1
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Roy RK, Bera A, Patra N. Insights into Allosteric Inhibition of the AcrB Efflux Pump: Role of Distinct Binding Pockets, Protomer Preferences, and Crosstalk Disruption. J Chem Inf Model 2024. [PMID: 39011748 DOI: 10.1021/acs.jcim.4c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
AcrB, a key component in bacterial efflux processes, exhibits distinct binding pockets that influence inhibitor interactions. In addition to the well-known distal binding pocket within the periplasmic domain, a noteworthy pocket amidst the transmembrane (TM) helices serves as an alternate binding site for inhibitors. The bacterial efflux mechanism involves a pivotal functional rotation of the TM protein, inducing conformational changes in each protomer and propelling drugs toward the outer membrane domain. Surprisingly, inhibitors binding to the TM domain display a preference for L protomers over T protomers. Metadynamics simulations elucidate that Lys940 in the TM domain of AcrB can adopt two conformations in L protomers, whereas the energy barrier for such transitions is higher in T protomers. This phenomenon results in stable inhibitor binding in l protomers. Upon a detailed analysis of unbinding pathways using random accelerated molecular dynamics and umbrella sampling, we have identified three distinct routes for ligand exit from the allosteric site, specifically involving regions within the TM domains─TM4, TM5, and TM10. To explore allosteric crosstalk, we focused on the following key residues: Val452 from the TM domain and Ala831 from the porter domain. Surprisingly, our findings reveal that inhibitor binding disrupts this communication. The shortest path connecting Val452 and Ala831 increases upon inhibitor binding, suggesting sabotage of the natural interdomain communication dynamics. This result highlights the intricate interplay between inhibitor binding and allosteric signaling within our studied system.
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Affiliation(s)
- Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Abhishek Bera
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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2
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Wilhelm J, Pos KM. Molecular insights into the determinants of substrate specificity and efflux inhibition of the RND efflux pumps AcrB and AdeB. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001438. [PMID: 38358391 PMCID: PMC10924465 DOI: 10.1099/mic.0.001438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Gram-negative bacterial members of the Resistance Nodulation and cell Division (RND) superfamily form tripartite efflux pump systems that span the cell envelope. One of the intriguing features of the multiple drug efflux members of this superfamily is their ability to recognize different classes of antibiotics, dyes, solvents, bile salts, and detergents. This review provides an overview of the molecular mechanisms of multiple drug efflux catalysed by the tripartite RND efflux system AcrAB-TolC from Eschericha coli. The determinants for sequential or simultaneous multiple substrate binding and efflux pump inhibitor binding are discussed. A comparison is made with the determinants for substrate binding of AdeB from Acinetobacter baumannii, which acts within the AdeABC multidrug efflux system. There is an apparent general similarity between the structures of AcrB and AdeB and their substrate specificity. However, the presence of distinct conformational states and different drug efflux capacities as revealed by single-particle cryo-EM and mutational analysis suggest that the drug binding and transport features exhibited by AcrB may not be directly extrapolated to the homolog AdeB efflux pump.
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Affiliation(s)
- Julia Wilhelm
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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3
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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4
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Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA. Physiological Functions of Bacterial "Multidrug" Efflux Pumps. Chem Rev 2021; 121:5417-5478. [PMID: 33761243 DOI: 10.1021/acs.chemrev.0c01226] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.
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Affiliation(s)
- Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Claire Maher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Liam D H Elbourne
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Ian T Paulsen
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
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5
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Rathi E, Kumar A, Kini SG. Computational approaches in efflux pump inhibitors: current status and prospects. Drug Discov Today 2020; 25:1883-1890. [PMID: 32712312 DOI: 10.1016/j.drudis.2020.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 01/02/2023]
Abstract
Treatment of bacterial infections is currently threatened by the development of antibiotic resistance and a poor pipeline of new antibiotics. Efflux pumps (EPs) are an integral part of the defense machinery of bacteria, preventing the entry of molecules, such as antibiotics, into the intracellular environment and resulting in antibiotic resistance. Therefore, research has focused on the discovery of novel EP inhibitors (EPIs), such as PAβN, D13-9001, and MBX2319. however, there are still no US Food and Drug Administration (FDA)-approved drugs targeting EPs because of the inadequate assimilation of the inhibitors. Here, we discuss the use of computational approaches for molecular mechanistic studies of EPIs to help direct future research.
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Affiliation(s)
- Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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6
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Atzori A, Malloci G, Cardamone F, Bosin A, Vargiu AV, Ruggerone P. Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli. Int J Mol Sci 2020; 21:E860. [PMID: 32013182 PMCID: PMC7037162 DOI: 10.3390/ijms21030860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/26/2020] [Indexed: 12/22/2022] Open
Abstract
The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism.
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Affiliation(s)
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy; (A.A.); (F.C.); (A.B.); (P.R.)
| | | | | | - Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy; (A.A.); (F.C.); (A.B.); (P.R.)
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7
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Kobylka J, Kuth MS, Müller RT, Geertsma ER, Pos KM. AcrB: a mean, keen, drug efflux machine. Ann N Y Acad Sci 2019; 1459:38-68. [PMID: 31588569 DOI: 10.1111/nyas.14239] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria are intrinsically resistant against cytotoxic substances by means of their outer membrane and a network of multidrug efflux systems, acting in synergy. Efflux pumps from various superfamilies with broad substrate preferences sequester and pump drugs across the inner membrane to supply the highly polyspecific and powerful tripartite resistance-nodulation-cell division (RND) efflux pumps with compounds to be extruded across the outer membrane barrier. In Escherichia coli, the tripartite efflux system AcrAB-TolC is the archetype RND multiple drug efflux pump complex. The homotrimeric inner membrane component acriflavine resistance B (AcrB) is the drug specificity and energy transduction center for the drug/proton antiport process. Drugs are bound and expelled via a cycle of mainly three consecutive states in every protomer, constituting a flexible alternating access channel system. This review recapitulates the molecular basis of drug and inhibitor binding, including mechanistic insights into drug efflux by AcrB. It also summarizes 17 years of mutational analysis of the gene acrB, reporting the effect of every substitution on the ability of E. coli to confer resistance toward antibiotics (http://goethe.link/AcrBsubstitutions). We emphasize the functional robustness of AcrB toward single-site substitutions and highlight regions that are more sensitive to perturbation.
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Affiliation(s)
- Jessica Kobylka
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Miriam S Kuth
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Reinke T Müller
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
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8
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Abstract
Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.
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9
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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] [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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10
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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. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 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] [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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