101
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Hussain S, Bernstein HD. The Bam complex catalyzes efficient insertion of bacterial outer membrane proteins into membrane vesicles of variable lipid composition. J Biol Chem 2018; 293:2959-2973. [PMID: 29311257 DOI: 10.1074/jbc.ra117.000349] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/06/2017] [Indexed: 12/29/2022] Open
Abstract
Most proteins that reside in the bacterial outer membrane (OM) have a distinctive "β-barrel" architecture, but the assembly of these proteins is poorly understood. The spontaneous assembly of OM proteins (OMPs) into pure lipid vesicles has been studied extensively but often requires non-physiological conditions and time scales and is strongly influenced by properties of the lipid bilayer, including surface charge, thickness, and fluidity. Furthermore, the membrane insertion of OMPs in vivo is catalyzed by a heterooligomer called the β-barrel assembly machinery (Bam) complex. To determine the role of lipids in the assembly of OMPs under more physiological conditions, we exploited an assay in which the Bam complex mediates their insertion into membrane vesicles. After reconstituting the Bam complex into vesicles that contain a variety of different synthetic lipids, we found that two model OMPs, EspP and OmpA, folded efficiently regardless of the lipid composition. Most notably, both proteins folded into membranes composed of a gel-phase lipid that mimics the rigid bacterial OM. Interestingly, we found that EspP, OmpA, and another model protein (OmpG) folded at significantly different rates and that an α-helix embedded inside the EspP β-barrel accelerates folding. Our results show that the Bam complex largely overcomes effects that lipids exert on OMP assembly and suggest that specific interactions between the Bam complex and an OMP influence its rate of folding.
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Affiliation(s)
- Sunyia Hussain
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0538
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0538.
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102
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Keeble AH, Banerjee A, Ferla MP, Reddington SC, Anuar INAK, Howarth M. Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics. Angew Chem Int Ed Engl 2017; 56:16521-16525. [PMID: 29024296 PMCID: PMC5814910 DOI: 10.1002/anie.201707623] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/15/2017] [Indexed: 12/19/2022]
Abstract
SpyTag is a peptide that forms a spontaneous amide bond with its protein partner SpyCatcher. This protein superglue is a broadly useful tool for molecular assembly, locking together biological building blocks efficiently and irreversibly in diverse architectures. We initially developed SpyTag and SpyCatcher by rational design, through splitting a domain from a Gram-positive bacterial adhesin. In this work, we established a phage-display platform to select for specific amidation, leading to an order of magnitude acceleration for interaction of the SpyTag002 variant with the SpyCatcher002 variant. We show that the 002 pair bonds rapidly under a wide range of conditions and at either protein terminus. SpyCatcher002 was fused to an intimin derived from enterohemorrhagic Escherichia coli. SpyTag002 reaction enabled specific and covalent decoration of intimin for live cell fluorescent imaging of the dynamics of the bacterial outer membrane as cells divide.
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Affiliation(s)
- Anthony H. Keeble
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Anusuya Banerjee
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Matteo P. Ferla
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | | | | | - Mark Howarth
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
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103
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Schiffrin B, Brockwell DJ, Radford SE. Outer membrane protein folding from an energy landscape perspective. BMC Biol 2017; 15:123. [PMID: 29268734 PMCID: PMC5740924 DOI: 10.1186/s12915-017-0464-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cell envelope is essential for the survival of Gram-negative bacteria. This specialised membrane is densely packed with outer membrane proteins (OMPs), which perform a variety of functions. How OMPs fold into this crowded environment remains an open question. Here, we review current knowledge about OMP folding mechanisms in vitro and discuss how the need to fold to a stable native state has shaped their folding energy landscapes. We also highlight the role of chaperones and the β-barrel assembly machinery (BAM) in assisting OMP folding in vivo and discuss proposed mechanisms by which this fascinating machinery may catalyse OMP folding.
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Affiliation(s)
- Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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104
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Keeble AH, Banerjee A, Ferla MP, Reddington SC, Anuar INAK, Howarth M. Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anthony H. Keeble
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Anusuya Banerjee
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Matteo P. Ferla
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Samuel C. Reddington
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | | | - Mark Howarth
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
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105
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Duncan AL, Reddy T, Koldsø H, Hélie J, Fowler PW, Chavent M, Sansom MSP. Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes. Sci Rep 2017; 7:16647. [PMID: 29192147 PMCID: PMC5709381 DOI: 10.1038/s41598-017-16865-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/15/2017] [Indexed: 01/07/2023] Open
Abstract
Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies of an inwardly rectifying potassium (Kir) channel which forms specific interactions with the regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency of protein molecules to cluster has the effect of organizing the membrane into dynamic compartments. At the same time, the diversity of lipids present has a marked effect on the clustering behavior of ion channels. Sub-diffusion of proteins and lipids is observed. Protein crowding alters the sub-diffusive behavior of proteins and lipids such as PIP2 which interact tightly with Kir channels. Protein crowding also affects bilayer properties, such as membrane undulations and bending rigidity, in a PIP2-dependent manner. This interplay between the diffusion and the dynamic organization of Kir channels may have important implications for channel function.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- T-6, MS K710, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- D. E. Shaw Research, 120 W 45th St., New York, NY, 10036, USA
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Semmle, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- IPBS-CNRS, Toulouse, Midi-Pyrénées, France
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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106
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Excessive aggregation of membrane proteins in the Martini model. PLoS One 2017; 12:e0187936. [PMID: 29131844 PMCID: PMC5683612 DOI: 10.1371/journal.pone.0187936] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 11/19/2022] Open
Abstract
The coarse-grained Martini model is employed extensively to study membrane protein oligomerization. While this approach is exceptionally promising given its computational efficiency, it is alarming that a significant fraction of these studies demonstrate unrealistic protein clusters, whose formation is essentially an irreversible process. This suggests that the protein-protein interactions are exaggerated in the Martini model. If this held true, then it would limit the applicability of Martini to study multi-protein complexes, as the rapidly clustering proteins would not be able to properly sample the correct dimerization conformations. In this work we first demonstrate the excessive protein aggregation by comparing the dimerization free energies of helical transmembrane peptides obtained with the Martini model to those determined from FRET experiments. Second, we show that the predictions provided by the Martini model for the structures of transmembrane domain dimers are in poor agreement with the corresponding structures resolved using NMR. Next, we demonstrate that the first issue can be overcome by slightly scaling down the Martini protein-protein interactions in a manner, which does not interfere with the other Martini interaction parameters. By preventing excessive, irreversible, and non-selective aggregation of membrane proteins, this approach renders the consideration of lateral dynamics and protein-lipid interactions in crowded membranes by the Martini model more realistic. However, this adjusted model does not lead to an improvement in the predicted dimer structures. This implicates that the poor agreement between the Martini model and NMR structures cannot be cured by simply uniformly reducing the interactions between all protein beads. Instead, a careful amino-acid specific adjustment of the protein-protein interactions is likely required.
