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Start Me Up: How Can Surrounding Gangliosides Affect Sodium-Potassium ATPase Activity and Steer towards Pathological Ion Imbalance in Neurons? Biomedicines 2022; 10:biomedicines10071518. [PMID: 35884824 PMCID: PMC9313118 DOI: 10.3390/biomedicines10071518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
Gangliosides, amphiphilic glycosphingolipids, tend to associate laterally with other membrane constituents and undergo extensive interactions with membrane proteins in cis or trans configurations. Studies of human diseases resulting from mutations in the ganglioside biosynthesis pathway and research on transgenic mice with the same mutations implicate gangliosides in the pathogenesis of epilepsy. Gangliosides are reported to affect the activity of the Na+/K+-ATPase, the ubiquitously expressed plasma membrane pump responsible for the stabilization of the resting membrane potential by hyperpolarization, firing up the action potential and ion homeostasis. Impaired Na+/K+-ATPase activity has also been hypothesized to cause seizures by several mechanisms. In this review we present different epileptic phenotypes that are caused by impaired activity of Na+/K+-ATPase or changed membrane ganglioside composition. We further discuss how gangliosides may influence Na+/K+-ATPase activity by acting as lipid sorting machinery providing the optimal stage for Na+/K+-ATPase function. By establishing a distinct lipid environment, together with other membrane lipids, gangliosides possibly modulate Na+/K+-ATPase activity and aid in “starting up” and “turning off” this vital pump. Therefore, structural changes of neuronal membranes caused by altered ganglioside composition can be a contributing factor leading to aberrant Na+/K+-ATPase activity and ion imbalance priming neurons for pathological firing.
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2
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Khalid S, Schroeder C, Bond PJ, Duncan AL. What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35294337 PMCID: PMC9558347 DOI: 10.1099/mic.0.001165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cell envelopes are compositionally complex and crowded and while highly dynamic in some areas, their molecular motion is very limited, to the point of being almost static in others. Therefore, it is no real surprise that studying them at high resolution across a range of temporal and spatial scales requires a number of different techniques. Details at atomistic to molecular scales for up to tens of microseconds are now within range for molecular dynamics simulations. Here we review how such simulations have contributed to our current understanding of the cell envelopes of Gram-negative bacteria.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Cyril Schroeder
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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3
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Huggins DJ, Biggin PC, Dämgen MA, Essex JW, Harris SA, Henchman RH, Khalid S, Kuzmanic A, Laughton CA, Michel J, Mulholland AJ, Rosta E, Sansom MSP, van der Kamp MW. Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1393] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- David J. Huggins
- TCM Group, Cavendish Laboratory University of Cambridge Cambridge UK
- Unilever Centre, Department of Chemistry University of Cambridge Cambridge UK
- Department of Physiology and Biophysics Weill Cornell Medical College New York NY
| | | | - Marc A. Dämgen
- Department of Biochemistry University of Oxford Oxford UK
| | - Jonathan W. Essex
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | - Sarah A. Harris
- School of Physics and Astronomy University of Leeds Leeds UK
- Astbury Centre for Structural and Molecular Biology University of Leeds Leeds UK
| | - Richard H. Henchman
- Manchester Institute of Biotechnology The University of Manchester Manchester UK
- School of Chemistry The University of Manchester Oxford UK
| | - Syma Khalid
- School of Chemistry University of Southampton Southampton UK
- Institute for Life Sciences University of Southampton Southampton UK
| | | | - Charles A. Laughton
- School of Pharmacy University of Nottingham Nottingham UK
- Centre for Biomolecular Sciences University of Nottingham Nottingham UK
| | - Julien Michel
- EaStCHEM school of Chemistry University of Edinburgh Edinburgh UK
| | - Adrian J. Mulholland
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
| | - Edina Rosta
- Department of Chemistry King's College London London UK
| | | | - Marc W. van der Kamp
- Centre of Computational Chemistry, School of Chemistry University of Bristol Bristol UK
- School of Biochemistry, Biomedical Sciences Building University of Bristol Bristol UK
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4
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Samsudin F, Boags A, Piggot TJ, Khalid S. Braun's Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall. Biophys J 2017; 113:1496-1504. [PMID: 28978443 DOI: 10.1016/j.bpj.2017.08.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/13/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022] Open
Abstract
Gram-negative bacteria such as Escherichia coli are protected by a complex cell envelope. The development of novel therapeutics against these bacteria necessitates a molecular level understanding of the structure-dynamics-function relationships of the various components of the cell envelope. We use atomistic MD simulations to reveal the details of covalent and noncovalent protein interactions that link the outer membrane to the aqueous periplasmic region. We show that the Braun's lipoprotein tilts and bends, and thereby lifts the cell wall closer to the outer membrane. Both monomers and dimers of the outer membrane porin OmpA can interact with peptidoglycan in the presence of Braun's lipoprotein, but in the absence of the latter, only dimers of OmpA show a propensity to form contacts with peptidoglycan. Our study provides a glimpse of how the molecular components of the bacterial cell envelope interact with each other to mediate cell wall attachment in E. coli.
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Affiliation(s)
- Firdaus Samsudin
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom; CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom.
