1
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Reany O, Romero-Ruiz M, Khurana R, Mondal P, Keinan E, Bayley H. Stochastic Sensing of Chloride Anions Using an α-Hemolysin Pore with a semiaza-Bambusuril Adapter. Angew Chem Int Ed Engl 2024; 63:e202406719. [PMID: 38850111 DOI: 10.1002/anie.202406719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/09/2024]
Abstract
Pores containing molecular adapters provide internal selective binding sites, thereby allowing the stochastic sensing of analytes. Herein, we demonstrate that semiaza-bambusuril (BU) acts as a non-covalent molecular adapter when lodged within the lumen of the wild-type α-hemolysin (WT-αHL) protein pore. Because the bambusurils are recognized as anion receptors, the anion binding site within the adapter-nanopore complex allows the detection of chloride anions, thus converting a non-selective pore into an anion sensor.
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Affiliation(s)
- Ofer Reany
- Department of Natural Sciences, The Open University of Israel, 1 University Road, Ra'anana, 4353701, Israel
| | - Mercedes Romero-Ruiz
- Department of Natural Sciences, The Open University of Israel, 1 University Road, Ra'anana, 4353701, Israel
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Raman Khurana
- Department of Natural Sciences, The Open University of Israel, 1 University Road, Ra'anana, 4353701, Israel
| | - Pravat Mondal
- Department of Natural Sciences, The Open University of Israel, 1 University Road, Ra'anana, 4353701, Israel
| | - Ehud Keinan
- The Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200001, Israel
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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2
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Baldelli M, Di Muccio G, Sauciuc A, Morozzo Della Rocca B, Viola F, Balme S, Bonini A, Maglia G, Chinappi M. Controlling Electroosmosis in Nanopores Without Altering the Nanopore Sensing Region. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401761. [PMID: 38860821 DOI: 10.1002/adma.202401761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Indexed: 06/12/2024]
Abstract
Nanopores are powerful tools for single-molecule sensing of biomolecules and nanoparticles. The signal coming from the molecule to be analyzed strongly depends on its interaction with the narrower section of the nanopore (constriction) that may be tailored to increase sensing accuracy. Modifications of nanopore constriction have also been commonly used to induce electroosmosis, that favors the capture of molecules in the nanopore under a voltage bias and independently of their charge. However, engineering nanopores for increasing both electroosmosis and sensing accuracy is challenging. Here it is shown that large electroosmotic flows can be achieved without altering the nanopore constriction. Using continuum electrohydrodynamic simulations, it is found that an external charged ring generates strong electroosmosis in cylindrical nanopores. Similarly, for conical nanopores it is shown that moving charges away from the cone tip still results in an electroosmotic flow (EOF), whose intensity reduces increasing the diameter of the nanopore section where charges are placed. This paradigm is applied to engineered biological nanopores showing, via atomistic simulations and experiments, that mutations outside the constriction induce a relatively intense electroosmosis. This strategy provides much more flexibility in nanopore design since electroosmosis can be controlled independently from the constriction, which can be optimized to improve sensing accuracy.
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Affiliation(s)
- Matteo Baldelli
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
| | - Giovanni Di Muccio
- Department of Mechanical and Aerospace Engineering, University of Rome Sapienza, Roma, 00184, Italy
| | - Adina Sauciuc
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | | | | | - Sébastien Balme
- Institut Europeen des Membranes, UMR5635, University of Montpellier ENCSM CNRS, Montpellier, 34095, France
| | - Andrea Bonini
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
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3
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Mereuta L, Bhatti H, Asandei A, Cimpanu A, Ying YL, Long YT, Luchian T. Controlling DNA Fragments Translocation across Nanopores with the Synergic Use of Site-Directed Mutagenesis, pH-Dependent Charge Tuning, and Electroosmotic Flow. ACS APPLIED MATERIALS & INTERFACES 2024; 16:40100-40110. [PMID: 39038810 PMCID: PMC11299134 DOI: 10.1021/acsami.4c03848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024]
Abstract
Biological and solid-state nanopores are at the core of transformative techniques and nanodevices, democratizing the examination of matter and biochemical reactions at the single-molecule level, with low cost, portability, and simplicity in operation. One of the crucial hurdles in such endeavors is the fast analyte translocation, which limits characterization, and a rich number of strategies have been explored over the years to overcome this. Here, by site-directed mutagenesis on the α-hemolysin protein nanopore (α-HL), sought to replace selected amino acids with glycine, electrostatic binding sites were induced on the nanopore's vestibule and constriction region and achieved in the most favorable case a 20-fold increase in the translocation time of short single-stranded DNA (ssDNA) at neutral pH, with respect to the wild-type (WT) nanopore. We demonstrated an efficient tool of controlling the ssDNA translocation time, via the interplay between the nanopore-ssDNA surface electrostatic interactions and electroosmotic flow, all mediated by the pH-dependent ionization of amino acids lining the nanopore's translocation pathway. Our data also reveal the nonmonotonic, pH-induced alteration of ssDNA average translocation time. Unlike mildly acidic conditions (pH ∼ 4.7), at a pH ∼ 2.8 maintained symmetrically or asymmetrically across the WT α-HL, we evidenced the manifestation of a dominant electroosmotic flow, determining the speeding up of the ssDNA translocation across the nanopore by counteracting the ssDNA-nanopore attractive electrostatic interactions. We envision potential applications of the presented approach by enabling easy-to-use, real-time detection of short ssDNA sequences, without the need for complex biochemical modifications to the nanopore to mitigate the fast translocation of such sequences.
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Affiliation(s)
- Loredana Mereuta
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Huma Bhatti
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Alina Asandei
- Interdisciplinary
Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Adina Cimpanu
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Yi-Lun Ying
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Tudor Luchian
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
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4
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Vikraman D, Majumdar BB, Sk S, Weichbrodt C, Fertig N, Winterhalter M, Mondal J, Mahendran KR. Conformational flexibility driving charge-selective substrate translocation across a bacterial transporter. Chem Sci 2024; 15:9333-9344. [PMID: 38903220 PMCID: PMC11186346 DOI: 10.1039/d4sc00345d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024] Open
Abstract
Bacterial membrane porins facilitate the translocation of small molecules while restricting large molecules, and this mechanism remains elusive at the molecular level. Here, we investigate the selective uptake of large cyclic sugars across an unusual passive membrane transporter, CymA, comprising a charged zone and a constricting N terminus segment. Using a combination of electrical recordings, protein mutagenesis and molecular dynamics simulations, we establish substrate translocation across CymA governed by the electrostatic pore properties and conformational dynamics of the constriction segment. Notably, we show that the variation in pH of the environment resulted in reversible modulation of the substrate binding site in the pore, thereby regulating charge-selective transport of cationic, anionic and neutral cyclic sugars. The quantitative kinetics of cyclic sugar translocation across CymA obtained in electrical recordings at different pHs are comparable with molecular dynamics simulations that revealed the transport pathway, energetics and favorable affinity sites in the pore for substrate binding. We further define the molecular basis of cyclic sugar translocation and establish that the constriction segment is flexible and can reside inside or outside the pore, regulating substrate translocation distinct from the ligand-gated transport mechanism. Our study provides novel insights into energy-independent large molecular membrane transport for targeted drug design strategies.
