact of the F610A mutation on the functionality of AcrB by means of computational techniques, using doxorubicin as substrate. We found that the compound slides deeply inside the binding pocket after mutation, increasing the strength of the interaction. During subsequent conformational alterations of the transporter, doxorubicin was either not extruded from the binding site or displaced along a direction other than the one associated with extrusion. Our study indicates how subtle interactions determine the functionality of multidrug transporters, since decreased transport might not be simplistically correlated to decreased substrate binding affinity.
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Affiliation(s)
- Attilio V Vargiu
- CNR-IOM, Unità SLACS, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato (CA), Italy.
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49
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Schulz R, Vargiu AV, Ruggerone P, Kleinekathöfer U. Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB. J Phys Chem B 2011; 115:8278-87. [DOI: 10.1021/jp200996x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Robert Schulz
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
| | - Attilio V. Vargiu
- CNR-IOM, Unità SLACS,
c/o Dipartimento di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.7, I-09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- CNR-IOM, Unità SLACS,
c/o Dipartimento di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.7, I-09042 Monserrato (CA), Italy
| | - Ulrich Kleinekathöfer
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
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50
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Schulz R, Vargiu AV, Collu F, Kleinekathöfer U, Ruggerone P. Functional rotation of the transporter AcrB: insights into drug extrusion from simulations. PLoS Comput Biol 2010; 6:e1000806. [PMID: 20548943 PMCID: PMC2883587 DOI: 10.1371/journal.pcbi.1000806] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 05/05/2010] [Indexed: 01/16/2023] Open
Abstract
The tripartite complex AcrAB-TolC is the major efflux system in Escherichia coli. It extrudes a wide spectrum of noxious compounds out of the bacterium, including many antibiotics. Its active part, the homotrimeric transporter AcrB, is responsible for the selective binding of substrates and energy transduction. Based on available crystal structures and biochemical data, the transport of substrates by AcrB has been proposed to take place via a functional rotation, in which each monomer assumes a particular conformation. However, there is no molecular-level description of the conformational changes associated with the rotation and their connection to drug extrusion. To obtain insights thereon, we have performed extensive targeted molecular dynamics simulations mimicking the functional rotation of AcrB containing doxorubicin, one of the two substrates that were co-crystallized so far. The simulations, including almost half a million atoms, have been used to test several hypotheses concerning the structure-dynamics-function relationship of this transporter. Our results indicate that, upon induction of conformational changes, the substrate detaches from the binding pocket and approaches the gate to the central funnel. Furthermore, we provide strong evidence for the proposed peristaltic transport involving a zipper-like closure of the binding pocket, responsible for the displacement of the drug. A concerted opening of the channel between the binding pocket and the gate further favors the displacement of the drug. This microscopically well-funded information allows one to identify the role of specific amino acids during the transitions and to shed light on the functioning of AcrB. In nature, bacteria have to resist several toxic threats to be able to survive, from bile acids in intestines up to antibiotics. The Escherichia coli bacterium, which usually is a commensal inhabitant of human intestines, can also acquire pathogenic properties which would harm the human body. To dispose of toxic compounds, E. coli has developed a protein machinery which is called “efflux pump”. Here, we studied the dynamics of the transporter protein AcrB, a component of the E. coli major efflux system, in complex with an antibiotic (doxorubicin). We used computer simulations to complement the existing experimental data. Our purpose was to gain more detailed insights into the pumping mechanism at the molecular level. In our simulations the drug leaves the binding pocket upon induction of functional rotation in the protein, although a complete extrusion was never observed. A peristaltic motion, which starts with a zipper-like closure of the interior of the protein, is an important step for the extrusion of the drug. Interestingly, such a peristaltic mechanism of pumping has been suggested before on the basis of structural data. The molecular details obtained in this study shall deepen the understanding of the functioning of the efflux pump.
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Affiliation(s)
- Robert Schulz
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
| | - Attilio V. Vargiu
- Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita' degli Studi di Cagliari, Monserrato, Italy
- * E-mail:
| | - Francesca Collu
- Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita' degli Studi di Cagliari, Monserrato, Italy
| | | | - Paolo Ruggerone
- Istituto Officina dei Materiali del CNR, UOS SLACS and Dipartimento di Fisica, Universita' degli Studi di Cagliari, Monserrato, Italy
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