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5
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Dutagaci B, Feig M. Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. J Chem Inf Model 2017; 57:3032-3042. [PMID: 29155578 DOI: 10.1021/acs.jcim.7b00510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane and identification of lipid-facing and inward-facing residues, followed by energy optimization of the implicit membrane model to obtain the hydrophobic length from the optimal membrane width. The latest HDGB version 3 (HDGBv3) and HDGB van der Waals (HDGBvdW) models were applied to a test set containing 15 proteins (seven β-barrel and eight α-helical proteins), for which matching membrane widths are available from experiment, and an additional set contains ten α-helical and ten β-barrel proteins without any experimental data. The results with the HDGB model compare favorably with predictions from methods used in the Orientations of Proteins in Membranes (OPM) and Protein Data Bank of Transmembrane Proteins (PDB-TM) databases.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University , 603 Wilson Road, Room BCH, 218, East Lansing, Michigan 48824, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , 603 Wilson Road, Room BCH, 218, East Lansing, Michigan 48824, United States
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6
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Ortiz-Suarez ML, Samsudin F, Piggot TJ, Bond PJ, Khalid S. Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations. Biophys J 2017; 111:1692-1702. [PMID: 27760356 PMCID: PMC5071624 DOI: 10.1016/j.bpj.2016.09.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/30/2016] [Accepted: 09/06/2016] [Indexed: 12/02/2022] Open
Abstract
OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein. To address this issue, we performed molecular-dynamics simulations of the full-length model of the OmpA dimer proposed by Robinson and co-workers. The N-terminal domains were embedded in an asymmetric model of the outer membrane, with lipopolysaccharide molecules in the outer leaflet and phospholipids in the inner leaflet. Our results reveal a large dimerization interface within the membrane environment, ensuring that the dimer is stable over the course of the simulations. The linker is flexible, expanding and contracting to pull the globular C-terminal domain up toward the membrane or push it down toward the periplasm, suggesting a possible mechanism for providing mechanical stability to the cell. The external loops were more stabilized than was observed in previous studies due to the extensive dimerization interface and presence of lipopolysaccharide molecules in our outer-membrane model, which may have functional consequences in terms of OmpA adhesion to host cells. In addition, the pore-gating behavior of the protein was modulated compared with previous observations, suggesting a possible role for dimerization in channel regulation.
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Affiliation(s)
- Maite L Ortiz-Suarez
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Thomas J Piggot
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Peter J Bond
- Bioinformatics Institute (A(∗)STAR), Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| | - Syma Khalid
- School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom.
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7
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Pothula KR, Dhanasekar NN, Lamichhane U, Younas F, Pletzer D, Benz R, Winterhalter M, Kleinekathöfer U. Single Residue Acts as Gate in OccK Channels. J Phys Chem B 2017; 121:2614-2621. [DOI: 10.1021/acs.jpcb.7b01787] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Karunakar R. Pothula
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Naresh N. Dhanasekar
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Usha Lamichhane
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Farhan Younas
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Daniel Pletzer
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Roland Benz
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Winterhalter
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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8
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Harris BJ, Cheng X, Frymier P. Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study. J Phys Chem B 2016; 120:599-609. [DOI: 10.1021/acs.jpcb.5b07812] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bradley J. Harris
- College
of Engineering and Computer Science, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Xiaolin Cheng
- Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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9
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Vega-Manriquez X, Huerta-Ascencio L, Martínez-Gómez D, López-Vidal Y, Verdugo-Rodríguez A. Influence of heat-labile serum components in the presence of OmpA on the outer membrane of Salmonella gallinarum. Arch Microbiol 2015; 198:161-9. [PMID: 26597854 DOI: 10.1007/s00203-015-1174-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 11/06/2015] [Accepted: 11/12/2015] [Indexed: 11/24/2022]
Abstract
Salmonella gallinarum is the causative agent of fowl typhoid. Being a Gram-negative bacteria, its outer membrane proteins (OMP) can be regulated by different microenvironments. S. gallinarum was cultured under the following conditions: nutrient broth (NB), NB supplemented with serum from specific pathogen-free birds (NBS) and NB with serum incubated at 56 °C prior to incubation with the bacteria (NBSD); OMP were subsequently extracted. Several changes were observed in the apparent expression of OMP, mainly a decrease in an OMP with a size of 30 kDa, approximately, under the NBS condition. In contrast, the same event was not observed in NB and NBSD when using one- and two-dimensional polyacrylamide gels (SDS-PAGE). Using the OMP with a size of 30 kDa, approximately, as antigen in indirect ELISA, we were able to differentiate serum from healthy and vaccinated birds, as well as birds infected with S. gallinarum and S. enteritidis. The amino-terminal of this protein was sequenced, showing 100 % identity with OmpA of S. typhimurium. Subsequently, we designed primers to amplify the gene by PCR. The partial sequence of the amplified gene showed 100 % identity with OmpA of S. gallinarum. (1) Heat-labile serum components influence the presence of OmpA in the OM of S. gallinarum; (2) by the way of ELISA, OmpA allows to specifically differentiate healthy from diseased birds.
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Affiliation(s)
- X Vega-Manriquez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, Mexico
| | - L Huerta-Ascencio
- Laboratorio de Microbiología Molecular, Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootencnia, Universidad Nacional Autónoma de México, Circuito exterior S/N, Ciudad Universitaria, UNAM CU, Coyoacan México, 04510, México City, Mexico
| | - D Martínez-Gómez
- Departamento de Producción Agrícola, Universidad Autónoma Metropolitana-Unidad Xochimilco, México City, Mexico
| | - Y López-Vidal
- Programa de Inmunología Molecular Microbiana, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, Mexico
| | - A Verdugo-Rodríguez
- Laboratorio de Microbiología Molecular, Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootencnia, Universidad Nacional Autónoma de México, Circuito exterior S/N, Ciudad Universitaria, UNAM CU, Coyoacan México, 04510, México City, Mexico.
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10
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Parkin J, Khalid S. Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from Pseudomonas aeruginosa. Biophys J 2015; 107:1853-1861. [PMID: 25418166 DOI: 10.1016/j.bpj.2014.08.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 01/11/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine.
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Affiliation(s)
- Jamie Parkin
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, United Kingdom.