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107
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Meuskens I, Michalik M, Chauhan N, Linke D, Leo JC. A New Strain Collection for Improved Expression of Outer Membrane Proteins. Front Cell Infect Microbiol 2017; 7:464. [PMID: 29164072 PMCID: PMC5681912 DOI: 10.3389/fcimb.2017.00464] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/20/2017] [Indexed: 02/02/2023] Open
Abstract
Almost all integral membrane proteins found in the outer membranes of Gram-negative bacteria belong to the transmembrane β-barrel family. These proteins are not only important for nutrient uptake and homeostasis, but are also involved in such processes as adhesion, protein secretion, biofilm formation, and virulence. As surface exposed molecules, outer membrane β-barrel proteins are also potential drug and vaccine targets. High production levels of heterologously expressed proteins are desirable for biochemical and especially structural studies, but over-expression and subsequent purification of membrane proteins, including outer membrane proteins, can be challenging. Here, we present a set of deletion mutants derived from E. coli BL21 Gold (DE3) designed for the over-expression of recombinant outer membrane proteins. These strains harbor deletions of four genes encoding abundant β-barrel proteins in the outer membrane (OmpA, OmpC, OmpF, and LamB), both single and in all combinations of double, triple, and quadruple knock-outs. The sequences encoding these outer membrane proteins were deleted completely, leaving only a minimal scar sequence, thus preventing the possibility of genetic reversion. Expression tests in the quadruple mutant strain with four test proteins, including a small outer membrane β-barrel protein and variants thereof as well as two virulence-related autotransporters, showed significantly improved expression and better quality of the produced proteins over the parent strain. Differences in growth behavior and aggregation in the presence of high salt were observed, but these phenomena did not negatively influence the expression in the quadruple mutant strain when handled as we recommend. The strains produced in this study can be used for outer membrane protein production and purification, but are also uniquely useful for labeling experiments for biophysical measurements in the native membrane environment.
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Affiliation(s)
- Ina Meuskens
- Section for Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway.,Interfaculty Institute for Biochemistry, Eberhard Karls University, Tübingen, Germany
| | - Marcin Michalik
- Section for Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nandini Chauhan
- Section for Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Section for Evolution and Genetics, Department of Biosciences, University of Oslo, Oslo, Norway
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108
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Abstract
The outer membrane (OM) excludes antibiotics such as vancomycin that kill gram-positive bacteria, and so is a major contributor to multidrug resistance in gram-negative bacteria. Yet, the OM is readily bypassed by protein bacteriocins, which are toxins released by bacteria to kill their neighbors during competition for resources. Discovered over 60 y ago, it has been a mystery how these proteins cross the OM to deliver their toxic payload. We have discovered how the bacteriocin pyocin S2 (pyoS2), which degrades DNA, enters Pseudomonas aeruginosa cells. PyoS2 tricks the iron transporter FpvAI into transporting it across the OM by a process that is remarkably similar to that used by its endogenous ligand, the siderophore ferripyoverdine. Unlike their descendants, mitochondria and plastids, bacteria do not have dedicated protein import systems. However, paradoxically, import of protein bacteriocins, the mechanisms of which are poorly understood, underpins competition among pathogenic and commensal bacteria alike. Here, using X-ray crystallography, isothermal titration calorimetry, confocal fluorescence microscopy, and in vivo photoactivatable cross-linking of stalled translocation intermediates, we demonstrate how the iron transporter FpvAI in the opportunistic pathogen Pseudomonas aeruginosa is hijacked to translocate the bacteriocin pyocin S2 (pyoS2) across the outer membrane (OM). FpvAI is a TonB-dependent transporter (TBDT) that actively imports the small siderophore ferripyoverdine (Fe-Pvd) by coupling to the proton motive force (PMF) via the inner membrane (IM) protein TonB1. The crystal structure of the N-terminal domain of pyoS2 (pyoS2NTD) bound to FpvAI (Kd = 240 pM) reveals that the pyocin mimics Fe-Pvd, inducing the same conformational changes in the receptor. Mimicry leads to fluorescently labeled pyoS2NTD being imported into FpvAI-expressing P. aeruginosa cells by a process analogous to that used by bona fide TBDT ligands. PyoS2NTD induces unfolding by TonB1 of a force-labile portion of the plug domain that normally occludes the central channel of FpvAI. The pyocin is then dragged through this narrow channel following delivery of its own TonB1-binding epitope to the periplasm. Hence, energized nutrient transporters in bacteria also serve as rudimentary protein import systems, which, in the case of FpvAI, results in a protein antibiotic 60-fold bigger than the transporter’s natural substrate being translocated across the OM.
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109
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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110
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Chaturvedi D, Mahalakshmi R. Transmembrane β-barrels: Evolution, folding and energetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2467-2482. [PMID: 28943271 DOI: 10.1016/j.bbamem.2017.09.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022]
Abstract
The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.
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Affiliation(s)
- Deepti Chaturvedi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
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111
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Kim S, Patel DS, Park S, Slusky J, Klauda JB, Widmalm G, Im W. Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophys J 2017; 111:1750-1760. [PMID: 27760361 DOI: 10.1016/j.bpj.2016.09.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/19/2016] [Accepted: 09/06/2016] [Indexed: 01/05/2023] Open
Abstract
Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties. In addition, different neutralizing ion types (Ca2+, K+, and Na+) are considered to examine the ion's influence on the membrane properties. The trajectory analysis shows that (1) the area per lipid is mostly correlated to the acyl chain number, and the area per lipid increases as a function of the acyl chain number; (2) the hydrophobic thickness is mainly determined by the average acyl chain length with slight dependence on the acyl chain number, and the hydrophobic thickness generally increases with the average acyl chain length; (3) a good correlation is observed among the area per lipid, hydrophobic thickness, and acyl chain order; and (4) although the influence of neutralizing ion types on the area per lipid and hydrophobic thickness is minimal, Ca2+ stays longer on the membrane surface than K+ or Na+, consequently leading to lower lateral diffusion and a higher compressibility modulus, which agrees well with available experiments.
