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Vendrell-Fernández S, Lozano-Picazo P, Cuadros-Sánchez P, Tejero-Ojeda MM, Giraldo R. Conversion of the OmpF Porin into a Device to Gather Amyloids on the E. coli Outer Membrane. ACS Synth Biol 2022; 11:655-667. [PMID: 34852197 DOI: 10.1021/acssynbio.1c00347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein amyloids are ubiquitous in natural environments. They typically originate from microbial secretions or spillages from mammals infected by prions, currently raising concerns about their infectivity and toxicity in contexts such as gut microbiota or soils. Exploiting the self-assembly potential of amyloids for their scavenging, here, we report the insertion of an amyloidogenic sequence stretch from a bacterial prion-like protein (RepA-WH1) in one of the extracellular loops (L5) of the abundant Escherichia coli outer membrane porin OmpF. The expression of this grafted porin enables bacterial cells to trap on their envelopes the same amyloidogenic sequence when provided as an extracellular free peptide. Conversely, when immobilized on a surface as bait, the full-length prion-like protein including the amyloidogenic peptide can catch bacteria displaying the L5-grafted OmpF. Polyphenolic molecules known to inhibit amyloid assembly interfere with peptide recognition by the engineered OmpF, indicating that this is compatible with the kind of homotypic interactions expected for amyloid assembly. Our study suggests that synthetic porins may provide suitable scaffolds for engineering biosensor and clearance devices to tackle the threat posed by pathogenic amyloids.
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Affiliation(s)
- Sol Vendrell-Fernández
- Department of Microbial Biotechnology, National Centre for Biotechnology (CSIC), c/ Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain
| | - Paloma Lozano-Picazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), c/ Ramiro de Maeztu 9, Campus Moncloa, 28040 Madrid, Spain
| | - Paula Cuadros-Sánchez
- Department of Microbial Biotechnology, National Centre for Biotechnology (CSIC), c/ Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain
| | - María M. Tejero-Ojeda
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), c/ Ramiro de Maeztu 9, Campus Moncloa, 28040 Madrid, Spain
| | - Rafael Giraldo
- Department of Microbial Biotechnology, National Centre for Biotechnology (CSIC), c/ Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), c/ Ramiro de Maeztu 9, Campus Moncloa, 28040 Madrid, Spain
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2
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Acharya A, Prajapati JD, Kleinekathöfer U. Improved Sampling and Free Energy Estimates for Antibiotic Permeation through Bacterial Porins. J Chem Theory Comput 2021; 17:4564-4577. [PMID: 34138557 DOI: 10.1021/acs.jctc.1c00369] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Antibiotics enter into bacterial cells via protein channels that serve as low-energy pathways through the outer membrane, which is otherwise impenetrable. Insights into the molecular mechanisms underlying the transport processes are vital for the development of effective antibacterials. A much-desired prerequisite is an accurate and reproducible determination of free energy surfaces for antibiotic translocation, enabling quantitative and meaningful comparisons of permeation mechanisms for different classes of antibiotics. Inefficient sampling along the orthogonal degrees of freedom, for example, in umbrella sampling and metadynamics approaches, is however a key limitation affecting the accuracy and the convergence of free energy estimates. To overcome this limitation, two sampling methods have been employed in the present study that, respectively, combine umbrella sampling and metadynamics-style biasing schemes with temperature acceleration for improved sampling along orthogonal degrees of freedom. As a model for the transport of bulky solutes, the ciprofloxacin-OmpF system has been selected. The well-tempered metadynamics approach with multiple walkers is compared with its "temperature-accelerated" variant in terms of improvements in sampling and convergence of free energy estimates. We find that the inclusion of collective variables governing solute degrees of freedom and solute-water interactions within the sampling scheme largely alleviates sampling issues. Concerning improved sampling and convergence of free energy estimates from independent simulations, the temperature-accelerated sliced sampling approach that combines umbrella sampling with temperature-accelerated molecular dynamics performs even better as shown for the ciprofloxacin-OmpF system.