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11
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Iftemi S, De Zotti M, Formaggio F, Toniolo C, Stella L, Luchian T. Electrophysiology investigation of Trichogin GA IV activity in planar lipid membranes reveals ion channels of well-defined size. Chem Biodivers 2015; 11:1069-77. [PMID: 25044592 DOI: 10.1002/cbdv.201300334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 11/07/2022]
Abstract
Trichogin GA IV, an antimicrobial peptaibol, exerts its function by augmenting membrane permeability, but the molecular aspects of its pore-forming mechanism are still debated. Several lines of evidence indicate a 'barrel-stave' channel structure, similar to that of alamethicin, but the length of a trichogin helix is too short to span a normal bilayer. Herein, we present electrophysiology measurements in planar bilayers, showing that trichogin does form channels of a well-defined size (R=4.2⋅10(9) Ω; corresponding at least to a trimeric aggregate) that span the membrane and allow ion diffusion, but do not exhibit voltage-dependent rectification, unlike those of alamethicin.
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Affiliation(s)
- Sorana Iftemi
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru I. Cuza University, 11, Blvd. Carol I, RO-700506 Iasi (phone: +40-232-201191)
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12
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Harris BJ, Cheng X, Frymier P. All-atom molecular dynamics simulation of a photosystem i/detergent complex. J Phys Chem B 2014; 118:11633-45. [PMID: 25233289 DOI: 10.1021/jp507157e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.
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Affiliation(s)
- Bradley J Harris
- Department of Chemical and Biomolecular Engineering, ‡Department of Biochemistry and Cellular and Molecular Biology, §Sustainable Energy Education and Research Center, and ∥Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee , Knoxville, Tennessee 37996, United States
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13
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Ishida H, Garcia-Herrero A, Vogel HJ. The periplasmic domain of Escherichia coli outer membrane protein A can undergo a localized temperature dependent structural transition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3014-24. [PMID: 25135663 DOI: 10.1016/j.bbamem.2014.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 01/21/2023]
Abstract
Gram-negative bacteria such as Escherichia coli are surrounded by two membranes with a thin peptidoglycan (PG)-layer located in between them in the periplasmic space. The outer membrane protein A (OmpA) is a 325-residue protein and it is the major protein component of the outer membrane of E. coli. Previous structure determinations have focused on the N-terminal fragment (residues 1-171) of OmpA, which forms an eight stranded transmembrane β-barrel in the outer membrane. Consequently it was suggested that OmpA is composed of two independently folded domains in which the N-terminal β-barrel traverses the outer membrane and the C-terminal domain (residues 180-325) adopts a folded structure in the periplasmic space. However, some reports have proposed that full-length OmpA can instead refold in a temperature dependent manner into a single domain forming a larger transmembrane pore. Here, we have determined the NMR solution structure of the C-terminal periplasmic domain of E. coli OmpA (OmpA(180-325)). Our structure reveals that the C-terminal domain folds independently into a stable globular structure that is homologous to the previously reported PG-associated domain of Neisseria meningitides RmpM. Our results lend credence to the two domain structure model and a PG-binding function for OmpA, and we could indeed localize the PG-binding site on the protein through NMR chemical shift perturbation experiments. On the other hand, we found no evidence for binding of OmpA(180-325) with the TonB protein. In addition, we have also expressed and purified full-length OmpA (OmpA(1-325)) to study the structure of the full-length protein in micelles and nanodiscs by NMR spectroscopy. In both membrane mimetic environments, the recombinant OmpA maintains its two domain structure that is connected through a flexible linker. A series of temperature-dependent HSQC experiments and relaxation dispersion NMR experiments detected structural destabilization in the bulge region of the periplasmic domain of OmpA above physiological temperatures, which may induce dimerization and play a role in triggering the previously reported larger pore formation.
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Affiliation(s)
- Hiroaki Ishida
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Alicia Garcia-Herrero
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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14
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Marcoux J, Politis A, Rinehart D, Marshall DP, Wallace MI, Tamm LK, Robinson CV. Mass spectrometry defines the C-terminal dimerization domain and enables modeling of the structure of full-length OmpA. Structure 2014; 22:781-90. [PMID: 24746938 DOI: 10.1016/j.str.2014.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/26/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
The transmembrane domain of the outer membrane protein A (OmpA) from Escherichia coli is an excellent model for structural and folding studies of β-barrel membrane proteins. However, full-length OmpA resists crystallographic efforts, and the link between its function and tertiary structure remains controversial. Here we use site-directed mutagenesis and mass spectrometry of different constructs of OmpA, released in the gas phase from detergent micelles, to define the minimal region encompassing the C-terminal dimer interface. Combining knowledge of the location of the dimeric interface with molecular modeling and ion mobility data allows us to propose a low-resolution model for the full-length OmpA dimer. Our model of the dimer is in remarkable agreement with experimental ion mobility data, with none of the unfolding or collapse observed for full-length monomeric OmpA, implying that dimer formation stabilizes the overall structure and prevents collapse of the flexible linker that connects the two domains.
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Affiliation(s)
- Julien Marcoux
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Argyris Politis
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Dennis Rinehart
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - David P Marshall
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Mark I Wallace
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK.