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Affiliation(s)
- Seonghoon Kim
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Joanna Slusky
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland, College Park, Maryland
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
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112
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Zerbe K, Moehle K, Robinson JA. Protein Epitope Mimetics: From New Antibiotics to Supramolecular Synthetic Vaccines. Acc Chem Res 2017; 50:1323-1331. [PMID: 28570824 DOI: 10.1021/acs.accounts.7b00129] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein epitope mimetics provide powerful tools to study biomolecular recognition in many areas of chemical biology. They may also provide access to new biologically active molecules and potentially to new classes of drug and vaccine candidates. Here we highlight approaches for the design of folded, structurally defined epitope mimetics, by incorporating backbone and side chains of hot residues onto a stable constrained scaffold. Using robust synthetic methods, the structural, biological, and physical properties of epitope mimetics can be optimized, by variation of both side chain and backbone chemistry. To illustrate the potential of protein epitope mimetics in medicinal chemistry and biotechnology, we present studies in two areas of infectology; the discovery of new antibiotics targeting essential outer membrane (OM) proteins in Gram-negative bacteria and the design of supramolecular synthetic vaccines. The discovery of new antibiotics with novel mechanisms of action, in particular to combat infections caused by Gram-negative pathogens, represents a major challenge in medicinal chemistry. We were inspired by naturally occurring cationic antimicrobial peptides to design structurally related peptidomimetics and to optimize their antimicrobial properties through library synthesis and screening. Through these efforts, we could show that antimicrobial β-hairpin mimetics may have structures and properties that facilitate interactions with essential bacterial β-barrel OM proteins. One recently discovered family of antimicrobial peptidomimetics targets the β-barrel protein LptD in Pseudomonas spp. This protein plays a key role in lipopolysaccaride (LPS) transport to the cell surface during OM biogenesis. Through a highly selective interaction with LptD, the peptidomimetic blocks LPS transport, resulting in nanomolar antimicrobial activity against the important human pathogen P. aeruginosa. Epitope mimetics may also have great potential in the field of vaccinology, where structural information on complexes between neutralizing antibodies and their cognate epitopes can be taken as a starting point for B cell epitope mimetic design. In order to generate potent immune responses, an effective method of delivering epitope mimetics to relevant cells and tissues in the immune system is also required. For this, engineered synthetic nanoparticles (synthetic virus-like particles, SVLPs) prepared using supramolecular chemistry can be designed with optimal surface properties for efficient dendritic cell-mediated delivery of folded B-cell and linear T-cell epitopes, along with ligands for pattern recognition receptors, into lymphoid tissues. In this way, multivalent display of the epitope mimetics occurs over the surface of the nanoparticle, suitable for cross-linking B cell receptors. In this highly immunogenic format, strong epitope-specific humoral immune responses can be elicited that target infections caused by pathogenic microorganisms. Other potential applications of epitope mimetics in next-generation therapeutics are also discussed.
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Affiliation(s)
- Katja Zerbe
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kerstin Moehle
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - John A. Robinson
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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113
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Irudayanathan FJ, Wang N, Wang X, Nangia S. Architecture of the paracellular channels formed by claudins of the blood–brain barrier tight junctions. Ann N Y Acad Sci 2017; 1405:131-146. [DOI: 10.1111/nyas.13378] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 01/31/2023]
Affiliation(s)
| | - Nan Wang
- Department of Biomedical and Chemical Engineering Syracuse University Syracuse New York
| | - Xiaoyi Wang
- Department of Biomedical and Chemical Engineering Syracuse University Syracuse New York
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering Syracuse University Syracuse New York
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114
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Iyer BR, Zadafiya P, Vetal PV, Mahalakshmi R. Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein. J Biol Chem 2017; 292:12351-12365. [PMID: 28592485 PMCID: PMC5519381 DOI: 10.1074/jbc.m117.789446] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/02/2017] [Indexed: 01/07/2023] Open
Abstract
The free energy of water-to-interface amino acid partitioning is a major contributing factor in membrane protein folding and stability. The interface residues at the C terminus of transmembrane β-barrels form the β-signal motif required for assisted β-barrel assembly in vivo but are believed to be less important for β-barrel assembly in vitro. Here, we experimentally measured the thermodynamic contribution of all 20 amino acids at the β-signal motif to the unassisted folding of the model β-barrel protein PagP. We obtained the partitioning free energy for all 20 amino acids at the lipid-facing interface (ΔΔG0w,i(φ)) and the protein-facing interface (ΔΔG0w,i(π)) residues and found that hydrophobic amino acids are most favorably transferred to the lipid-facing interface, whereas charged and polar groups display the highest partitioning energy. Furthermore, the change in non-polar surface area correlated directly with the partitioning free energy for the lipid-facing residue and inversely with the protein-facing residue. We also demonstrate that the interface residues of the β-signal motif are vital for in vitro barrel assembly, because they exhibit a side chain–specific energetic contribution determined by the change in nonpolar accessible surface. We further establish that folding cooperativity and hydrophobic collapse are balanced at the membrane interface for optimal stability of the PagP β-barrel scaffold. We conclude that the PagP C-terminal β-signal motif influences the folding cooperativity and stability of the folded β-barrel and that the thermodynamic contributions of the lipid- and protein-facing residues in the transmembrane protein β-signal motif depend on the nature of the amino acid side chain.
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Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India
| | - Punit Zadafiya
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India
| | - Pallavi Vijay Vetal
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India.
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115
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Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. J Phys Chem Lett 2017; 8:2513-2518. [PMID: 28467715 DOI: 10.1021/acs.jpclett.7b00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology: multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.
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Affiliation(s)
- Alister Boags
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street, 138671 Singapore
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, 117543 Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
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116
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Gunasinghe SD, Webb CT, Elgass KD, Hay ID, Lithgow T. Super-Resolution Imaging of Protein Secretion Systems and the Cell Surface of Gram-Negative Bacteria. Front Cell Infect Microbiol 2017; 7:220. [PMID: 28611954 PMCID: PMC5447050 DOI: 10.3389/fcimb.2017.00220] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/12/2017] [Indexed: 12/28/2022] Open
Abstract
Gram-negative bacteria have a highly evolved cell wall with two membranes composed of complex arrays of integral and peripheral proteins, as well as phospholipids and glycolipids. In order to sense changes in, respond to, and exploit their environmental niches, bacteria rely on structures assembled into or onto the outer membrane. Protein secretion across the cell wall is a key process in virulence and other fundamental aspects of bacterial cell biology. The final stage of protein secretion in Gram-negative bacteria, translocation across the outer membrane, is energetically challenging so sophisticated nanomachines have evolved to meet this challenge. Advances in fluorescence microscopy now allow for the direct visualization of the protein secretion process, detailing the dynamics of (i) outer membrane biogenesis and the assembly of protein secretion systems into the outer membrane, (ii) the spatial distribution of these and other membrane proteins on the bacterial cell surface, and (iii) translocation of effector proteins, toxins and enzymes by these protein secretion systems. Here we review the frontier research imaging the process of secretion, particularly new studies that are applying various modes of super-resolution microscopy.