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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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3
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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: 81] [Impact Index Per Article: 27.0] [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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4
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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5
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Schmitt C, Bafna JA, Schmid B, Klingl S, Baier S, Hemmis B, Wagner R, Winterhalter M, Voll LM. Manipulation of charge distribution in the arginine and glutamate clusters of the OmpG pore alters sugar specificity and ion selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183021. [PMID: 31306626 DOI: 10.1016/j.bbamem.2019.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023]
Abstract
OmpG is a general diffusion pore in the E. coli outer membrane with a molecular architecture comprising a 14-stranded β-barrel scaffold and unique structural features. In contrast to other non-specific porins, OmpG lacks a central constriction zone and has an exceptionally wide pore diameter of about 13 Å. The equatorial plane of OmpG harbors an annulus of four alternating basic and acidic patches whose function is only poorly characterized. We have investigated the role of charge distribution for ion selectivity and sugar transport with the help of OmpG variants mutated in the annulus. Substituting the glutamate residues of the annulus for histidines or alanines led to a strong reduction in cation selectivity. Replacement of the glutamates in the annulus by histidine residues also disfavored the passage of pentoses and hexoses relative to disaccharides. Our results demonstrate that despite the wide pore diameter, an annulus only consisting of two opposing basic patches confers reduced cation and monosaccharide transport compared to OmpG wild type. Furthermore, randomization of charged residues in the annulus had the potential to abolish pH-dependency of sugar transport. Our results indicate that E15, E31, R92, R111 and R211 in the annulus form electrostatic interactions with R228, E229 and D232 in loop L6 that influence pH-dependency of sugar transport.
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Affiliation(s)
- Christine Schmitt
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany; Department Biology, Division of Plant Physiology, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany.
| | - Benedikt Schmid
- Division of Biotechnology and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany.
| | - Stefan Klingl
- Division of Biotechnology and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany.
| | - Steffen Baier
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Birgit Hemmis
- Department of Biology and Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany
| | - Richard Wagner
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany; Department of Biology and Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany.
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany.
| | - Lars M Voll
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany; Department Biology, Division of Plant Physiology, Philipps-University Marburg, D-35043 Marburg, Germany.
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6
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Lopes-Rodrigues M, Zanuy D, Alemán C, Michaux C, Perpète EA. 3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes. J Biomol Struct Dyn 2018; 37:3923-3935. [DOI: 10.1080/07391102.2018.1529627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Eric A. Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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7
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Hollingsworth SA, Dror RO. Molecular Dynamics Simulation for All. Neuron 2018; 99:1129-1143. [PMID: 30236283 PMCID: PMC6209097 DOI: 10.1016/j.neuron.2018.08.011] [Citation(s) in RCA: 963] [Impact Index Per Article: 160.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022]
Abstract
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery has expanded dramatically in recent years. These simulations capture the behavior of proteins and other biomolecules in full atomic detail and at very fine temporal resolution. Major improvements in simulation speed, accuracy, and accessibility, together with the proliferation of experimental structural data, have increased the appeal of biomolecular simulation to experimentalists-a trend particularly noticeable in, although certainly not limited to, neuroscience. Simulations have proven valuable in deciphering functional mechanisms of proteins and other biomolecules, in uncovering the structural basis for disease, and in the design and optimization of small molecules, peptides, and proteins. Here we describe, in practical terms, the types of information MD simulations can provide and the ways in which they typically motivate further experimental work.
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Affiliation(s)
- Scott A Hollingsworth
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
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8
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Solov'eva T, Likhatskaya G, Khomenko V, Guzev K, Kim N, Bystritskaya E, Novikova O, Stenkova A, Rakin A, Isaeva M. The impact of length variations in the L2 loop on the structure and thermal stability of non-specific porins: The case of OmpCs from the Yersinia pseudotuberculosis complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:515-525. [PMID: 29038023 DOI: 10.1016/j.bbamem.2017.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/25/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
Porins are integral proteins of the outer membranes of gram-negative bacteria. In membranes, they exist as homotrimers and the L2 loops contribute to their stability. Comparison of OmpC porins of the Yersinia pseudotuberculosis complex with other enterobacterial porins demonstrated L2 loop length diversity, which is caused by varying numbers of dipeptide/tripeptide repeats. The OmpC porins are highly homologous to each other, and they can be subdivided into five isoforms based on their L2 loop structure. Optical spectroscopy and SDS-PAGE experiments revealed that particularities of the L2 loops affected the structure and thermal stability of the porins. Thermal denaturation studies showed that porins with shorter loops, compared to porins with longer loops, had more stable tertiary and less stable secondary and quaternary structures. According to our comparative modeling results, the L2 loops differ in their structure by adopting different spatial positions and forming different polar bonds with a neighbor monomer. The replacement of asparagine with arginine at the C-terminus of the L2 loop shifts the loop upwards and causes the loss of contacts with the arginine clusters within the pores. The increase in the length of these loops ensures that they shift down toward the pore and restore their contacts with arginines on the channel wall, as is the case in classical nonspecific porins. Despite the fact that the surface charge density varies considerably among the OmpC porins, the L2 loops form a typical negatively charged region in the center of the trimer.