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15
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Fleites LA, Mensi I, Gargani D, Zhang S, Rott P, Gabriel DW. Xanthomonas albilineans OmpA1 appears to be functionally modular and both the OMC and C-like domains are necessary for leaf scald disease of sugarcane. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1200-1210. [PMID: 23758144 DOI: 10.1094/mpmi-01-13-0002-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Several EZ-Tn5 insertions in gene locus XALc_0557 (OmpA1) of the sugarcane leaf scald pathogen Xanthomonas albilineans XaFL07-1 were previously found to strongly affect pathogenicity and endophytic stalk colonization. XALc_0557 has a predicted OmpA N-terminal outer membrane channel (OMC) domain and an OmpA C-like domain. Further analysis of mutant M468, with an EZ-Tn5 insertion in the upstream OMC domain coding region, revealed impaired epiphytic and endophytic leaf survival, impaired resistance to sodium dodecyl sulfate (SDS), structural defects in the outer membrane (OM), and hyperproduction of OM vesicles. Cloned full-length XALc_0557 complemented M468 for all phenotypes tested, including pathogenicity, resistance to SDS, and ability to survive both endophytically and epiphytically. Another construct, pCT47.3, which expressed only the C-like domain of XALc_0557, restored resistance to SDS in M468 but failed to complement any other mutant phenotype, indicating that the C-like domain functioned independently of the OMC domain to help maintain OM integrity. pCT47.3 also complemented pathogenicity, resistance to SDS, and stalk colonization in mutant M1152, which carries an EZ-Tn5 insert in the C-like coding region, indicating that both predicted domains are modular and necessary but neither is sufficient for X. albilineans pathogenicity, endophytic survival in, and epiphytic survival on sugarcane.
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16
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The role of short-chain conjugated poly-(R)-3-hydroxybutyrate (cPHB) in protein folding. Int J Mol Sci 2013; 14:10727-48. [PMID: 23702844 PMCID: PMC3709699 DOI: 10.3390/ijms140610727] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/25/2023] Open
Abstract
Poly-(R)-3-hydroxybutyrate (PHB), a linear polymer of R-3-hydroxybutyrate (R-3HB), is a fundamental constituent of biological cells. Certain prokaryotes accumulate PHB of very high molecular weight (10,000 to >1,000,000 residues), which is segregated within granular deposits in the cytoplasm; however, all prokaryotes and all eukaryotes synthesize PHB of medium-chain length (~100-200 residues) which resides within lipid bilayers or lipid vesicles, and PHB of short-chain length (<12 residues) which is conjugated to proteins (cPHB), primarily proteins in membranes and organelles. The physical properties of cPHB indicate it plays important roles in the targeting and folding of cPHB-proteins. Here we review the occurrence, physical properties and molecular characteristics of cPHB, and discuss its influence on the folding and structure of outer membrane protein A (OmpA) of Escherichia coli.
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17
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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18
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Piggot TJ, Piñeiro Á, Khalid S. Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. J Chem Theory Comput 2012; 8:4593-609. [DOI: 10.1021/ct3003157] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas J. Piggot
- School of Chemistry, University
of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Ángel Piñeiro
- Department of Applied Physics,
University of Santiago de Compostela, Campus Vida, 15782, Santiago
de Compostela, Spain
| | - Syma Khalid
- School of Chemistry, University
of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
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19
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Yin F, Kindt JT. Hydrophobic mismatch and lipid sorting near OmpA in mixed bilayers: atomistic and coarse-grained simulations. Biophys J 2012; 102:2279-87. [PMID: 22677381 DOI: 10.1016/j.bpj.2012.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 04/02/2012] [Accepted: 04/04/2012] [Indexed: 11/24/2022] Open
Abstract
To understand the effects of lipid composition on membrane protein function in a mixture as complex as a biomembrane, one must know whether the lipid composition local to the protein differs from the mean lipid composition. In this study, we simulated the transmembrane domain of a β-barrel protein, OmpA, in mixtures of lipids of different tail lengths under conditions of negative hydrophobic mismatch, i.e., local bilayer thinning. We modeled the influence of OmpA on the local lipid composition both at a coarse-grained (CG) resolution using conventional molecular dynamics, and at an atomistic resolution within the semi-grand canonical ensemble using mutation moves to rapidly approach an equilibrium lateral distribution of lipids. Moderate enrichment of the shorter tail component (either DDPC in DDPC/DMPC mixtures or DMPC in DMPC/DSPC mixtures) extending 2-3 nm away from the protein surface was observed with both the atomistic and CG models. The similarity in trends suggests that the more computationally economical CG models capture the essential features of lipid sorting induced by hydrophobic mismatch.
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Affiliation(s)
- Fuchang Yin
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
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20
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Yang Y, Auguin D, Delbecq S, Dumas E, Molle G, Molle V, Roumestand C, Saint N. Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an oligomeric channel in the mycobacterial cell wall. Proteins 2011; 79:645-61. [PMID: 21117233 DOI: 10.1002/prot.22912] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The pore-forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor required for acid resistance in host phagosomes. In this study, we determined the 3D structure of OmpATb by NMR in solution. We found that OmpATb is composed of two independent domains separated by a proline-rich hinge region. As expected, the high-resolution structure of the C-terminal domain (OmpATb(198-326)) revealed a module structurally related to other OmpA-like proteins from Gram-negative bacteria. The N-terminal domain of OmpATb (73-204), which is sufficient to form channels in planar lipid bilayers, exhibits a fold, which belongs to the α+β sandwich class fold. Its peculiarity is to be composed of two overlapping subdomains linked via a BON (Bacterial OsmY and Nodulation) domain initially identified in bacterial proteins predicted to interact with phospholipids. Although OmpATb(73-204) is highly water soluble, current-voltage measurements demonstrate that it is able to form conducting pores in model membranes. A HADDOCK modeling of the NMR data gathered on the major monomeric form and on the minor oligomeric populations of OmpATb(73-204) suggest that OmpATb(73-204) can form oligomeric rings able to insert into phospholipid membrane, similar to related proteins from the Type III secretion systems, which form multisubunits membrane-associated rings at the basal body of the secretion machinery.