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Affiliation(s)
- Devika Vikraman
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
- Manipal Academy of Higher Education Manipal Karnataka-576104 India
| | | | - Sharavanakkumar Sk
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | | | | | - Mathias Winterhalter
- School of Science, Constructor University Campus Ring 1 28759 Bremen Germany
- Center for Hybrid Nanostructures (CHyN), Universität Hamburg Luruper Chaussee 149 Hamburg 22761 Germany
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad Telangana-500046 India
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
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5
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Satheesan R, Vikraman D, Jayan P, Vijayan V, Chimerel C, Mahendran KR. Sensing PEGylated Peptide Conformations Using a Protein Nanopore. NANO LETTERS 2024; 24:3566-3574. [PMID: 38316144 DOI: 10.1021/acs.nanolett.3c03247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Membrane pores are exploited for the stochastic sensing of various analytes, and here, we use electrical recordings to explore the interaction of PEGylated peptides of different sizes with a protein pore, CymA. This wide-diameter natural pore comprises densely filled charged residues, facilitating electrophoretic binding of polyethylene glycol (PEG) tagged with a nonaarginine peptide. The small PEG 200 peptide conjugates produced monodisperse blockages and exhibited voltage-dependent translocation across the pores. Notably, the larger PEG 1000 and 2000 peptide conjugates yielded heterogeneous blockages, indicating a multitude of PEG conformations hindering their translocation through the pore. Furthermore, a much larger PEG 5000 peptide occludes the pore entrance, resulting in complete closure. The competitive binding of different PEGylated peptides with the same pore produced specific blockage signals reflecting their identity, size, and conformation. Our proposed model of sensing distinct polypeptide conformations corresponds to disordered protein unfolding, suggesting that this pore can find applications in proteomics.
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Affiliation(s)
- Remya Satheesan
- Membrane Biology Laboratory, Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Devika Vikraman
- Membrane Biology Laboratory, Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Parvathy Jayan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Kerala 695551, India
| | - Vinesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala PO, Vithura, Kerala 695551, India
| | - Catalin Chimerel
- Automation Department, Faculty of Electrical Engineering and Computer Science, Transilvania University of Brasov, Brasov 500036, Romania
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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6
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Zhao Y, Su Z, Zhang X, Wu D, Wu Y, Li G. Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1454-1467. [PMID: 38415741 DOI: 10.1039/d3ay02040a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.
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Affiliation(s)
- Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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7
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Vikraman D, Satheesan R, Rajendran M, Kumar NA, Johnson JB, R SK, Mahendran KR. Selective Translocation of Cyclic Sugars through Dynamic Bacterial Transporter. ACS Sens 2022; 7:1766-1776. [PMID: 35671512 DOI: 10.1021/acssensors.2c00943] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selective translocation of molecules through membrane pores is an integral process in cells. We present a bacterial sugar transporter, CymA of unusual structural conformation due to a dynamic N terminus segment in the pore, reducing its diameter. We quantified the translocation kinetics of various cyclic sugars of different charge, size, and symmetry across native and truncated CymA devoid of the N terminus using single-channel recordings. The chemically divergent cyclic hexasaccharides bind to the native and truncated pore with high affinity and translocate effectively. Specifically, these sugars bind and translocate rapidly through truncated CymA compared to native CymA. In contrast, larger cyclic heptasaccharides and octasaccharides do not translocate but bind to native and truncated CymA with distinct binding kinetics highlighting the importance of molecular charge, size and symmetry in translocation consistent with liposome assays. Based on the sugar-binding kinetics, we suggest that the N terminus most likely resides inside the native CymA barrel, regulating the transport rate of cyclic sugars. Finally, we present native CymA as a large nanopore sensor for the simultaneous single-molecule detection of various sugars at high resolution, establishing its functional versatility. This natural pore is expected to have several applications in nanobiotechnology and will help further our understanding of the fundamental mechanism of molecular transport.
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Affiliation(s)
- Devika Vikraman
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Remya Satheesan
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mangaiyarkarasi Rajendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Nisha Asok Kumar
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.,Pathogen Biology, Virology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - John Bernet Johnson
- Pathogen Biology, Virology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Smrithi Krishnan R
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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8
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Acharya A, Prajapati JD, Kleinekathöfer U. Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions. J Phys Chem B 2022; 126:3995-4008. [PMID: 35616602 DOI: 10.1021/acs.jpcb.2c01173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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9
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Prajapati JD, Pangeni S, Aksoyoglu MA, Winterhalter M, Kleinekathöfer U. Changes in Salt Concentration Modify the Translocation of Neutral Molecules through a ΔCymA Nanopore in a Non-monotonic Manner. ACS NANO 2022; 16:7701-7712. [PMID: 35435659 DOI: 10.1021/acsnano.1c11471] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The voltage-dependent transport through biological and artificial nanopores is being used in many applications such as DNA or protein sequencing and sensing. The primary approach to determine the transport has been to measure the temporal ion current fluctuations caused by solutes when applying external voltages. Crossing the nanoscale confinement in the presence of an applied electric field primarily relies on two factors, i.e., the electrophoretic drag and electroosmosis. The electroosmotic flow (EOF) is a voltage-dependent ion-associated flow of solvent molecules, i.e., usually water, and depends on many factors, such as pH, temperature, pore diameter, and also the concentration of ions. The exact interplay between these factors is so far poorly understood. In this joint experimental and computational study, we have investigated the dependence of the EOF on the concentration of the buffer salt by probing the transport of α-cyclodextrin molecules through the ΔCymA channel. For five different KCl concentrations in the range between 0.125 and 2 M, we performed applied-field molecular dynamics simulations and analyzed the ionic flow and the EOF across the ΔCymA pore. To our surprise, the concentration-dependent net ionic flux changes non-monotonically and nonlinearly and the EOF is seen to follow the same pattern. On the basis of these findings, we were able to correlate the concentration-dependent EOF with experimental kinetic constants for the translocation of α-cyclodextrin through the ΔCymA nanopore. Overall, the results further improve our understanding of the EOF-mediated transport through nanopores and show that the EOF needs to seriously be taken into consideration when analyzing the permeation of (neutral) substrates through nanopores.
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Affiliation(s)
| | - Sushil Pangeni
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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10
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Combined Pressure-Driven and Electroosmotic Slip Flow through Elliptic Cylindrical Microchannels: The Effect of the Eccentricity of the Channel Cross-Section. Symmetry (Basel) 2022. [DOI: 10.3390/sym14050999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Electroosmotic force has been used extensively to manipulate fluid flow in a microfluidic system with various channel shapes, especially an elliptic cylinder. However, developing a computational domain and simulating fluid flow for a system involving an elliptic channel consumes a large amount of time. Moreover, the mathematical expression for the fluid velocity of electroosmotic flow in an elliptic channel may be given in the form of the Mathieu functions that have difficulty in achieving the numerical result. In addition, there is clear scientific evidence that confirms the slippage of fluid at the solid-fluid interface in a microscale system. In this study, we present the mathematical model of combined pressure-driven and electroosmotic flow through elliptic microchannels under the slip-fluid condition. From the practical point of view in fluidics, the effect of the eccentricity of the channel cross-section is investigated on the volumetric flow rate to overcome the difficulty. The results show that the substitution of the equivalent circular channel for an elliptic channel provides a valid flow rate under the situation that the areas of both channel cross-sections are equal and the eccentricity of the elliptic cross-section is less than 0.5. Additionally, the flow rate obtained from the substitution is more accurate when the slip length increases or the pressure-gradient-to-external-electric-field ratio decreases.