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Affiliation(s)
- T Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - G Likhatskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - V Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - K Guzev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - N Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - E Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - O Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - A Stenkova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia
| | - A Rakin
- Institute for Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Naumburger Str. 96 a, 07743 Jena, Germany
| | - M Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022 Prospect 100-let Vladivostoku 159, Vladivostok, Russia.
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Patel DS, Re S, Wu EL, Qi Y, Klebba PE, Widmalm G, Yeom MS, Sugita Y, Im W. Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. Biophys J 2016; 110:930-8. [PMID: 26910429 DOI: 10.1016/j.bpj.2016.01.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.
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Affiliation(s)
- Dhilon S Patel
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Emilia L Wu
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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Samaniego-Barrón L, Luna-Castro S, Piña-Vázquez C, Suárez-Güemes F, de la Garza M. Two outer membrane proteins are bovine lactoferrin-binding proteins in Mannheimia haemolytica A1. Vet Res 2016; 47:93. [PMID: 27599994 PMCID: PMC5013584 DOI: 10.1186/s13567-016-0378-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/14/2016] [Indexed: 11/10/2022] Open
Abstract
Mannheimia haemolytica is a Gram negative bacterium that is part of the bovine respiratory disease, which causes important economic losses in the livestock industry. In the present work, the interaction between M. haemolytica A1 and bovine lactoferrin (BLf) was studied. This iron-chelating glycoprotein is part of the mammalian innate-immune system and is present in milk and mucosal secretions; Lf is also contained in neutrophils secondary granules, which release this glycoprotein at infection sites. It was evidenced that M. haemolytica was not able to use iron-charged BLf (BholoLf) as a sole iron source; nevertheless, iron-lacked BLf (BapoLf) showed a bactericidal effect against M. haemolytica with MIC of 4.88 ± 1.88 and 7.31 ± 1.62 μM for M. haemolytica strain F (field isolate) and M. haemolytica strain R (reference strain), respectively. Through overlay assays and 2-D electrophoresis, two OMP of 32.9 and 34.2 kDa with estimated IP of 8.18 and 9.35, respectively, were observed to bind both BapoLf and BholoLf; these OMP were identified by Maldi-Tof as OmpA (heat-modifiable OMP) and a membrane protein (porin). These M. haemolytica BLf binding proteins could be interacting in vivo with both forms of BLf depending on the iron state of the bovine.
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Affiliation(s)
- Luisa Samaniego-Barrón
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico
| | - Sarahí Luna-Castro
- Facultad de Medicina Veterinaria y Zootecnia Dr. Norberto Treviño Zapata, Universidad Autónoma de Tamaulipas, Carretera a Cd. Mante Km 5, CP 87000 Ciudad Victoria, Tamaulipas Mexico
| | - Carolina Piña-Vázquez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico
| | - Francisco Suárez-Güemes
- Departamento de Microbiología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Cd. Universitaria, Coyoacán, CP 04510 Ciudad de México, Mexico
| | - Mireya de la Garza
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico
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11
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- 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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12
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Lidón López M, Queralt-Martín M, Alcaraz A. Experimental demonstration of charge inversion in a protein channel in the presence of monovalent cations. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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13
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Pongprayoon P. How do the protonation states of E296 and D312 in OmpF and D299 and D315 in homologous OmpC affect protein structure and dynamics? Simulation studies. Comput Biol Chem 2014; 53PB:226-234. [PMID: 25462331 DOI: 10.1016/j.compbiolchem.2014.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 10/24/2022]
Abstract
In this study, the structural and dynamic properties of two major porins (OmpF and OmpC) in Escherichia coli are investigated using molecular dynamics (MD) simulations. Both porins have the extracellular loop L3 folded halfway through the pore to form a constriction area. The solute influx and efflux are controlled by the L3 movement. E296 and D312 in OmpF and homologous D299 and D315 in OmpC located on the barrel wall are found to play a key role in L3 gating activity. All possible charged states of both E296(D299) and D312(315) are applied in this study to observe changes in overall structure and especially L3 movement. The results show that different protonation states of both residues cause the large-scale deviations in structure and pore cavity especially in OmpF. Fully charged E296(D299) and D312(315) increase the protein flexibility significantly. Deprotonating at least one of E296(D299) and D312(315) helps to fasten L3 to the barrel wall and maintain pore size. Lacking of interactions with D312(315) can lead to the pore closure in OmpF. Comparing with OmpC, not only is OmpF less stable, but it is also more sensitive to the charge states of both E296(D299) and D312(315).