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Affiliation(s)
- Yinshan Yang
- Centre de Biochimie Structurale, CNRS UMR 5048, Université Montpellier 1 et 2, F34090 Montpellier, France
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21
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22
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Yuan H, Jameson CJ, Murad S. Diffusion of gases across lipid membranes with OmpA channel: a molecular dynamics study. Mol Phys 2010. [DOI: 10.1080/00268976.2010.484396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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OmpA of uropathogenic Escherichia coli promotes postinvasion pathogenesis of cystitis. Infect Immun 2009; 77:5245-51. [PMID: 19797074 DOI: 10.1128/iai.00670-09] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Type 1 pilus directs bladder epithelial binding and invasion by uropathogenic Escherichia coli (UPEC) in the initial stage of cystitis, but the bacterial determinants of postinvasion events in the pathogenesis of cystitis are largely undetermined. We show here that the UPEC outer membrane protein A (OmpA), a monomeric, major, integral protein component of the bacterial outer membrane, functions as a critical determinant of intracellular virulence for UPEC, promoting persistent infection within bladder epithelium. Using a murine urinary tract infection (UTI) model, we demonstrate that whereas deletion of the UPEC ompA gene did not disrupt initial epithelial binding and invasion by UPEC, it did preclude completion of the intracellular bacterial community (IBC) pathway, accompanied by diminishing bacterial loads in the bladder. This defect in epithelial persistence of the ompA mutant was enhanced in competitive infections with wild-type UPEC. Microscopic examinations revealed that the ompA mutant formed significantly fewer IBCs, and those that were initiated were unable to progress past the early stages of maturation. These defects could be corrected by complementation of ompA. In addition, expression of ompA during wild-type UTI was sharply increased at time points correlated with IBC development and the arrival of host immune effector cells. Our findings establish OmpA as a key UPEC virulence factor that functions after epithelial invasion to facilitate IBC maturation and chronic bacterial persistence.
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24
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Fast-time scale dynamics of outer membrane protein A by extended model-free analysis of NMR relaxation data. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:68-76. [PMID: 19665446 DOI: 10.1016/j.bbamem.2009.07.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 07/22/2009] [Indexed: 11/20/2022]
Abstract
In order to better understand the dynamics of an integral membrane protein, backbone amide (15)N NMR dynamics measurements of the beta-barrel membrane protein OmpA have been performed at three magnetic fields. A total of nine relaxation data sets were globally analyzed using an extended model-free formalism. The diffusion tensor was found to be prolate axially symmetric with an axial ratio of 5.75, indicating a possible rotation of the protein within the micelle. The generalized order parameters gradually decreased from the mid-plane towards the two ends of the barrel, counteracting the dynamic gradient of the lipids in a matching bilayer, and were dramatically reduced in the extracellular loops. Large-scale internal motions on the ns time scale indicate that entire loops most likely undergo concerted ("sea anemone"-like) motions emanating from their anchoring points on the barrel. The case of OmpA in DPC micelles also illustrates inherent limitations of analyzing the data with even the most sophisticated current models of the model-free formalism. It is likely that conformational exchange processes on the ms-mus also play a role in describing the motions of some residues, but their analysis did not produce unique results that could be independently verified.
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25
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Wan S, Coveney PV. A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes. J Comput Chem 2009; 30:1038-50. [PMID: 18942723 DOI: 10.1002/jcc.21130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The monotopic proteins COX-1 and -2 in dimeric form bound to lipid bilayer membranes are studied using molecular dynamics simulations within an aqueous environment. The 25-ns simulations are performed for both isozymes with arachidonic acid bound in the cyclooxygenase sites. The interactions between the enzymes and the lipids are analyzed, providing insight into the attachment mechanism of monotopic proteins to membranes. Our study reveals some key differences between the two isozymes that include the orientations at which they sit on the surface of the membranes and the depths to which they embed within the membranes. The differences in membrane association of the isozymes indicate that they may integrate distinctively with the same membrane, and/or with different membranes or their lipid components. Our results indicate that arachidonic acid can be bound in the cyclooxygenase active site in distinct catalytically competent conformations that lead to certain hydroperoxy acids; and the arachidonic acid and/or cyclooxygenase sites undergo a conformational change which makes only one subunit of each homodimer catalytically active.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1A 0HE, United Kingdom
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26
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Abstract
Bacterial outer membrane porins have a robust beta-barrel structure and therefore show potential for use as stochastic sensors based on single-molecule detection. The monomeric porin OmpG is especially attractive compared with multisubunit proteins because appropriate modifications of the pore can be easily achieved by mutagenesis. However, the gating of OmpG causes transient current blockades in single-channel recordings that would interfere with analyte detection. To eliminate this spontaneous gating activity, we used molecular dynamics simulations to identify regions of OmpG implicated in the gating. Based on our findings, two approaches were used to enhance the stability of the open conformation by site-directed mutagenesis. First, the mobility of loop 6 was reduced by introducing a disulfide bond between the extracellular ends of strands beta12 and beta13. Second, the interstrand hydrogen bonding between strands beta11 and beta12 was optimized by deletion of residue D215. The OmpG porin with both stabilizing mutations exhibited a 95% reduction in gating activity. We used this mutant for the detection of adenosine diphosphate at the single-molecule level, after equipping the porin with a cyclodextrin molecular adapter, thereby demonstrating its potential for use in stochastic sensing applications.