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Affiliation(s)
- Sachith D Gunasinghe
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash UniversityClayton, VIC, Australia
| | - Chaille T Webb
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash UniversityClayton, VIC, Australia
| | | | - Iain D Hay
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash UniversityClayton, VIC, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash UniversityClayton, VIC, Australia
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117
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Bergmiller T, Andersson AMC, Tomasek K, Balleza E, Kiviet DJ, Hauschild R, Tkačik G, Guet CC. Biased partitioning of the multidrug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Science 2017; 356:311-315. [DOI: 10.1126/science.aaf4762] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/30/2016] [Accepted: 03/13/2017] [Indexed: 12/22/2022]
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118
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Barrett TC, Mok WWK, Brynildsen MP. Biased inheritance protects older bacteria from harm. Science 2017; 356:247-248. [PMID: 28428383 DOI: 10.1126/science.aan0348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Theresa C Barrett
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Wendy W K Mok
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. .,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
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119
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Patel DS, Qi Y, Im W. Modeling and simulation of bacterial outer membranes and interactions with membrane proteins. Curr Opin Struct Biol 2017; 43:131-140. [DOI: 10.1016/j.sbi.2017.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/08/2016] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
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120
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Maingi V, Burns JR, Uusitalo JJ, Howorka S, Marrink SJ, Sansom MSP. Stability and dynamics of membrane-spanning DNA nanopores. Nat Commun 2017; 8:14784. [PMID: 28317903 PMCID: PMC5364398 DOI: 10.1038/ncomms14784] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023] Open
Abstract
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine. Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.
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Affiliation(s)
- Vishal Maingi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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121
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Ionescu SA, Lee S, Housden NG, Kaminska R, Kleanthous C, Bayley H. Orientation of the OmpF Porin in Planar Lipid Bilayers. Chembiochem 2017; 18:554-562. [PMID: 28094462 DOI: 10.1002/cbic.201600644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 12/27/2022]
Abstract
The outer-membrane protein OmpF is an abundant trimeric general diffusion porin that plays a central role in the transport of antibiotics and colicins across the outer membrane of E. coli. Individual OmpF trimers in planar lipid bilayers (PLBs) show one of two current-voltage asymmetries, thus implying that insertion occurs with either the periplasmic or the extracellular end first. A method for establishing the orientation of OmpF in PLB was developed, based on targeted covalent modification with membrane-impermeant reagents of peripheral cysteine residues introduced near the periplasmic or the extracellular entrance. By correlating the results of the modification experiments with measurements of current asymmetry or the sidedness of binding of the antibiotic enrofloxacin, OmpF orientation could be quickly determined in subsequent experiments under a variety of conditions. Our work will allow the precise interpretation of past and future studies of antibiotic permeation and protein translocation through OmpF and related porins.
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Affiliation(s)
- Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Sejeong Lee
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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122
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Chebaro Y, Sirigu S, Amal I, Lutzing R, Stote RH, Rochette-Egly C, Rochel N, Dejaegere A. Allosteric Regulation in the Ligand Binding Domain of Retinoic Acid Receptorγ. PLoS One 2017; 12:e0171043. [PMID: 28125680 PMCID: PMC5268703 DOI: 10.1371/journal.pone.0171043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/13/2017] [Indexed: 11/29/2022] Open
Abstract
Retinoic acid (RA) plays key roles in cell differentiation and growth arrest through nuclear retinoic acid receptors (RARs), which are ligand-dependent transcription factors. While the main trigger of RAR activation is the binding of RA, phosphorylation of the receptors has also emerged as an important regulatory signal. Phosphorylation of the RARγ N-terminal domain (NTD) is known to play a functional role in neuronal differentiation. In this work, we investigated the phosphorylation of RARγ ligand binding domain (LBD), and present evidence that the phosphorylation status of the LBD affects the phosphorylation of the NTD region. We solved the X-ray structure of a phospho-mimetic mutant of the LBD (RARγ S371E), which we used in molecular dynamics simulations to characterize the consequences of the S371E mutation on the RARγ structural dynamics. Combined with simulations of the wild-type LBD, we show that the conformational equilibria of LBD salt bridges (notably R387-D340) are affected by the S371E mutation, which likely affects the recruitment of the kinase complex that phosphorylates the NTD. The molecular dynamics simulations also showed that a conservative mutation in this salt bridge (R387K) affects the dynamics of the LBD without inducing large conformational changes. Finally, cellular assays showed that the phosphorylation of the NTD of RARγ is differentially regulated by retinoic acid in RARγWT and in the S371N, S371E and R387K mutants. This multidisciplinary work highlights an allosteric coupling between phosphorylations of the LBD and the NTD of RARγ and supports the importance of structural dynamics involving electrostatic interactions in the regulation of RARs activity.
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Affiliation(s)
- Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Serena Sirigu
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Ismail Amal
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Régis Lutzing
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Roland H. Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
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123
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Lill Y, Jordan LD, Smallwood CR, Newton SM, Lill MA, Klebba PE, Ritchie K. Confined Mobility of TonB and FepA in Escherichia coli Membranes. PLoS One 2016; 11:e0160862. [PMID: 27935943 PMCID: PMC5147803 DOI: 10.1371/journal.pone.0160862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/26/2016] [Indexed: 01/21/2023] Open
Abstract
The important process of nutrient uptake in Escherichia coli, in many cases, involves transit of the nutrient through a class of beta-barrel proteins in the outer membrane known as TonB-dependent transporters (TBDTs) and requires interaction with the inner membrane protein TonB. Here we have imaged the mobility of the ferric enterobactin transporter FepA and TonB by tracking them in the membranes of live E. coli with single-molecule resolution at time-scales ranging from milliseconds to seconds. We employed simple simulations to model/analyze the lateral diffusion in the membranes of E.coli, to take into account both the highly curved geometry of the cell and artifactual effects expected due to finite exposure time imaging. We find that both molecules perform confined lateral diffusion in their respective membranes in the absence of ligand with FepA confined to a region 0.180−0.007+0.006 μm in radius in the outer membrane and TonB confined to a region 0.266−0.009+0.007 μm in radius in the inner membrane. The diffusion coefficient of these molecules on millisecond time-scales was estimated to be 21−5+9 μm2/s and 5.4−0.8+1.5 μm2/s for FepA and TonB, respectively, implying that each molecule is free to diffuse within its domain. Disruption of the inner membrane potential, deletion of ExbB/D from the inner membrane, presence of ligand or antibody to FepA and disruption of the MreB cytoskeleton was all found to further restrict the mobility of both molecules. Results are analyzed in terms of changes in confinement size and interactions between the two proteins.