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Affiliation(s)
- Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
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14
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Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J Am Chem Soc 2014; 135:16561-8. [PMID: 24106986 DOI: 10.1021/ja407783a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.
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Affiliation(s)
- Balasundaresan Dhakshnamoorthy
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Brigitte K Ziervogel
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Lydia Blachowicz
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
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15
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Queralt-Martín M, Verdiá-Báguena C, Aguilella VM, Alcaraz A. Electrostatic interactions drive the nonsteric directional block of OmpF channel by La3+. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:15320-15327. [PMID: 24256306 DOI: 10.1021/la402700m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Ion channels regulate the transport of molecules and the electric signal transduction in living cells by means of complex and even highly sophisticated mechanisms. We focus here on the crucial role that polyvalent ions, well-known modulators of many biological nanosystems, play in ion channel function. In particular, we show that trace amounts of lanthanum are able to block the bacterial porin OmpF, a large biological pore of Escherichia coli wide enough to exchange antibiotics and other larger molecules. The underlying mechanism has a strong directional character: it is sensitive to the sign of the applied voltage and to the side of the blocker addition. We explore these channel features by combining planar lipid bilayer electrophysiology at the single channel level, site-directed mutagenesis, and inductively coupled plasma mass spectrometry (ICP-MS). In contrast to other well-described channel blockers, which seem to occlude the narrower part of the pore, we envisage a nonsteric mechanism based on electrostatic interactions.
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Affiliation(s)
- María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , 12071 Castellón, Spain
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16
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Kattner C, Zaucha J, Jaenecke F, Zachariae U, Tanabe M. Identification of a cation transport pathway in Neisseria meningitidis PorB. Proteins 2013; 81:830-40. [PMID: 23255122 DOI: 10.1002/prot.24241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/06/2012] [Accepted: 12/08/2012] [Indexed: 11/10/2022]
Abstract
Neisseria meningitidis is the main causative agent of bacterial meningitis. In its outer membrane, the trimeric Neisserial porin PorB is responsible for the diffusive transport of essential hydrophilic solutes across the bilayer. Previous molecular dynamics simulations based on the recent crystal structure of PorB have suggested the presence of distinct solute translocation pathways through this channel. Although PorB has been electrophysiologically characterized as anion-selective, cation translocation through nucleotide-bound PorB during pathogenesis is thought to be instrumental for host cell death. As a result, we were particularly interested in further characterizing cation transport through the pore. We combined a structural approach with additional computational analysis. Here, we present two crystal structures of PorB at 2.1 and 2.65 Å resolution. The new structures display additional electron densities around the protruding loop 3 (L3) inside the pore. We show that these electron densities can be identified as monovalent cations, in our case Cs(+), which are tightly bound to the inner channel. Molecular dynamics simulations reveal further ion interactions and the free energy landscape for ions inside PorB. Our results suggest that the crystallographically identified locations of Cs(+) form a cation transport pathway inside the pore. This finding suggests how positively charged ions are translocated through PorB when the channel is inserted into mitochondrial membranes during Neisserial infection, a process which is considered to dissipate the mitochondrial transmembrane potential gradient and thereby induce apoptosis.