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27
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Carpenter T, Khalid S, Sansom MSP. A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2831-40. [PMID: 17888868 DOI: 10.1016/j.bbamem.2007.07.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 07/06/2007] [Accepted: 07/26/2007] [Indexed: 10/22/2022]
Abstract
PmOmpA is a two-domain outer membrane protein from Pasteurella multocida. The N-terminal domain of PmOmpA is a homologue of the transmembrane beta-barrel domain of OmpA from Escherichia coli, whilst the C-terminal domain of PmOmpA is a homologue of the extra-membrane Neisseria meningitidis RmpM C-terminal domain. This enables a model of a complete two domain PmOmpA to be constructed and its conformational dynamics explored via MD simulations of the protein embedded within two different phospholipid bilayers (DMPC and DMPE). The conformational stability of the transmembrane beta-barrel is similar to that of a homology model of OprF from Pseudomonas aeruginosa in bilayer simulations. There is a degree of water penetration into the interior of the beta-barrel, suggestive of a possible transmembrane pore. Although the PmOmpA model is stable over 20 ns simulations, retaining its secondary structure and fold integrity throughout, substantial flexibility is observed in a short linker region between the N- and the C-terminal domains. At low ionic strength, the C-terminal domain moves to interact electrostatically with the lipid bilayer headgroups. This study demonstrates that computational approaches may be applied to more complex, multi-domain outer membrane proteins, rather than just to transmembrane beta-barrels, opening the possibility of in silico proteomics approaches to such proteins.
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28
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Aykanat T, Benan Dincturk H. An outer membrane protein A (ompA) homologue from the photosynthetic purple sulfur bacterium Allochromatium vinosum. Microbiol Res 2007; 162:341-6. [PMID: 16644194 DOI: 10.1016/j.micres.2006.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2006] [Indexed: 11/30/2022]
Abstract
A 991 bp DNA fragment, consisting of a 225 amino acid reading frame homologous to outer membrane protein coding ompA gene, was cloned from a purple sulfur bacterium Allochromatium vinosum. The homology analysis revealed up to 51% similarity to other bacterial species. The absence of branching within diazotrophs or other taxonomically related groups shows the structural importance of the protein regardless of the metabolism and evolution of the species.
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Affiliation(s)
- Tutku Aykanat
- Department of Molecular Biology and Genetics, Faculty of Sciences and Letters, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
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29
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Smith SGJ, Mahon V, Lambert MA, Fagan RP. A molecular Swiss army knife: OmpA structure, function and expression. FEMS Microbiol Lett 2007; 273:1-11. [PMID: 17559395 DOI: 10.1111/j.1574-6968.2007.00778.x] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The OmpA outer membrane protein of Escherichia coli and other enterobacteria is a multifaceted protein. This protein is expressed to very high levels and ompA is tightly regulated at the posttranscriptional level. It can function as an adhesin and invasin, participate in biofilm formation, act as both an immune target and evasin, and serves as a receptor for several bacteriophages. Many of these properties are due to four short protein loops that emanate from the protein to the outside of the cell. Herein it is described how the structure of this protein relates to its many functions.
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Affiliation(s)
- Stephen G J Smith
- Department of Clinical Microbiology, Trinity College Dublin, St James's Hospital, Dublin, Ireland.
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30
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Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MSP. Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:131-41. [PMID: 17551722 DOI: 10.1007/s00249-007-0185-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 05/07/2007] [Accepted: 05/08/2007] [Indexed: 11/26/2022]
Abstract
The structures of three bacterial outer membrane proteins (OmpA, OmpX and PagP) have been determined by both X-ray diffraction and NMR. We have used multiple (7 x 15 ns) MD simulations to compare the conformational dynamics resulting from the X-ray versus the NMR structures, each protein being simulated in a lipid (DMPC) bilayer. Conformational drift was assessed via calculation of the root mean square deviation as a function of time. On this basis the 'quality' of the starting structure seems mainly to influence the simulation stability of the transmembrane beta-barrel domain. Root mean square fluctuations were used to compare simulation mobility as a function of residue number. The resultant residue mobility profiles were qualitatively similar for the corresponding X-ray and NMR structure-based simulations. However, all three proteins were generally more mobile in the NMR-based than in the X-ray simulations. Principal components analysis was used to identify the dominant motions within each simulation. The first two eigenvectors (which account for >50% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal alpha-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a approximately 10 ns timescale.
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Affiliation(s)
- Katherine Cox
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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31
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Khalid S, Bond PJ, Carpenter T, Sansom MSP. OmpA: gating and dynamics via molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:1871-80. [PMID: 17601489 DOI: 10.1016/j.bbamem.2007.05.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 05/23/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
Outer membrane proteins (OMPs) of Gram-negative bacteria have a variety of functions including passive transport, active transport, catalysis, pathogenesis and signal transduction. Whilst the structures of approximately 25 OMPs are currently known, there is relatively little known about their dynamics in different environments. The outer membrane protein, OmpA from Escherichia coli has been studied extensively in different environments both experimentally and computationally, and thus provides an ideal test case for the study of the dynamics and environmental interactions of outer membrane proteins. We review molecular dynamics simulations of OmpA and its homologues in a variety of different environments and discuss possible mechanisms of pore gating. The transmembrane domain of E. coli OmpA shows subtle differences in dynamics and interactions between a detergent micelle and a lipid bilayer environment. Simulations of the crystallographic unit cell reveal a micelle-like network of detergent molecules interacting with the protein monomers. Simulation and modelling studies emphasise the role of an electrostatic-switch mechanism in the pore-gating mechanism. Simulation studies have been extended to comparative models of OmpA homologues from Pseudomonas aeruginosa (OprF) and Pasteurella multocida (PmOmpA), the latter model including the periplasmic C-terminal domain.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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33
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Abstract
Mobility of extracellular loops may play an important role in the function of outer membrane proteins from Gram-negative bacteria. Molecular dynamics simulations of OpcA from Neisseria meningitidis, embedded in a lipid bilayer, have been used to explore the relationship between the crystal structure and dynamic function of this protein. The results suggest that the crystal environment may constrain the membrane protein structure in a nonphysiological state. The presence of lipids and physiological salt concentrations result in changes in the conformation of the extracellular loops of OpcA, leading to opening of a pore, and to modulation of the molecular surface implicated in recognition of proteoglycan. These changes may be related to the role of OpcA in pathogenesis via modulation of the conformation of a possible sialic acid binding site.