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Affiliation(s)
- Yoriko Lill
- Department of Physics, Purdue University, West Lafayette, Indiana, United States of America
| | - Lorne D. Jordan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Chuck R. Smallwood
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Salete M. Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Phillip E. Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail: (PEK); (KR)
| | - Ken Ritchie
- Department of Physics, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (PEK); (KR)
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124
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Hedger G, Rouse SL, Domański J, Chavent M, Koldsø H, Sansom MSP. Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes. Biochemistry 2016; 55:6238-6249. [PMID: 27786441 PMCID: PMC5120876 DOI: 10.1021/acs.biochem.6b00751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
The exchange of ADP
and ATP across the inner mitochondrial membrane
is a fundamental cellular process. This exchange is facilitated by
the adenine nucleotide translocase, the structure and function of
which are critically dependent on the signature phospholipid of mitochondria,
cardiolipin (CL). Here we employ multiscale molecular dynamics simulations
to investigate CL interactions within a membrane environment. Using
simulations at both coarse-grained and atomistic resolutions, we identify
three CL binding sites on the translocase, in agreement with those
seen in crystal structures and inferred from nuclear magnetic resonance
measurements. Characterization of the free energy landscape for lateral
lipid interaction via potential of mean force calculations demonstrates
the strength of interaction compared to those of binding sites on
other mitochondrial membrane proteins, as well as their selectivity
for CL over other phospholipids. Extending the analysis to other members
of the family, yeast Aac2p and mouse uncoupling protein 2, suggests
a degree of conservation. Simulation of large patches of a model mitochondrial
membrane containing multiple copies of the translocase shows that
CL interactions persist in the presence of protein–protein
interactions and suggests CL may mediate interactions between translocases.
This study provides a key example of how computational microscopy
may be used to shed light on regulatory lipid–protein interactions.
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Affiliation(s)
- George Hedger
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Sarah L Rouse
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - Jan Domański
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,D. E. Shaw Research , 120 West 45th Street, 39th Floor, New York, New York 10036, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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125
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Outer Membrane Vesicle Production Facilitates LPS Remodeling and Outer Membrane Maintenance in Salmonella during Environmental Transitions. mBio 2016; 7:mBio.01532-16. [PMID: 27795394 PMCID: PMC5082901 DOI: 10.1128/mbio.01532-16] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The ability of Gram-negative bacteria to carefully modulate outer membrane (OM) composition is essential to their survival. However, the asymmetric and heterogeneous structure of the Gram-negative OM poses unique challenges to the cell’s successful adaption to rapid environmental transitions. Although mechanisms to recycle and degrade OM phospholipid material exist, there is no known mechanism by which to remove unfavorable lipopolysaccharide (LPS) glycoforms, except slow dilution through cell growth. As all Gram-negative bacteria constitutively shed OM vesicles (OMVs), we propose that cells may utilize OMV formation as a way to selectively remove environmentally disadvantageous LPS species. We examined the native kinetics of OM composition during physiologically relevant environmental changes in Salmonella enterica, a well-characterized model system for activation of PhoP/Q and PmrA/B two-component systems (TCSs). In response to acidic pH, toxic metals, antimicrobial peptides, and lack of divalent cations, these TCSs modify the LPS lipid A and core, lengthen the O antigen, and upregulate specific OM proteins. An environmental change to PhoP/Q- and PmrA/B-activating conditions simultaneously induced the addition of modified species of LPS to the OM, downregulation of previously dominant species of LPS, greater OMV production, and increased OMV diameter. Comparison of the relative abundance of lipid A species present in the OM and the newly budded OMVs following two sets of rapid environmental shifts revealed the retention of lipid A species with modified phosphate moieties in the OM concomitant with the selective loss of palmitoylated species via vesiculation following exposure to moderately acidic environmental conditions. All Gram-negative bacteria alter the structural composition of LPS present in their OM in response to various environmental stimuli. We developed a system to track the native dynamics of lipid A change in Salmonella enterica serovar Typhimurium following an environmental shift to PhoP/Q- and PmrA/B-inducing conditions. We show that growth conditions influence OMV production, size, and lipid A content. We further demonstrate that the lipid A content of OMVs does not fit a stochastic model of content selection, revealing the significant retention of lipid A species containing covalent modifications that mask their 1- and 4′-phosphate moieties under host-like conditions. Furthermore, palmitoylation of the lipid A to form hepta-acylated species substantially increases the likelihood of its incorporation into OMVs. These results highlight a role for the OMV response in OM remodeling and maintenance processes in Gram-negative bacteria.
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126
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Chavent M, Duncan AL, Sansom MS. Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. Curr Opin Struct Biol 2016; 40:8-16. [PMID: 27341016 PMCID: PMC5404110 DOI: 10.1016/j.sbi.2016.06.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 11/21/2022]
Abstract
Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Sp Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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127
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Iadanza MG, Higgins AJ, Schiffrin B, Calabrese AN, Brockwell DJ, Ashcroft AE, Radford SE, Ranson NA. Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM. Nat Commun 2016; 7:12865. [PMID: 27686148 PMCID: PMC5056442 DOI: 10.1038/ncomms12865] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/04/2016] [Indexed: 02/06/2023] Open
Abstract
The β-barrel assembly machinery (BAM) is a ∼203 kDa complex of five proteins (BamA-E), which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a 'lateral gating' motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex and interactions between BamA, B, D and E, and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM.