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11
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Niu H, Li MY, Ying YL, Long YT. An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport. Chem Sci 2022; 13:2456-2461. [PMID: 35310483 PMCID: PMC8864703 DOI: 10.1039/d1sc06459b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
Reading the primary sequence directly using nanopores remains challenging due to the complex building blocks of 20 proteinogenic amino acids and the corresponding sophisticated structures. Compared to the uniformly negatively charged polynucleotides, biological nanopores hardly provide effective ionic current responses to all heterogeneously charged peptides under nearly physiological pH conditions. Herein, we precisely design a N226Q/S228K mutant aerolysin which creates a new electrostatic constriction named R3 in-between two natural sensing regions for controlling the capture and translocation of heterogeneously charged peptides. At nearly physiological pH, the decoration of positive charges at this constriction gives a large velocity of electroosmotic flow (EOF), leading to a maximum 8-fold increase in frequency for the heterogeneously charged peptides with the net charge from +1 to -3. Even the duration time of the negatively charged peptide Aβ35-25D4 in N226Q/S228K AeL also rises from 0.07 ± 0.01 ms to 0.63 ± 0.01 ms after introducing the third electrostatic constriction. Therefore, the N226Q/S228K aerolysin nanopore with three electrostatic constrictions realizes the dual goals of both capturing and decelerating heterogeneously charged peptides without labelling, even for the folded peptides.
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Affiliation(s)
- Hongyan Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Meng-Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
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12
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Liu Y, Wang K, Wang Y, Wang L, Yan S, Du X, Zhang P, Chen HY, Huang S. Machine Learning Assisted Simultaneous Structural Profiling of Differently Charged Proteins in a Mycobacterium smegmatis Porin A (MspA) Electroosmotic Trap. J Am Chem Soc 2022; 144:757-768. [PMID: 34994548 DOI: 10.1021/jacs.1c09259] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The nanopore is emerging as a means of single-molecule protein sensing. However, proteins demonstrate different charge properties, which complicates the design of a sensor that can achieve simultaneous sensing of differently charged proteins. In this work, we introduce an asymmetric electrolyte buffer combined with the Mycobacterium smegmatis porin A (MspA) nanopore to form an electroosmotic flow (EOF) trap. Apo- and holo-myoglobin, which differ in only a single heme, can be fully distinguished by this method. Direct discrimination of lysozyme, apo/holo-myoglobin, and the ACTR/NCBD protein complex, which are basic, neutral, and acidic proteins, respectively, was simultaneously achieved by the MspA EOF trap. To automate event classification, multiple event features were extracted to build a machine learning model, with which a 99.9% accuracy is achieved. The demonstrated method was also applied to identify single molecules of α-lactalbumin and β-lactoglobulin directly from whey protein powder. This protein-sensing strategy is useful in direct recognition of a protein from a mixture, suggesting its prospective use in rapid and sensitive detection of biomarkers or real-time protein structural analysis.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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13
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Bartsch A, Ives CM, Kattner C, Pein F, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C, Llabrés S. An antibiotic-resistance conferring mutation in a neisserial porin: Structure, ion flux, and ampicillin binding. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183601. [PMID: 33675718 PMCID: PMC8047873 DOI: 10.1016/j.bbamem.2021.183601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/13/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022]
Abstract
Gram-negative bacteria cause the majority of highly drug-resistant bacterial infections. To cross the outer membrane of the complex Gram-negative cell envelope, antibiotics permeate through porins, trimeric channel proteins that enable the exchange of small polar molecules. Mutations in porins contribute to the development of drug-resistant phenotypes. In this work, we show that a single point mutation in the porin PorB from Neisseria meningitidis, the causative agent of bacterial meningitis, can strongly affect the binding and permeation of beta-lactam antibiotics. Using X-ray crystallography, high-resolution electrophysiology, atomistic biomolecular simulation, and liposome swelling experiments, we demonstrate differences in drug binding affinity, ion selectivity and drug permeability of PorB. Our work further reveals distinct interactions between the transversal electric field in the porin eyelet and the zwitterionic drugs, which manifest themselves under applied electric fields in electrophysiology and are altered by the mutation. These observations may apply more broadly to drug-porin interactions in other channels. Our results improve the molecular understanding of porin-based drug-resistance in Gram-negative bacteria.
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Affiliation(s)
- Annika Bartsch
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Christof Kattner
- ZIK HALOmem, Membrane Protein Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Straße 3, 06120 Halle (Saale), Germany
| | - Florian Pein
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077 Göttingen, Germany
| | - Manuel Diehn
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077 Göttingen, Germany
| | - Mikio Tanabe
- Institute of Materials Structure Science, Structural Biology Research Center, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077 Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077 Göttingen, Germany; Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany.
| | - Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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14
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Pangeni S, Prajapati JD, Bafna J, Nilam M, Nau WM, Kleinekathöfer U, Winterhalter M. Permeation eines 5.1‐kDa‐Peptides durch einen Proteinkanal: Molekulare Basis der Translokation von Protamin durch CymA aus
Klebsiella Oxytoca
**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sushil Pangeni
- Department of Life Sciences and Chemistry Jacobs University 28759 Bremen Deutschland
| | | | - Jayesh Bafna
- Department of Life Sciences and Chemistry Jacobs University 28759 Bremen Deutschland
| | - Mohamed Nilam
- Department of Life Sciences and Chemistry Jacobs University 28759 Bremen Deutschland
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University 28759 Bremen Deutschland
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences Jacobs University Bremen 28759 Bremen Deutschland
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry Jacobs University 28759 Bremen Deutschland
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15
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Pangeni S, Prajapati JD, Bafna J, Nilam M, Nau WM, Kleinekathöfer U, Winterhalter M. Large-Peptide Permeation Through a Membrane Channel: Understanding Protamine Translocation Through CymA from Klebsiella Oxytoca*. Angew Chem Int Ed Engl 2021; 60:8089-8094. [PMID: 33580541 PMCID: PMC8049027 DOI: 10.1002/anie.202016943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/13/2022]
Abstract
Quantifying the passage of the large peptide protamine (Ptm) across CymA, a passive channel for cyclodextrin uptake, is in the focus of this study. Using a reporter-pair-based fluorescence membrane assay we detected the entry of Ptm into liposomes containing CymA. The kinetics of the Ptm entry was independent of its concentration suggesting that the permeation through CymA is the rate-limiting factor. Furthermore, we reconstituted single CymA channels into planar lipid bilayers and recorded the ion current fluctuations in the presence of Ptm. To this end, we were able to resolve the voltage-dependent entry of single Ptm peptide molecules into the channel. Extrapolation to zero voltage revealed about 1-2 events per second and long dwell times, in agreement with the liposome study. Applied-field and steered molecular dynamics simulations added an atomistic view of the permeation events. It can be concluded that a concentration gradient of 1 μm Ptm leads to a translocation rate of about one molecule per second and per channel.