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Affiliation(s)
- Christof Kattner
- HALOmem, Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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17
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Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J 2013; 32:728-41. [PMID: 23403925 PMCID: PMC3590989 DOI: 10.1038/emboj.2013.17] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 01/07/2013] [Indexed: 12/14/2022] Open
Abstract
To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.
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18
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Abstract
The structure of OmpF porin in complex with three common antibiotics (zwitterionic ampicillin, anionic ertapenem, and di-anionic carbenicillin) was determined using X-ray crystallography. The three antibiotics are found to bind within the extracellular and periplasmic pore vestibules, away from the narrow OmpF constriction zone. Using the X-ray structures as a starting point, nonequilibrium molecular dynamics simulations with an applied membrane voltage show that ionic current through the OmpF channel is blocked with bound ampicillin, but not with bound carbenicillin. The susceptibility of Escherichia coli expressing OmpF mutants to ampicillin and carbenicillin was also experimentally characterized using microbiologic assays. These results show that general diffusion by OmpF porins allows for transfer of molecules with varied charged states and give insights into the design of more efficient antibiotics. A better understanding of this mechanism will shed light on nature's way of devising channels able to enhance the transport of molecules through membranes.
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Affiliation(s)
- Brigitte K Ziervogel
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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19
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Divalent Metal Ion Transport across Large Biological Ion Channels and Their Effect on Conductance and Selectivity. Biochem Res Int 2012; 2012:245786. [PMID: 23008773 PMCID: PMC3449104 DOI: 10.1155/2012/245786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/17/2022] Open
Abstract
Electrophysiological characterization of large protein channels, usually displaying multi-ionic transport and weak ion selectivity, is commonly performed at physiological conditions (moderate gradients of KCl solutions at decimolar concentrations buffered at neutral pH). We extend here the characterization of the OmpF porin, a wide channel of the outer membrane of E. coli, by studying the effect of salts of divalent cations on the transport properties of the channel. The regulation of divalent cations concentration is essential in cell metabolism and understanding their effects is of key importance, not only in the channels specifically designed to control their passage but also in other multiionic channels. In particular, in porin channels like OmpF, divalent cations modulate the efficiency of molecules having antimicrobial activity. Taking advantage of the fact that the OmpF channel atomic structure has been resolved both in water and in MgCl2 aqueous solutions, we analyze the single channel conductance and the channel selectivity inversion aiming to separate the role of the electrolyte itself, and the counterion accumulation induced by the protein channel charges and other factors (binding, steric effects, etc.) that being of minor importance in salts of monovalent cations become crucial in the case of divalent cations.
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20
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Balasubramaniam D, Arockiasamy A, Kumar PD, Sharma A, Krishnaswamy S. Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi. J Struct Biol 2012; 178:233-44. [PMID: 22525817 DOI: 10.1016/j.jsb.2012.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 04/03/2012] [Accepted: 04/07/2012] [Indexed: 11/25/2022]
Abstract
OmpF is a major general diffusion porin of Salmonella typhi, a Gram-negative bacterium, which is an obligatory human pathogen causing typhoid. The structure of S. typhi Ty21a OmpF (PDB Id: 3NSG) determined at 2.8 Å resolution by X-ray crystallography shows a 16-stranded β-barrel with three β-barrel monomers associated to form a trimer. The packing observed in S. typhi Ty21a rfOmpF crystals has not been observed earlier in other porin structures. The variations seen in the loop regions provide a starting point for using the S. typhi OmpF for structure-based multi-valent vaccine design. Along one side of the S. typhi Ty21a OmpF pore there exists a staircase arrangement of basic residues (20R, 60R, 62K, 65R, 77R, 130R and 16K), which also contribute, to the electrostatic potential in the pore. This structure suggests the presence of asymmetric electrostatics in the porin oligomer. Moreover, antibiotic translocation, permeability and reduced uptake in the case of mutants can be understood based on the structure paving the way for designing new antibiotics.