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34
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Hong H, Szabo G, Tamm LK. Electrostatic couplings in OmpA ion-channel gating suggest a mechanism for pore opening. Nat Chem Biol 2006; 2:627-35. [PMID: 17041590 DOI: 10.1038/nchembio827] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 08/30/2006] [Indexed: 11/08/2022]
Abstract
The molecular forces that drive structural transitions between the open and closed states of channels and transporters are not well understood. The gate of the OmpA channel is formed by the central Glu52-Arg138 salt bridge, which can open to form alternate ion pairs with Lys82 and Glu128. To gain deeper insight into the channel-opening mechanism, we measured interaction energies between the relevant side chains by double-mutant cycle analysis and correlated these with the channel activities of corresponding point mutants. The closed central salt bridge has a strong interaction energy of -5.6 kcal mol(-1), which can be broken by forming the open-state salt bridge Glu52-Lys82 (DeltaDeltaG(Inter) = -3.5 kcal mol(-1)) and a weak interaction between Arg138 and Glu128 (DeltaDeltaG(Inter) = -0.6 kcal mol(-1)). A covalent disulfide bond in place of the central salt bridge completely blocks the channel. Growth assays indicate that this gating mechanism could physiologically contribute to the osmoprotection of Escherichia coli cells from environmental stress.
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Affiliation(s)
- Heedeok Hong
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, PO Box 800736, Charlottesville, Virginia 22908-0736, USA
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35
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Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI. Positioning of proteins in membranes: a computational approach. Protein Sci 2006; 15:1318-33. [PMID: 16731967 PMCID: PMC2242528 DOI: 10.1110/ps.062126106] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene-like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water-soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were approximately 1 A and 2 degrees, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 A depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26 degrees in asymmetric structures. Calculated hydrophobic boundaries of proteins are located approximately 5 A lower than lipid phosphates and correspond to the zero membrane depth parameter of spin-labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/.
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Affiliation(s)
- Andrei L Lomize
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.
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36
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Haubertin DY, Madaoui H, Sanson A, Guérois R, Orlowski S. Molecular dynamics simulations of E. coli MsbA transmembrane domain: formation of a semipore structure. Biophys J 2006; 91:2517-31. [PMID: 16782794 PMCID: PMC1562368 DOI: 10.1529/biophysj.106.084020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human P-glycoprotein (MDR1/P-gp) is an ATP-binding cassette (ABC) transporter involved in cellular response to chemical stress and failures of anticancer chemotherapy. In the absence of a high-resolution structure for P-gp, we were interested in the closest P-gp homolog for which a crystal structure is available: the bacterial ABC transporter MsbA. Here we present the molecular dynamics simulations performed on the transmembrane domain of the open-state MsbA in a bilayer composed of palmitoyl oleoyl phosphatidylethanolamine lipids. The system studied contained more than 90,000 atoms and was simulated for 50 ns. This simulation shows that the open-state structure of MsbA can be stable in a membrane environment and provides invaluable insights into the structural relationships between the protein and its surrounding lipids. This study reveals the formation of a semipore-like structure stabilized by two key phospholipids which interact with the hinge region of the protein during the entire simulation. Multiple sequence alignments of ABC transporters reveal that one of the residues involved in the interaction with these two phospholipids are under a strong selection pressure specifically applied on the bacterial homologs of MsbA. Hence, comparison of molecular dynamics simulation and phylogenetic data appears as a powerful approach to investigate the functional relevance of molecular events occurring during simulations.
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Affiliation(s)
- David Y Haubertin
- Service de Biophysique des Fonctions Membranaires, Département de Biologie Joliot-Curie and URA 2096 CNRS, Direction des Sciences du Vivant/Commissariat á l'Energie Atomique (CEA), Centre de Saclay, 91191 Gif-sur-Yvette cedex, France
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37
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Khalid S, Bond PJ, Deol SS, Sansom MSP. Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa. Proteins 2006; 63:6-15. [PMID: 16397890 DOI: 10.1002/prot.20845] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OprF is a major outer membrane protein from Pseudomonas aeruginosa, a homolog of OmpA from Escherichia coli. The N-terminal domains of both proteins have been demonstrated to form low conductance channels in lipid bilayers. Homology models, consisting of an eight-stranded beta-barrel, of the N-terminal domain OprF have been constructed based on the crystal structure of the corresponding domain from E. coli OmpA. OprF homology models have been evaluated via a set (6 x 10 ns) of simulations of the beta-barrel embedded within a solvated dimyristoyl-phosphatidylcholine (DMPC) bilayer. The conformational stability of the models is similar to that of the crystal structure of OmpA in comparable simulations. There is a degree of water penetration into the pore-like center of the OprF barrel. The presence of an acidic/basic (E8/K121) side-chain interaction within the OprF barrel may form a "gate" able to close/open a central pore. Lipid-protein interactions within the simulations were analyzed and revealed that aromatic side-chains (Trp, Tyr) of OprF interact with lipid headgroups. Overall, the behavior of the OprF model in simulations supports the suggestion that this molecule is comparable to OmpA. The simulations help to explain the mechanism of formation of low conductance pores within the outer membrane.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Bond PJ, Faraldo-Gómez JD, Deol SS, Sansom MSP. Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA. Proc Natl Acad Sci U S A 2006; 103:9518-23. [PMID: 16766663 PMCID: PMC1480439 DOI: 10.1073/pnas.0600398103] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics (MD) simulations are used to explore the dynamics of a membrane protein in its crystal environment. A 50-ns-duration simulation (at a temperature of 300 K) is performed for the crystallographic unit cell of the bacterial outer membrane protein OmpA. The unit cell contains four protein molecules, plus detergent molecules and water. An excellent correlation between simulated and experimental values of crystallographic B factors is observed. Effectively, 0.2 micros of protein trajectories are obtained, allowing a critical assessment of simulation quality. Some deficiency in conformational sampling is demonstrated, but averaging over multiple trajectories improves this limitation. The previously undescribed structure and dynamics of detergent molecules in a unit cell are reported here, providing insight into the interactions important in the formation and stabilization of the crystalline environment at room temperature. In particular, we show that at room temperature the detergent molecules form a dynamic, extended micellar structure spreading over adjacent OmpA monomers within the crystal.