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Affiliation(s)
- Sushil Pangeni
- Department of Life Sciences and ChemistryJacobs University28759BremenGermany
| | | | - Jayesh Bafna
- Department of Life Sciences and ChemistryJacobs University28759BremenGermany
| | - Mohamed Nilam
- Department of Life Sciences and ChemistryJacobs University28759BremenGermany
| | - Werner M. Nau
- Department of Life Sciences and ChemistryJacobs University28759BremenGermany
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16
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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17
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Lei Z, Karim A. The challenges and applications of nanotechnology against bacterial resistance. J Vet Pharmacol Ther 2020; 44:281-297. [PMID: 33277732 DOI: 10.1111/jvp.12936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
Bacterial resistance to the antibiotics develops rapidly and is increasingly serious health concern in the world. It is an insoluble topic due to the multiple resistant mechanisms. The overexpression of relative activities of the efflux pump has proven to be a frequent and important source of bacterial resistance. Efflux transporters in the membrane from the resistant bacteria could play a key role to inhibit the intracellular drug intake and impede the drug activities. However, nanoparticles (NPs), one of the most frequently used encapsulation materials, could increase the intracellular accumulation of the drug and inhibit the transporter activity effectively. The rational and successful application of nanotechnology is a key factor in overcoming bacterial resistance. Furthermore, nanoparticles such as metallic, carbon nanotubes and so on, may prevent the development of drug resistance and be associated with antibiotic agents, inhibiting biofilm formation or increasing the access into the target cell and exterminating the bacteria eventually. In the current study, the mechanisms of bacterial resistance are discussed and summarized. Additionally, the opportunities and challenges in the use of nanoparticles against bacterial resistance are also illuminated. At the same time, the use of nanoparticles to combat multidrug-resistant bacteria is also investigated by coupling natural antimicrobials or other alternatives. In short, we have provided a new perspective for the application of nanoparticles against multidrug-resistant bacteria.
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Affiliation(s)
- Zhiqun Lei
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Aman Karim
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
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18
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Winterhalter M. Antibiotic uptake through porins located in the outer membrane of Gram-negative bacteria. Expert Opin Drug Deliv 2020; 18:449-457. [PMID: 33161750 DOI: 10.1080/17425247.2021.1847080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Introduction: Making selective inhibitors of novel Gram-negative targets is not a substantial challenge - getting them into Gram-negative bacteria to reach their lethal target is the bottleneck. Poor permeability of the antibiotic requires high concentration causing off target activity. The lack of simple experimental techniques to measure antibiotic uptake as well as the local concentration at the target site creates a particular bottleneck in understanding and in improving the antibiotic activity.Areas covered: Here we recall current approaches to quantify the uptake. For a few antibiotics with known evidence for channel-limited permeation, the flux across a single OmpF or OmpC channel has been measured. For a typical concentration gradient of 1 µM of antibiotics the uptake varies between one up to few hundred molecules per second and per channel.Expert opinion: The current research effort is on quantifying the flux for a larger list of compounds on a cellular (mass spectra, fluorescence) or at single channel level (electrophysiology). A larger dataset of single channel permeabilities under various condition will be a powerful tool for understanding and improving the activity of antibiotics.
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19
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Prajapati JD, Kleinekathöfer U. Voltage-Dependent Transport of Neutral Solutes through Nanopores: A Molecular View. J Phys Chem B 2020; 124:10718-10731. [PMID: 33175522 DOI: 10.1021/acs.jpcb.0c08401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The permeation of (neutral) molecules through nanopores in the presence of external voltages depends on several factors including pore electrostatics, electrophoretic force, and electro-osmotic drag. In earlier single-channel electrophysiology experiments, voltage-dependent asymmetric transport of neutral α-cyclodextrin (α-CD) molecules through the biological nanopore ΔCymA was observed. The voltage-dependent ion-associated flow of water, the so-called electro-osmotic flow, has been suggested to be the key factor behind the observed asymmetric behavior. The influence of pore electrostatics and electrophoretic force and their interplay with the electro-osmotic drag with varying buffers and voltages has not yet been analyzed at the molecular level. Hence, the detailed physical mechanism behind this intriguing permeation process is in part still unclear. In the present study, we have performed 36 μs all-atom free energy calculations by combining applied-field molecular dynamics simulations with metadynamics techniques. The influence of several ionic conditions as well as external voltages on the permeation of α-CD molecules across the ΔCymA pore has been investigated. To decipher the thermodynamic and kinetic details, the lowest energy paths and the permeation times for α-CD translocation have been estimated. In the presence of KCl or MgCl2 salts, the charge of the cations is found to control the direction and magnitude of the electro-osmotic flow, which in turn strongly affects α-CD permeation. Overall, the present findings significantly improve the fundamental understanding of the voltage-dependent transport of neutral solutes across nanopores.
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Affiliation(s)
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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20
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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21
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Prajapati JD, Mele C, Aksoyoglu MA, Winterhalter M, Kleinekathöfer U. Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field. J Chem Inf Model 2020; 60:3188-3203. [DOI: 10.1021/acs.jcim.0c00389] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Crystal Mele
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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22
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Bafna JA, Pangeni S, Winterhalter M, Aksoyoglu MA. Electroosmosis Dominates Electrophoresis of Antibiotic Transport Across the Outer Membrane Porin F. Biophys J 2020; 118:2844-2852. [PMID: 32348725 DOI: 10.1016/j.bpj.2020.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/12/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
We report that the dynamics of antibiotic capture and transport across a voltage-biased OmpF nanopore is dominated by the electroosmotic flow rather than the electrophoretic force. By reconstituting an OmpF porin in an artificial lipid bilayer and applying an electric field across it, we are able to elucidate the permeation of molecules and their mechanism of transport. This field gives rise to an electrophoretic force acting directly on a charged substrate but also indirectly via coupling to all other mobile ions, causing an electroosmotic flow. The directionality and magnitude of this flow depends on the selectivity of the channel. Modifying the charge state of three different substrates (norfloxacin, ciprofloxacin, and enoxacin) by varying the pH between 6 and 9 while the charge and selectivity of OmpF is conserved allows us to work under conditions in which electroosmotic flow and electrophoretic forces add or oppose. This configuration allows us to identify and distinguish the contributions of the electroosmotic flow and the electrophoretic force on translocation. Statistical analysis of the resolvable dwell times reveals rich kinetic details regarding the direction and the stochastic movement of antibiotics inside the nanopore. We quantitatively describe the electroosmotic velocity component experienced by the substrates and their diffusion coefficients inside the porin with an estimate of the energy barrier experienced by the molecules caused by the interaction with the channel wall, which slows down the permeation by several orders of magnitude.