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Affiliation(s)
- D Balasubramaniam
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625 021, India
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21
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Numata J, Juneja A, Diestler DJ, Knapp EW. Influence of Spacer–Receptor Interactions on the Stability of Bivalent Ligand–Receptor Complexes. J Phys Chem B 2012; 116:2595-604. [DOI: 10.1021/jp211383s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jorge Numata
- Department of Biology, Chemistry
and Pharmacy, Institute of Chemistry and Biochemistry, Fabeckstrasse 36A, D-14195 Berlin, Germany
| | - Alok Juneja
- Department of Biology, Chemistry
and Pharmacy, Institute of Chemistry and Biochemistry, Fabeckstrasse 36A, D-14195 Berlin, Germany
- Department of Biosciences and
Nutrition, Karolinska Institutet, SE-141
83 Huddinge, Sweden
| | - Dennis J. Diestler
- Department of Biology, Chemistry
and Pharmacy, Institute of Chemistry and Biochemistry, Fabeckstrasse 36A, D-14195 Berlin, Germany
- University of Nebraska-Lincoln, Lincoln, Nebraska 68583,
United States
| | - Ernst-Walter Knapp
- Department of Biology, Chemistry
and Pharmacy, Institute of Chemistry and Biochemistry, Fabeckstrasse 36A, D-14195 Berlin, Germany
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22
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23
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Calero C, Faraudo J, Aguilella-Arzo M. First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:021908. [PMID: 21405864 DOI: 10.1103/physreve.83.021908] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Indexed: 05/30/2023]
Abstract
We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force F(eff) can be obtained after appropriate subdivision of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson-Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.
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Affiliation(s)
- Carles Calero
- Institut de Ciència dels Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain.
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24
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Queralt-Martín M, García-Giménez E, Mafé S, Alcaraz A. Divalent cations reduce the pH sensitivity of OmpF channel inducing the pKashift of key acidic residues. Phys Chem Chem Phys 2011; 13:563-9. [DOI: 10.1039/c0cp01325k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Aguilella VM, Queralt-Martín M, Aguilella-Arzo M, Alcaraz A. Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity. Integr Biol (Camb) 2010; 3:159-72. [PMID: 21132209 DOI: 10.1039/c0ib00048e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion channels are hollow proteins that have evolved to exhibit discrimination between charged solutes. This property, known as ion selectivity is critical for several biological functions. By using the bacterial porin OmpF as a model system of wide protein channels, we demonstrate that significant insights can be gained when selectivity measurements are combined with electrodiffusion continuum models and simulations based on the atomic structure. A correct interpretation of the mechanisms ruling the many sources of channel discrimination is a first, indispensable step for the understanding of the controlled movement of ions into or out of cells characteristic of many physiological processes. We conclude that the scattered information gathered from several independent approaches should be appropriately merged to provide a unified and coherent picture of the channel selectivity.
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Affiliation(s)
- Vicente M Aguilella
- Dept. Physics, Lab. Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain.
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26
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Faraudo J, Calero C, Aguilella-Arzo M. Ionic partition and transport in multi-ionic channels: a molecular dynamics simulation study of the OmpF bacterial porin. Biophys J 2010; 99:2107-15. [PMID: 20923644 PMCID: PMC3042589 DOI: 10.1016/j.bpj.2010.07.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/29/2010] [Accepted: 07/30/2010] [Indexed: 11/15/2022] Open
Abstract
We performed all-atom molecular dynamics simulations studying the partition of ions and the ionic current through the bacterial porin OmpF and two selected mutants. The study is motivated by new, interesting experimental findings concerning their selectivity and conductance behavior at neutral pH. The mutations considered here are designed to study the effect of removal of negative charges present in the constriction zone of the wild-type OmpF channel (which contains, on one side, a cluster with three positive residues, and on the other side, two negatively charged residues). Our results show that these mutations induce an exclusion of cations from the constriction zone of the channel, substantially reducing the flow of cations. In fact, the partition of ions inside the mutant channels is strongly inhomogeneous, with regions containing an excess of cations and regions containing an excess of anions. Interestingly, the overall number of cations inside the channel is larger than the number of anions, this excess being different for each protein channel. We found that the differences in ionic charge inside these channels are justified by the differences in electric charge between the wild-type OmpF and the mutants, following an electroneutral balance.
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Affiliation(s)
- Jordi Faraudo
- Institut de Ciència de Materials de Barcelona, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Carles Calero
- Institut de Ciència de Materials de Barcelona, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
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