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Affiliation(s)
- Matthew G. Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Anna J. Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
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128
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Fowler PW, Hélie J, Duncan A, Chavent M, Koldsø H, Sansom MSP. Membrane stiffness is modified by integral membrane proteins. SOFT MATTER 2016; 12:7792-7803. [PMID: 27722554 PMCID: PMC5314686 DOI: 10.1039/c6sm01186a] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/25/2016] [Indexed: 05/12/2023]
Abstract
The ease with which a cell membrane can bend and deform is important for a wide range of biological functions. Peripheral proteins that induce curvature in membranes (e.g. BAR domains) have been studied for a number of years. Little is known, however, about the effect of integral membrane proteins on the stiffness of a membrane (characterised by the bending rigidity, Kc). We demonstrate by computer simulation that adding integral membrane proteins at physiological densities alters the stiffness of the membrane. First we establish that the coarse-grained MARTINI forcefield is able to accurately reproduce the bending rigidity of a small patch of 1500 phosphatidyl choline lipids by comparing the calculated value to both experiment and an atomistic simulation of the same system. This enables us to simulate the dynamics of large (ca. 50 000 lipids) patches of membrane using the MARTINI coarse-grained description. We find that altering the lipid composition changes the bending rigidity. Adding integral membrane proteins to lipid bilayers also changes the bending rigidity, whilst adding a simple peripheral membrane protein has no effect. Our results suggest that integral membrane proteins can have different effects, and in the case of the bacterial outer membrane protein, BtuB, the greater the density of protein, the larger the reduction in stiffness.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Anna Duncan
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
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129
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Hartel AJW, Glogger M, Jones NG, Abuillan W, Batram C, Hermann A, Fenz SF, Tanaka M, Engstler M. N-glycosylation enables high lateral mobility of GPI-anchored proteins at a molecular crowding threshold. Nat Commun 2016; 7:12870. [PMID: 27641538 PMCID: PMC5031801 DOI: 10.1038/ncomms12870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/09/2016] [Indexed: 01/17/2023] Open
Abstract
The protein density in biological membranes can be extraordinarily high, but the impact of molecular crowding on the diffusion of membrane proteins has not been studied systematically in a natural system. The diversity of the membrane proteome of most cells may preclude systematic studies. African trypanosomes, however, feature a uniform surface coat that is dominated by a single type of variant surface glycoprotein (VSG). Here we study the density-dependence of the diffusion of different glycosylphosphatidylinositol-anchored VSG-types on living cells and in artificial membranes. Our results suggest that a specific molecular crowding threshold (MCT) limits diffusion and hence affects protein function. Obstacles in the form of heterologous proteins compromise the diffusion coefficient and the MCT. The trypanosome VSG-coat operates very close to its MCT. Importantly, our experiments show that N-linked glycans act as molecular insulators that reduce retarding intermolecular interactions allowing membrane proteins to function correctly even when densely packed.
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Affiliation(s)
- Andreas J. W. Hartel
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Marius Glogger
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Nicola G. Jones
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
| | - Christopher Batram
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Anne Hermann
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Susanne F. Fenz
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
- Institute for Integrated Cell-Material Science (WPI iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Markus Engstler
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
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130
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Wang X, Jiang F, Zheng J, Chen L, Dong J, Sun L, Zhu Y, Liu B, Yang J, Yang G, Jin Q. The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri. Open Biol 2016; 6:rsob.160073. [PMID: 27655730 PMCID: PMC5043575 DOI: 10.1098/rsob.160073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022] Open
Abstract
Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support that PldA, which is widespread across Gram-negative bacteria, is an important factor for the bacterial life cycle, particularly in human pathogens.
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Affiliation(s)
- Xia Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Feng Jiang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jianhua Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Guowei Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
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131
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Fowler PW, Williamson JJ, Sansom MSP, Olmsted PD. Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics. J Am Chem Soc 2016; 138:11633-42. [PMID: 27574865 PMCID: PMC5025830 DOI: 10.1021/jacs.6b04880] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Characterizing
the nanoscale dynamic organization within lipid
bilayer
membranes is central
to our understanding of cell membranes at a molecular level. We investigate
phase separation and communication across leaflets in ternary lipid
bilayers, including saturated lipids with between 12 and 20 carbons
per tail. Coarse-grained molecular dynamics simulations reveal a novel
two-step kinetics due to hydrophobic mismatch, in which the initial
response of the apposed leaflets upon quenching is to increase local
asymmetry (antiregistration), followed by dominance of symmetry (registration)
as the bilayer equilibrates. Antiregistration can become thermodynamically
preferred if domain size is restricted below ∼20 nm, with implications
for the symmetry of rafts and nanoclusters in cell membranes, which
have similar reported sizes. We relate our findings to theory derived
from a semimicroscopic model in which the leaflets experience a “direct”
area-dependent coupling, and an “indirect” coupling
that arises from hydrophobic mismatch and is most important at domain
boundaries. Registered phases differ in composition from antiregistered
phases, consistent with a direct coupling between the leaflets. Increased
hydrophobic mismatch purifies the phases, suggesting that it contributes
to the molecule-level lipid immiscibility. Our results demonstrate
an interplay of competing interleaflet couplings that affect phase
compositions and kinetics, and lead to a length scale that
can influence lateral and transverse bilayer organization within cells.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford, OX1 3QU, U.K
| | - John J Williamson
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University , 37th and O Streets, N.W., Washington, D.C. 20057, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford, OX1 3QU, U.K
| | - Peter D Olmsted
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University , 37th and O Streets, N.W., Washington, D.C. 20057, United States
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132
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Lelimousin M, Limongelli V, Sansom MSP. Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations. J Am Chem Soc 2016; 138:10611-22. [PMID: 27459426 PMCID: PMC5010359 DOI: 10.1021/jacs.6b05602] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The epidermal growth
factor receptor (EGFR) is a dimeric membrane
protein that regulates key aspects of cellular function. Activation
of the EGFR is linked to changes in the conformation of the transmembrane
(TM) domain, brought about by changes in interactions of the TM helices
of the membrane lipid bilayer. Using an advanced computational approach
that combines Coarse-Grained molecular dynamics and well-tempered
MetaDynamics (CG-MetaD), we characterize the large-scale motions
of the TM helices, simulating multiple association and dissociation
events between the helices in membrane, thus leading to a free energy
landscape of the dimerization process. The lowest energy state of
the TM domain is a right-handed dimer structure in which the TM helices
interact through the N-terminal small-X3-small sequence
motif. In addition to this state, which is thought to correspond to
the active form of the receptor, we have identified further low-energy
states that allow us to integrate with a high level of detail a range
of previous experimental observations. These conformations may lead
to the active state via two possible activation pathways, which involve
pivoting and rotational motions of the helices, respectively. Molecular
dynamics also reveals correlation between the conformational changes
of the TM domains and of the intracellular juxtamembrane domains,
paving the way for a comprehensive understanding of EGFR signaling
at the cell membrane.
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Affiliation(s)
- Mickaël Lelimousin
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,CERMAV, Université Grenoble Alpes and CNRS , BP 53, F-38041 Grenoble Cedex 9, France
| | - Vittorio Limongelli
- Università della Svizzera Italiana (USI), Faculty of Informatics, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13, CH-6900 Lugano, Switzerland.,Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, I-80131 Naples, Italy
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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133
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Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis. Proc Natl Acad Sci U S A 2016; 113:E5034-43. [PMID: 27493217 DOI: 10.1073/pnas.1602382113] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion.