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Affiliation(s)
- Jayesh A Bafna
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sushil Pangeni
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | | | - M Alphan Aksoyoglu
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
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23
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Golla VK, Prajapati JD, Joshi M, Kleinekathöfer U. Exploration of Free Energy Surfaces Across a Membrane Channel Using Metadynamics and Umbrella Sampling. J Chem Theory Comput 2020; 16:2751-2765. [PMID: 32167296 DOI: 10.1021/acs.jctc.9b00992] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To reach their site of action, it is essential for antibiotic molecules to cross the bacterial outer membrane. The progress of enhanced sampling techniques in molecular dynamics simulations enables us to understand these translocations at an atomic level. To this end, calculations of free energy surfaces for these permeation processes are of key importance. Herein, we investigate the translocation of a variety of anionic solutes through the outer membrane pore OprO of the Gram-negative bacterium Pseudomonas aeruginosa using the metadynamics and umbrella sampling techniques at the all-atom level. Free energy calculations have been performed employing these two distinct methods in order to illustrate the difference in computed free energies, if any. The investigated solutes range from a single atomic chloride ion over a multiatomic monophosphate ion to a more bulky fosmidomycin antibiotic. The role of complexity of the permeating solutes in estimating accurate free energy profiles is demonstrated by performing extensive convergence analysis. For simple monatomic ions, good agreement between the well-tempered metadynamics and the umbrella sampling approaches is achieved, while for the permeation of the monophosphate ion differences start to appear. In the case of larger molecules such as fosmidomycin it is a tough challenge to achieve converged free energy profiles. This issue is mainly due to neglecting orthogonal degrees of freedom during the free energy calculations. Nevertheless, the freely driven metadynamics approach leads to clearly advantageous results. Additionally, atomistic insights of the translocation mechanisms of all three solutes are discussed.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Manas Joshi
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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24
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Vikraman D, Satheesan R, Kumar KS, Mahendran KR. Nanopore Passport Control for Substrate-Specific Translocation. ACS NANO 2020; 14:2285-2295. [PMID: 31976649 DOI: 10.1021/acsnano.9b09408] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membrane protein pores have demonstrated applications in nanobiotechnology and single-molecule chemistry for effective detection of biomolecules. Here, we define the molecular basis of carbohydrate polymers translocation through a substrate-specific bacterial nanopore, CymA, which has a 15-residue N terminus segment inside the pore, restricting its diameter. Using single-channel recordings, we determined the kinetics of cationic cyclic oligosaccharide binding and elucidated the translocation mechanism across the pore in real-time. The cationic cyclic hexasaccharide binds to the densely packed negatively charged residues at the extracellular side of the pore with high affinity, facilitating its entry into the pore driven by the applied voltage. Further, the dissociation rate constant increased with increasing voltages, indicating unidirectional translocation toward the pore exit. Specifically, a larger cationic cyclic octasaccharide rapidly blocked the pore more effectively, resulting in the complete closure of the pore with increasing voltage, implying only strong binding. Further, we show that uncharged oligosaccharides exclusively bind to the extracellular side of the pore and the electroosmotic flow most likely drives their translocation. We propose that CymA favors selective translocation of cyclic hexasaccharide and linear maltooligosaccharides due to an asymmetrical charge pattern and the N terminus that regulates the substrate transport. We suggest that this substrate-specific nanopore with sophisticated geometry will be useful for complex biopolymer characterization.
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Affiliation(s)
- Devika Vikraman
- Membrane Biology Laboratory, Interdisciplinary Research Program , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram 695014 , India
| | - Remya Satheesan
- Membrane Biology Laboratory, Interdisciplinary Research Program , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram 695014 , India
- Manipal Academy of Higher Education , Manipal , Karnataka , 576104 , India
| | - K Santhosh Kumar
- Membrane Biology Laboratory, Interdisciplinary Research Program , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram 695014 , India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Interdisciplinary Research Program , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram 695014 , India
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25
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Zernia S, van der Heide NJ, Galenkamp NS, Gouridis G, Maglia G. Current Blockades of Proteins inside Nanopores for Real-Time Metabolome Analysis. ACS NANO 2020; 14:2296-2307. [PMID: 32003969 PMCID: PMC7045694 DOI: 10.1021/acsnano.9b09434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 05/14/2023]
Abstract
Biological nanopores are emerging as powerful and low-cost sensors for real-time analysis of biological samples. Proteins can be incorporated inside the nanopore, and ligand binding to the protein adaptor yields changes in nanopore conductance. In order to understand the origin of these conductance changes and develop sensors for detecting metabolites, we tested the signal originating from 13 different protein adaptors. We found that the quality of the protein signal depended on both the size and charge of the protein. The engineering of a dipole within the surface of the adaptor reduced the current noise by slowing the protein dynamics within the nanopore. Further, the charge of the ligand and the induced conformational changes of the adaptor defined the conductance changes upon metabolite binding, suggesting that the protein resides in an electrokinetic minimum within the nanopore, the position of which is altered by the ligand. These results represent an important step toward understanding the dynamics of the electrophoretic trapping of proteins inside nanopores and will allow developing next-generation sensors for metabolome analysis.
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Affiliation(s)
- Sarah Zernia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giorgos Gouridis
- Rega
Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Box 1037, 3000 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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26
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Porins and small-molecule translocation across the outer membrane of Gram-negative bacteria. Nat Rev Microbiol 2019; 18:164-176. [DOI: 10.1038/s41579-019-0294-2] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
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27
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Breaching the Barrier: Quantifying Antibiotic Permeability across Gram-negative Bacterial Membranes. J Mol Biol 2019; 431:3531-3546. [DOI: 10.1016/j.jmb.2019.03.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022]
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28
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Pieńko T, Trylska J. Computational Methods Used to Explore Transport Events in Biological Systems. J Chem Inf Model 2019; 59:1772-1781. [DOI: 10.1021/acs.jcim.8b00974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tomasz Pieńko
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, S. Banacha 1a, 02-097 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
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29
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Wang J, Bafna JA, Bhamidimarri SP, Winterhalter M. Permeation von kleinen Molekülen durch Membrankanäle: Chemische Modifikation zur Quantifizierung des Transports über OmpF. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jiajun Wang
- Department of Life Sciences und Chemistry Jacobs University Campus Ring 1 28759 Bremen Deutschland
| | - Jayesh Arun Bafna
- Department of Life Sciences und Chemistry Jacobs University Campus Ring 1 28759 Bremen Deutschland
| | | | - Mathias Winterhalter
- Department of Life Sciences und Chemistry Jacobs University Campus Ring 1 28759 Bremen Deutschland
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30
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Wang J, Bafna JA, Bhamidimarri SP, Winterhalter M. Small‐Molecule Permeation across Membrane Channels: Chemical Modification to Quantify Transport across OmpF. Angew Chem Int Ed Engl 2019; 58:4737-4741. [DOI: 10.1002/anie.201814489] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Jiajun Wang
- Department of Life Sciences and Chemistry Jacobs University Campus Ring 1 28759 Bremen Germany
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry Jacobs University Campus Ring 1 28759 Bremen Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry Jacobs University Campus Ring 1 28759 Bremen Germany
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31
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Bartsch A, Llabrés S, Pein F, Kattner C, Schön M, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C. High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB. Sci Rep 2019; 9:1264. [PMID: 30718567 PMCID: PMC6362148 DOI: 10.1038/s41598-018-37066-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
The permeation of most antibiotics through the outer membrane of Gram-negative bacteria occurs through porin channels. To design drugs with increased activity against Gram-negative bacteria in the face of the antibiotic resistance crisis, the strict constraints on the physicochemical properties of the permeants imposed by these channels must be better understood. Here we show that a combination of high-resolution electrophysiology, new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding events between the β-lactam antibiotic ampicillin and the porin PorB from the pathogenic bacterium Neisseria meningitidis. In particular, an asymmetry often seen in the electrophysiological characteristics of ligand-bound channels is utilised to characterise the binding site and molecular interactions in detail, based on the principles of electro-osmotic flow through the channel. Our results provide a rationale for the determinants that govern the binding and permeation of zwitterionic antibiotics in porin channels.