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134
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Dynamic periplasmic chaperone reservoir facilitates biogenesis of outer membrane proteins. Proc Natl Acad Sci U S A 2016; 113:E4794-800. [PMID: 27482090 DOI: 10.1073/pnas.1601002113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Outer membrane protein (OMP) biogenesis is critical to bacterial physiology because the cellular envelope is vital to bacterial pathogenesis and antibiotic resistance. The process of OMP biogenesis has been studied in vivo, and each of its components has been studied in isolation in vitro. This work integrates parameters and observations from both in vivo and in vitro experiments into a holistic computational model termed "Outer Membrane Protein Biogenesis Model" (OMPBioM). We use OMPBioM to assess OMP biogenesis mathematically in a global manner. Using deterministic and stochastic methods, we are able to simulate OMP biogenesis under varying genetic conditions, each of which successfully replicates experimental observations. We observe that OMPs have a prolonged lifetime in the periplasm where an unfolded OMP makes, on average, hundreds of short-lived interactions with chaperones before folding into its native state. We find that some periplasmic chaperones function primarily as quality-control factors; this function complements the folding catalysis function of other chaperones. Additionally, the effective rate for the β-barrel assembly machinery complex necessary for physiological folding was found to be higher than has currently been observed in vitro. Overall, we find a finely tuned balance between thermodynamic and kinetic parameters maximizes OMP folding flux and minimizes aggregation and unnecessary degradation. In sum, OMPBioM provides a global view of OMP biogenesis that yields unique insights into this essential pathway.
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135
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Plummer AM, Fleming KG. From Chaperones to the Membrane with a BAM! Trends Biochem Sci 2016; 41:872-882. [PMID: 27450425 DOI: 10.1016/j.tibs.2016.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/13/2016] [Accepted: 06/20/2016] [Indexed: 01/17/2023]
Abstract
Outer membrane proteins (OMPs) play a central role in the integrity of the outer membrane of Gram-negative bacteria. Unfolded OMPs (uOMPs) transit across the periplasm, and subsequent folding and assembly are crucial for biogenesis. Chaperones and the essential β-barrel assembly machinery (BAM) complex facilitate these processes. In vitro studies suggest that some chaperones sequester uOMPs in internal cavities during their periplasmic transit to prevent deleterious aggregation. Upon reaching the outer membrane, the BAM complex acts catalytically to accelerate uOMP folding. Complementary in vivo experiments have revealed the localization and activity of the BAM complex in living cells. Completing an understanding of OMP biogenesis will require a holistic view of the interplay among the individual components discussed here.
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Affiliation(s)
- Ashlee M Plummer
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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136
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Structural and biophysical analysis of nuclease protein antibiotics. Biochem J 2016; 473:2799-812. [PMID: 27402794 PMCID: PMC5264503 DOI: 10.1042/bcj20160544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/07/2016] [Indexed: 01/28/2023]
Abstract
Protein antibiotics (bacteriocins) are a large and diverse family of multidomain toxins that kill specific Gram-negative bacteria during intraspecies competition for resources. Our understanding of the mechanism of import of such potent toxins has increased significantly in recent years, especially with the reporting of several structures of bacteriocin domains. Less well understood is the structural biochemistry of intact bacteriocins and how these compare across bacterial species. Here, we focus on endonuclease (DNase) bacteriocins that target the genomes of Escherichia coli and Pseudomonas aeruginosa, known as E-type colicins and S-type pyocins, respectively, bound to their specific immunity (Im) proteins. First, we report the 3.2 Å structure of the DNase colicin ColE9 in complex with its ultra-high affinity Im protein, Im9. In contrast with Im3, which when bound to the ribonuclease domain of the homologous colicin ColE3 makes contact with the translocation (T) domain of the toxin, we find that Im9 makes no such contact and only interactions with the ColE9 cytotoxic domain are observed. Second, we report small-angle X-ray scattering data for two S-type DNase pyocins, S2 and AP41, into which are fitted recently determined X-ray structures for isolated domains. We find that DNase pyocins and colicins are both highly elongated molecules, even though the order of their constituent domains differs. We discuss the implications of these architectural similarities and differences in the context of the translocation mechanism of protein antibiotics through the cell envelope of Gram-negative bacteria.
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137
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Fleming KG. A combined kinetic push and thermodynamic pull as driving forces for outer membrane protein sorting and folding in bacteria. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0026. [PMID: 26370938 DOI: 10.1098/rstb.2015.0026] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vitro folding studies of outer membrane beta-barrels have been invaluable in revealing the lipid effects on folding rates and efficiencies as well as folding free energies. Here, the biophysical results are summarized, and these kinetic and thermodynamic findings are considered in terms of the requirements for folding in the context of the cellular environment. Because the periplasm lacks an external energy source the only driving forces for sorting and folding available within this compartment are binding or folding free energies and their associated rates. These values define functions for periplasmic chaperones and suggest a biophysical mechanism for the BAM complex.
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Affiliation(s)
- Karen G Fleming
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
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138
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Classifying β-Barrel Assembly Substrates by Manipulating Essential Bam Complex Members. J Bacteriol 2016; 198:1984-92. [PMID: 27161117 DOI: 10.1128/jb.00263-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The biogenesis of the outer membrane (OM) of Escherichia coli is a conserved and vital process. The assembly of integral β-barrel outer membrane proteins (OMPs), which represent a major component of the OM, depends on periplasmic chaperones and the heteropentameric β-barrel assembly machine (Bam complex) in the OM. However, not all OMPs are affected by null mutations in the same chaperones or nonessential Bam complex members, suggesting there are categories of substrates with divergent requirements for efficient assembly. We have previously demonstrated two classes of substrates, one comprising large, low-abundance, and difficult-to-assemble substrates that are heavily dependent on SurA and also Skp and FkpA, and the other comprising relatively simple and abundant substrates that are not as dependent on SurA but are strongly dependent on BamB for assembly. Here, we describe novel mutations in bamD that lower levels of BamD 10-fold and >25-fold without altering the sequence of the mature protein. We utilized these mutations, as well as a previously characterized mutation that lowers wild-type BamA levels, to reveal a third class of substrates. These mutations preferentially cause a marked decrease in the levels of multimeric proteins. This susceptibility of multimers to lowered quantities of Bam machines in the cell may indicate that multiple Bam complexes are needed to efficiently assemble multimeric proteins into the OM. IMPORTANCE The outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, serves as a selective permeability barrier that prevents the uptake of toxic molecules and antibiotics. Integral β-barrel proteins (OMPs) are assembled by the β-barrel assembly machine (Bam), components of which are conserved in mitochondria, chloroplasts, and all Gram-negative bacteria, including many clinically relevant pathogenic species. Bam is essential for OM biogenesis and accommodates a diverse array of client proteins; however, a mechanistic model that accounts for the selectivity and broad substrate range of Bam is lacking. Here, we show that the assembly of multimeric OMPs is more strongly affected than that of monomeric OMPs when essential Bam complex components are limiting, suggesting that multiple Bam complexes are needed to assemble multimeric proteins.