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Affiliation(s)
- Annika Bartsch
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Nethergate, Dundee, DD1 5EH, UK
| | - Florian Pein
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Christof Kattner
- ZIK HALOmem, Membrane Protein Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Straße 3, 06120, Halle (Saale), Germany
- Juno Therapeutics GmbH, Göttingen, Germany
| | - Markus Schön
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Manuel Diehn
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Mikio Tanabe
- Institute of Materials Structure Science, Structural Biology Research Center, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Nethergate, Dundee, DD1 5EH, UK.
- Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4NH, UK.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany.
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32
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Bhamidimarri SP, Zahn M, Prajapati JD, Schleberger C, Söderholm S, Hoover J, West J, Kleinekathöfer U, Bumann D, Winterhalter M, van den Berg B. A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii. Structure 2019; 27:268-280.e6. [DOI: 10.1016/j.str.2018.10.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/19/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022]
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33
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Abstract
The transport of small molecules across membranes is essential for the import of nutrients and other energy sources into the cell and, for the export of waste and other potentially harmful byproducts out of the cell. While hydrophobic molecules are permeable to membranes, ions and other small polar molecules require transport via specialized membrane transport proteins . The two major classes of membrane transport proteins are transporters and channels. With our focus here on porins-major class of non-specific diffusion channel proteins , we will highlight some recent structural biology reports and functional assays that have substantially contributed to our understanding of the mechanism that mediates uptake of small molecules, including antibiotics, across the outer membrane of Enterobacteriaceae . We will also review advances in the regulation of porin expression and porin biogenesis and discuss these pathways as new therapeutic targets.
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Affiliation(s)
- Muriel Masi
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | | | - Jean-Marie Pagès
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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34
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Dumont E, Vergalli J, Pajovic J, Bhamidimarri SP, Morante K, Wang J, Lubriks D, Suna E, Stavenger RA, Winterhalter M, Réfrégiers M, Pagès JM. Mechanistic aspects of maltotriose-conjugate translocation to the Gram-negative bacteria cytoplasm. Life Sci Alliance 2018; 2:e201800242. [PMID: 30620010 PMCID: PMC6311466 DOI: 10.26508/lsa.201800242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Small molecule accumulation in Gram-negative bacteria is a key challenge to discover novel antibiotics, because of their two membranes and efflux pumps expelling toxic molecules. An approach to overcome this challenge is to hijack uptake pathways so that bacterial transporters shuttle the antibiotic to the cytoplasm. Here, we have characterized maltodextrin-fluorophore conjugates that can pass through both the outer and inner membranes mediated by components of the Escherichia coli maltose regulon. Single-channel electrophysiology recording demonstrated that the compounds permeate across the LamB channel leading to accumulation in the periplasm. We have also demonstrated that a maltotriose conjugate distributes into both the periplasm and cytoplasm. In the cytoplasm, the molecule activates the maltose regulon and triggers the expression of maltose binding protein in the periplasmic space indicating that the complete maltose entry pathway is induced. This maltotriose conjugate can (i) reach the periplasmic and cytoplasmic compartments to significant internal concentrations and (ii) auto-induce its own entry pathway via the activation of the maltose regulon, representing an interesting prototype to deliver molecules to the cytoplasm of Gram-negative bacteria.
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Affiliation(s)
- Estelle Dumont
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Service de Santé des Armées, Institut de Recherche Biomédicale des Armées, Membranes et Cibles Thérapeutiques, Marseille, France
| | - Julia Vergalli
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Service de Santé des Armées, Institut de Recherche Biomédicale des Armées, Membranes et Cibles Thérapeutiques, Marseille, France
| | - Jelena Pajovic
- DISCO Beamline, Synchrotron Soleil, Saint-Aubin, France.,University of Belgrade, Faculty of Physics, Belgrade, Serbia
| | - Satya P Bhamidimarri
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Koldo Morante
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Jiajun Wang
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | | | - Edgars Suna
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert A Stavenger
- Antibacterial Discovery Performance Unit, Infectious Diseases Discovery, GlaxoSmithKline, Collegeville, PA, USA
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | | | - Jean-Marie Pagès
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Service de Santé des Armées, Institut de Recherche Biomédicale des Armées, Membranes et Cibles Thérapeutiques, Marseille, France
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35
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Solano CJF, Prajapati JD, Pothula KR, Kleinekathöfer U. Brownian Dynamics Approach Including Explicit Atoms for Studying Ion Permeation and Substrate Translocation across Nanopores. J Chem Theory Comput 2018; 14:6701-6713. [DOI: 10.1021/acs.jctc.8b00917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Carlos J. F. Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Jigneshkumar D. Prajapati
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Karunakar R. Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
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36
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Santos RS, Figueiredo C, Azevedo NF, Braeckmans K, De Smedt SC. Nanomaterials and molecular transporters to overcome the bacterial envelope barrier: Towards advanced delivery of antibiotics. Adv Drug Deliv Rev 2018; 136-137:28-48. [PMID: 29248479 DOI: 10.1016/j.addr.2017.12.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 01/13/2023]
Abstract
With the dramatic consequences of bacterial resistance to antibiotics, nanomaterials and molecular transporters have started to be investigated as alternative antibacterials or anti-infective carrier systems to improve the internalization of bactericidal drugs. However, the capability of nanomaterials/molecular transporters to overcome the bacterial cell envelope is poorly understood. It is critical to consider the sophisticated architecture of bacterial envelopes and reflect how nanomaterials/molecular transporters can interact with these envelopes, being the major aim of this review. The first part of this manuscript overviews the permeability of bacterial envelopes and how it limits the internalization of common antibiotic and novel oligonucleotide drugs. Subsequently we critically discuss the mechanisms that allow nanomaterials/molecular transporters to overcome the bacterial envelopes, focusing on the most promising ones to this end - siderophores, cyclodextrins, metal nanoparticles, antimicrobial/cell-penetrating peptides and fusogenic liposomes. This review may stimulate drug delivery and microbiology scientists in designing effective nanomaterials/molecular transporters against bacterial infections.
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37
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Terrasse R, Winterhalter M. Translocation of small molecules through engineered outer-membrane channels from Gram-negative bacteria. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:111. [PMID: 30238205 DOI: 10.1140/epje/i2018-11721-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Selective permeability is a key feature of biological membranes. It is controlled by the physico-chemical properties of the lipid bilayer and by channel-forming membrane proteins. Here we focus on the permeation of small molecules across channel-forming proteins in Gram-negative bacteria called porins and present a new approach based on artificial amino acids. We introduced Hco, a fluorescent amino acid with characteristic excitation and emission wavelengths, into OmpF and measured FRET from Hco to dissolved Bocillin FL using solubilized OmpF porins. We examined four variants of OmpF and by doing so, we were able to show that small molecules, like Bocillin FL, are remaining long enough in the porin in order to undergo FRET and produce a reproducible fluorescence signal. This finding opens the way to quantify translocation in the future by the simultaneous detection of resistive pulses and differential fluorescence with FRET as an example.
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Affiliation(s)
- Rémi Terrasse
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719, Bremen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719, Bremen, Germany.
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38
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Satheesan R, R SK, Mahendran KR. Controlling Interactions of Cyclic Oligosaccharides with Hetero-Oligomeric Nanopores: Kinetics of Binding and Release at the Single-Molecule Level. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801192. [PMID: 30009552 DOI: 10.1002/smll.201801192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Controlling the molecular interactions through protein nanopores is crucial for effectively detecting single molecules. Here, the development of a hetero-oligomeric nanopore derived from Nocardia farcinica porin AB (NfpAB) is discussed for single-molecule sensing of biopolymers. Using single-channel recording, the interaction of cyclic oligosaccharides such as cationic cyclodextrins (CDs) of different symmetries and charges with NfpAB is measured. Studies of the transport kinetics of CDs reveal asymmetric geometry and charge distribution of NfpAB. The applied potential promotes the attachment of the cationic CDs to the negatively charged pore surface due to electrostatic interaction. Further, the attached CDs are released from the pore by reversing the applied potential in time-resolved blockages. Release of CDs from the pore depends on its charge, size, and magnitude of the applied potential. The kinetics of CD attachment and release is controlled by fine-tuning the applied potential demonstrating the successful molecular transport across these nanopores. It is suggested that such controlled molecular interactions with protein nanopores using organic templates can be useful for several applications in nanopore technology and single-molecule chemistry.
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Affiliation(s)
- Remya Satheesan
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Smrithi Krishnan R
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
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39
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Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae. Structure 2018; 26:708-721.e4. [PMID: 29657131 DOI: 10.1016/j.str.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/15/2018] [Accepted: 03/16/2018] [Indexed: 01/26/2023]
Abstract
The outer membranes (OM) of many Gram-negative bacteria contain general porins, which form nonspecific, large-diameter channels for the diffusional uptake of small molecules required for cell growth and function. While the porins of Enterobacteriaceae (e.g., E. coli OmpF and OmpC) have been extensively characterized structurally and biochemically, much less is known about their counterparts in Vibrionaceae. Vibrio cholerae, the causative agent of cholera, has two major porins, OmpU and OmpT, for which no structural information is available despite their importance for the bacterium. Here we report high-resolution X-ray crystal structures of V. cholerae OmpU and OmpT complemented with molecular dynamics simulations. While similar overall to other general porins, the channels of OmpU and OmpT have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels. Together with electrophysiological and in vitro transport data, our results illuminate small-molecule uptake within the Vibrionaceae.
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40
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Abstract
Collective antibiotic drug resistance is a global threat, especially with respect to Gram-negative bacteria. The low permeability of the bacterial outer cell wall has been identified as a challenging barrier that prevents a sufficient antibiotic effect to be attained at low doses of the antibiotic. The Gram-negative bacterial cell envelope comprises an outer membrane that delimits the periplasm from the exterior milieu. The crucial mechanisms of antibiotic entry via outer membrane includes general diffusion porins (Omps) responsible for hydrophilic antibiotics and lipid-mediated pathway for hydrophobic antibiotics. The protein and lipid arrangements of the outer membrane have had a strong impact on the understanding of bacteria and their resistance to many types of antibiotics. Thus, one of the current challenges is effective interpretation at the molecular basis of the outer membrane permeability. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in solute influx. Moreover, it aims toward further understanding and exploration of prospects to improve our knowledge of physicochemical limitations that direct the translocation of antibiotics via bacterial outer membrane.
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Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen, Germany.,Consultation Division, RSGBIOGEN, New Delhi, India
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41
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Cressiot B, Greive SJ, Si W, Pascoa TC, Mojtabavi M, Chechik M, Jenkins HT, Lu X, Zhang K, Aksimentiev A, Antson AA, Wanunu M. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. ACS NANO 2017; 11:11931-11945. [PMID: 29120602 PMCID: PMC5963890 DOI: 10.1021/acsnano.7b06980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics, and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein's insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal's DNA-ratchet function.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Wei Si
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Tomas C. Pascoa
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Xueguang Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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42
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Liu Z, Ghai I, Winterhalter M, Schwaneberg U. Engineering Enhanced Pore Sizes Using FhuA Δ1-160 from E. coli Outer Membrane as Template. ACS Sens 2017; 2:1619-1626. [PMID: 29052976 DOI: 10.1021/acssensors.7b00481] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biological membranes are the perfect example of a molecular filter using membrane channels to control the permeability of small water-soluble molecules. To allow filtering of larger hydrophilic molecules we started from the known mutant channel FhuA Δ1-160 in which the cork domain closing the channel had been removed. Here we further expand the pore diameter by copying the amino acid sequence of two β-strands in a stepwise manner increasing the total number of β-strands from 22 to 34. The pore size of the respective expanded channel protein was characterized by single-channel conductance. Insertion of additional β-strands increased the pore conductance but also induced more ion current flickering on the millisecond scale. Further, polymer exclusion measurements were performed by analyzing single-channel conductance in the presence of differently sized polyethylene glycol of known polymer random coil radii. The conclusion from channel conductance of small channel penetrating polymers versus larger excluded ones suggested an increase in pore radii from 1.6 nm for FhuA Δ1-160 up to a maximum of about 2.7 nm for +8 β insertion. Integration of more β-strand caused instability of the channel and exclusion of smaller sized polymer. FhuA Δ1-160 + 10 β and FhuA Δ1-160 + 12 β effective radius decreased to 1.4 and 1.3 nm, respectively, showing the limitations of this approach.