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139
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Horne JE, Radford SE. A growing toolbox of techniques for studying β-barrel outer membrane protein folding and biogenesis. Biochem Soc Trans 2016; 44:802-9. [PMID: 27284045 PMCID: PMC4900752 DOI: 10.1042/bst20160020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/21/2023]
Abstract
Great strides into understanding protein folding have been made since the seminal work of Anfinsen over 40 years ago, but progress in the study of membrane protein folding has lagged behind that of their water soluble counterparts. Researchers in these fields continue to turn to more advanced techniques such as NMR, mass spectrometry, molecular dynamics (MD) and single molecule methods to interrogate how proteins fold. Our understanding of β-barrel outer membrane protein (OMP) folding has benefited from these advances in the last decade. This class of proteins must traverse the periplasm and then insert into an asymmetric lipid membrane in the absence of a chemical energy source. In this review we discuss old, new and emerging techniques used to examine the process of OMP folding and biogenesis in vitro and describe some of the insights and new questions these techniques have revealed.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K.
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140
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Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2390-2400. [PMID: 26946244 DOI: 10.1016/j.bbamem.2016.02.037] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 11/22/2022]
Abstract
Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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141
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Vassallo CN, Wall D. Tissue repair in myxobacteria: A cooperative strategy to heal cellular damage. Bioessays 2016; 38:306-15. [PMID: 26898360 DOI: 10.1002/bies.201500132] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Damage repair is a fundamental requirement of all life as organisms find themselves in challenging and fluctuating environments. In particular, damage to the barrier between an organism and its environment (e.g. skin, plasma membrane, bacterial cell envelope) is frequent because these organs/organelles directly interact with the external world. Here, we discuss the general strategies that bacteria use to cope with damage to their cell envelope and their repair limits. We then describe a novel damage-coping mechanism used by multicellular myxobacteria. We propose that cell-cell transfer of membrane material within a population serves as a wound-healing strategy and provide evidence for its utility. We suggest that--similar to how tissues in eukaryotes have evolved cooperative methods of damage repair--so too have some bacteria that live a multicellular lifestyle.
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Affiliation(s)
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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142
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Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1753-9. [PMID: 26826270 DOI: 10.1016/j.bbamem.2016.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/06/2023]
Abstract
Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. 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)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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143
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Urfer M, Bogdanovic J, Lo Monte F, Moehle K, Zerbe K, Omasits U, Ahrens CH, Pessi G, Eberl L, Robinson JA. A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli. J Biol Chem 2015; 291:1921-1932. [PMID: 26627837 DOI: 10.1074/jbc.m115.691725] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 01/05/2023] Open
Abstract
Increasing antibacterial resistance presents a major challenge in antibiotic discovery. One attractive target in Gram-negative bacteria is the unique asymmetric outer membrane (OM), which acts as a permeability barrier that protects the cell from external stresses, such as the presence of antibiotics. We describe a novel β-hairpin macrocyclic peptide JB-95 with potent antimicrobial activity against Escherichia coli. This peptide exhibits no cellular lytic activity, but electron microscopy and fluorescence studies reveal an ability to selectively disrupt the OM but not the inner membrane of E. coli. The selective targeting of the OM probably occurs through interactions of JB-95 with selected β-barrel OM proteins, including BamA and LptD as shown by photolabeling experiments. Membrane proteomic studies reveal rapid depletion of many β-barrel OM proteins from JB-95-treated E. coli, consistent with induction of a membrane stress response and/or direct inhibition of the Bam folding machine. The results suggest that lethal disruption of the OM by JB-95 occurs through a novel mechanism of action at key interaction sites within clusters of β-barrel proteins in the OM. These findings open new avenues for developing antibiotics that specifically target β-barrel proteins and the integrity of the Gram-negative OM.
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Affiliation(s)
- Matthias Urfer
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich
| | - Jasmina Bogdanovic
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich
| | - Fabio Lo Monte
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich
| | - Kerstin Moehle
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich
| | - Katja Zerbe
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich
| | - Ulrich Omasits
- the Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard Hof 1, 8093 Zurich, Switzerland
| | - Christian H Ahrens
- the Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics, and Bioinformatics and the Swiss Institute of Bioinformatics, Agroscope, Schloss 1, 8820 Wädenswil, Switzerland, and
| | - Gabriella Pessi
- the Department of Microbiology, Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Leo Eberl
- the Department of Microbiology, Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - John A Robinson
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich,.
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144
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Kleanthous C, Rassam P, Baumann CG. Protein-protein interactions and the spatiotemporal dynamics of bacterial outer membrane proteins. Curr Opin Struct Biol 2015; 35:109-15. [PMID: 26629934 PMCID: PMC4684144 DOI: 10.1016/j.sbi.2015.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/26/2015] [Accepted: 10/30/2015] [Indexed: 01/14/2023]
Abstract
We discuss spatiotemporal patterning in the bacterial outer membrane. Promiscuous interactions between outer membrane proteins govern their behaviour. Turnover and biogenesis of outer membrane proteins linked to formation of clusters. Implications of spatiotemporal patterning for bacterial physiology discussed.
It has until recently been unclear whether outer membrane proteins (OMPs) of Gram-negative bacteria are organized or distributed randomly. Studies now suggest promiscuous protein–protein interactions (PPIs) between β-barrel OMPs in Escherichia coli govern their local and global dynamics, engender spatiotemporal patterning of the outer membrane into micro-domains and are the basis of β-barrel protein turnover. We contextualize these latest advances, speculate on areas of bacterial cell biology that might be influenced by the organization of OMPs into supramolecular assemblies, and highlight the new questions and controversies this revised view of the bacterial outer membrane raises.
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Affiliation(s)
- Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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145
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Misra R. Entry and exit of bacterial outer membrane proteins. Trends Microbiol 2015; 23:452-4. [PMID: 26169444 DOI: 10.1016/j.tim.2015.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/02/2015] [Indexed: 01/29/2023]
Abstract
The sites of new outer membrane protein (OMP) deposition and the fate of pre-existing OMPs are still enigmatic despite numerous concerted efforts. Rassam et al. identified mid-cell regions as the primary entry points for new OMP insertion in clusters, driving the pre-existing OMP clusters towards cell poles for long-term storage.
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Affiliation(s)
- Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
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