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Affiliation(s)
- Zhanzhi Liu
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Ishan Ghai
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, 28719, Bremen, Germany
| | - Mathias Winterhalter
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, 28719, Bremen, Germany
| | - Ulrich Schwaneberg
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany
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43
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Biophysical characterization of E. coli TolC interaction with the known blocker hexaamminecobalt. Biochim Biophys Acta Gen Subj 2017; 1861:2702-2709. [DOI: 10.1016/j.bbagen.2017.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/26/2017] [Accepted: 07/22/2017] [Indexed: 11/18/2022]
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44
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Soysa HSM, Schulte A, Suginta W. Functional analysis of an unusual porin-like channel that imports chitin for alternative carbon metabolism in Escherichia coli. J Biol Chem 2017; 292:19328-19337. [PMID: 28972167 DOI: 10.1074/jbc.m117.812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli have the genetic potential to use chitin as a carbon source in the absence of glucose, importing it via the chitin-uptake channel EcChiP for processing by the glucosamine catabolic pathway. The chip gene is usually not expressed when E. coli are grown on glucose-enriched nutrients, providing a general regulatory mechanism for the pathway. EcChiP is unusual in that it is homologous to porins and monomeric instead of trimeric, the typical form of sugar-specific channels, making it unclear how this channel operates. We recently reported that EcChiP could form a stable channel in lipid membranes and that the channel is specific for chitooligosaccharides. This report describes the biophysical nature of sugar-channel interactions and the kinetics of sugar association and dissociation. Titrating EcChiP with chitohexaose resulted in protein fluorescence enhancement in a concentration-dependent manner, yielding a binding constant of 2.9 × 105 m-1, consistent with the value of 2.5 × 105 m-1 obtained from isothermal titration microcalorimetry. Analysis of the integrated heat change suggested that the binding process was endothermic and driven by entropy. Single-channel recordings confirmed the voltage dependence of the penetration of chitohexaose molecules into and their release from EcChiP. Once inside the pore, the sugar release rate (koff) from the affinity site increased with elevated voltage, regardless of the side of sugar addition. Our findings revealed distinct thermodynamic and kinetic features of the activity of sugar-specific EcChiP and advance our knowledge of the physiological possibility of chitin utilization by non-chitinolytic bacteria.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and
| | - Albert Schulte
- the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and .,the Center of Excellence in Advanced Functional Materials, Suranaree University of Technology Nakhon Ratchasima 30000, Thailand and
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45
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Prajapati JD, Fernández Solano CJ, Winterhalter M, Kleinekathöfer U. Characterization of Ciprofloxacin Permeation Pathways across the Porin OmpC Using Metadynamics and a String Method. J Chem Theory Comput 2017; 13:4553-4566. [PMID: 28816443 DOI: 10.1021/acs.jctc.7b00467] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The rapid spreading of antimicrobial resistance in Gram-negative bacteria has become a major threat for humans as well as animals. As one of the main factors involved, the permeability of the outer membrane has attracted a great deal of attention recently. However, the knowledge regarding the translocation mechanisms for most available antibiotics is so far rather limited. Here, a theoretical study concerning the diffusion route of ciprofloxacin across the outer membrane porin OmpC from E. coli is presented. To this end, we establish a protocol to characterize meaningful permeation pathways by combining metadynamics with the zero-temperature string method. It was found that the lowest-energy pathway requires a reorientation of ciprofloxacin in the extracellular side of the porin before reaching the constriction region with its carboxyl group ahead. Several affinity sites have been identified, and their metastability has been evaluated using unbiased simulations. Such a detailed understanding is potentially very helpful in guiding the development of next generation antibiotics.
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Affiliation(s)
- Jigneshkumar Dahyabhai Prajapati
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Carlos José Fernández Solano
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Mathias Winterhalter
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
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Bajaj H, Acosta Gutierrez S, Bodrenko I, Malloci G, Scorciapino MA, Winterhalter M, Ceccarelli M. Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules. ACS NANO 2017; 11:5465-5473. [PMID: 28485920 DOI: 10.1021/acsnano.6b08613] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.
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Affiliation(s)
- Harsha Bajaj
- Jacobs University Bremen , Campus Ring 1, D-28759 Bremen, Germany
| | | | - Igor Bodrenko
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | | | | | - Matteo Ceccarelli
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
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47
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Soundararajan G, Bhamidimarri SP, Winterhalter M. Understanding Carbapenem Translocation through OccD3 (OpdP) of Pseudomonas aeruginosa. ACS Chem Biol 2017; 12:1656-1664. [PMID: 28440622 DOI: 10.1021/acschembio.6b01150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa utilizes a plethora of substrate specific channels for the uptake of small nutrients. OccD3 (OpdP or PA4501) is an OprD-like arginine uptake channel of P. aeruginosa whose role has been implicated in carbapenem uptake. To understand the mechanism of selective permeation, we reconstituted single OccD3 channels in a planar lipid bilayer and characterized the interaction with Imipenem and Meropenem, analyzing the ion current fluctuation in the presence of substrates. We performed point mutations in the constriction region of OccD3 to understand the binding and translocation of antibiotic in OccD3. By mutating two key residues in the substrate binding sites of OccD3 (located in the internal loop L7 and basic ladder), we emphasize the importance of these residues. We show that carbapenem antibiotics follow a similar path as arginine through the constriction zone and the basic ladder to translocate across OccD3.
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Affiliation(s)
- Gowrishankar Soundararajan
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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48
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Guo Y, Jian F, Kang X. Nanopore sensor for copper ion detection using a polyamine decorated β-cyclodextrin as the recognition element. RSC Adv 2017. [DOI: 10.1039/c7ra00454k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A novel and simple nanopore sensing method has been developed for the detection of CuII ions using polyamine decorated cyclodextrin as the recognition element.
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Affiliation(s)
- Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
| | - Feifei Jian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry
- College of Chemistry & Materials Science
- Northwest University
- Xi'an 710127
- P. R. China
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Soysa HSM, Suginta W. Identification and Functional Characterization of a Novel OprD-like Chitin Uptake Channel in Non-chitinolytic Bacteria. J Biol Chem 2016; 291:13622-33. [PMID: 27226611 DOI: 10.1074/jbc.m116.728881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022] Open
Abstract
Chitoporin from the chitinolytic marine Vibrio has been characterized as a trimeric OmpC-like channel responsible for effective chitin uptake. In this study we describe the identification and characterization of a novel OprD-like chitoporin (so-called EcChiP) from Escherichia coli The gene was identified, cloned, and functionally expressed in the Omp-deficient E. coli BL21 (Omp8) Rosetta strain. On size exclusion chromatography, EcChiP had an apparent native molecular mass of 50 kDa, as predicted by amino acid sequencing and mass analysis, confirming that the protein is a monomer. Black lipid membrane reconstitution demonstrated that EcChiP could readily form stable, monomeric channels in artificial phospholipid membranes, with an average single channel conductance of 0.55 ± 0.01 nanosiemens and a slight preference for cations. Single EcChiP channels showed strong specificity, interacting with long chain chitooligosaccharides but not with maltooligosaccharides. Liposome swelling assays indicated the bulk permeation of neutral monosaccharides and showed the size exclusion limit of EcChiP to be ∼200-300 Da for small permeants that pass through by general diffusion while allowing long chain chitooligosaccharides to pass through by a facilitated diffusion process. Taking E. coli as a model, we offer the first evidence that non-chitinolytic bacteria can activate a quiescent ChiP gene to express a functional chitoporin, enabling them to take up chitooligosaccharides for metabolism as an immediate source of energy.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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