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Affiliation(s)
- Peter J. Bond
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - José D. Faraldo-Gómez
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Sundeep S. Deol
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
- To whom correspondence should be addressed. E-mail:
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Faraldo-Gómez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins 2006; 57:783-91. [PMID: 15317024 DOI: 10.1002/prot.20257] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the current report, we provide a quantitative analysis of the convergence of the sampling of conformational space accomplished in molecular dynamics simulations of membrane proteins of duration in the order of 10 nanoseconds. A set of proteins of diverse size and topology is considered, ranging from helical pores such as gramicidin and small beta-barrels such as OmpT, to larger and more complex structures such as rhodopsin and FepA. Principal component analysis of the C(alpha)-atom trajectories was employed to assess the convergence of the conformational sampling in both the transmembrane domains and the whole proteins, while the time-dependence of the average structure was analyzed to obtain single-domain information. The membrane-embedded regions, particularly those of small or structurally simple proteins, were found to achieve reasonable convergence. By contrast, extra-membranous domains lacking secondary structure are often markedly under-sampled, exhibiting a continuous structural drift. This drift results in a significant imprecision in the calculated B-factors, which detracts from any quantitative comparison to experimental data. In view of such limitations, we suggest that similar analyses may be valuable in simulation studies of membrane protein dynamics, in order to attach a level of confidence to any biologically relevant observations.
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Affiliation(s)
- José D Faraldo-Gómez
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA.
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40
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Nestorovich EM, Sugawara E, Nikaido H, Bezrukov SM. Pseudomonas aeruginosa porin OprF: properties of the channel. J Biol Chem 2006; 281:16230-7. [PMID: 16617058 PMCID: PMC2846715 DOI: 10.1074/jbc.m600650200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using ion channel reconstitution in planar lipid bilayers, we examined the channel-forming activity of subfractions of Pseudomonas aeruginosa OprF, which was shown to exist in two different conformations: a minority single domain conformer and a majority two-domain conformer (Sugawara, E., Nestorovich, E. M., Bezrukov, S. M., and Nikaido, H. (2006) J. Biol. Chem. 281, 16220-16229). With the fraction depleted for the single domain conformer, we were unable to detect formation of any channels with well defined conductance levels. With the unfractionated OprF, we saw only rare channel formation. However, with the single domain-enriched fraction of OprF, we observed regular insertion of channels with highly reproducible conductances. Single OprF channels demonstrate rich kinetic behavior exhibiting spontaneous transitions between several subconformations that differ in ionic conductance and radius measured in polymer exclusion experiments. Although we showed that the effective radius of the most conductive conformation exceeds that of the general outer membrane porin of Escherichia coli, OmpF, we also found that a single OprF channel mainly exists in weakly conductive subconformations and switches to the fully open state for a short time only. Therefore, the low permeability of OprF reported earlier may be due to two factors: mainly to the paucity of the single domain conformer in the OprF population and secondly to the predominance of weakly conductive subconformations within the single domain conformer.
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Affiliation(s)
- Ekaterina M. Nestorovich
- Laboratory of Physical and Structural Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892-0924
| | - Etsuko Sugawara
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Sergey M. Bezrukov
- Laboratory of Physical and Structural Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892-0924
- To whom correspondence should be addressed: Laboratory of Physical and Structural Biology, NICHD, National Institutes of Health, Bldg. 9 Rm. 1N124, 9 Memorial Dr., Bethesda, MD 20892-0924. Tel.: 301-402-4701; Fax: 301-496-2172;
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41
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Abstract
Interactions of lipids are central to the folding and stability of membrane proteins. Coarse-grained molecular dynamics simulations have been used to reveal the mechanisms of self-assembly of protein/membrane and protein/detergent complexes for representatives of two classes of membrane protein, namely, glycophorin (a simple alpha-helical bundle) and OmpA (a beta-barrel). The accuracy of the coarse-grained simulations is established via comparison with the equivalent atomistic simulations of self-assembly of protein/detergent micelles. The simulation of OmpA/bilayer self-assembly reveals how a folded outer membrane protein can be inserted in a bilayer. The glycophorin/bilayer simulation supports the two-state model of membrane folding, in which transmembrane helix insertion precedes dimer self-assembly within a bilayer. The simulations also suggest that a dynamic equilibrium exists between the glycophorin helix monomer and dimer within a bilayer. The simulated glycophorin helix dimer is remarkably close in structure to that revealed by NMR. Thus, coarse-grained methods may help to define mechanisms of membrane protein (re)folding and will prove suitable for simulation of larger scale dynamic rearrangements of biological membranes.
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Affiliation(s)
- Peter J. Bond
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
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42
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Hong H, Patel DR, Tamm LK, van den Berg B. The Outer Membrane Protein OmpW Forms an Eight-stranded β-Barrel with a Hydrophobic Channel. J Biol Chem 2006; 281:7568-77. [PMID: 16414958 DOI: 10.1074/jbc.m512365200] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Escherichia coli OmpW belongs to a family of small outer membrane proteins that are widespread in Gram-negative bacteria. Their functions are unknown, but recent data suggest that they may be involved in the protection of bacteria against various forms of environmental stress. To gain insight into the function of these proteins A we have determined the crystal structure of E. coli OmpW to 2.7-A resolution. The structure shows that OmpW forms an 8-stranded beta-barrel with a long and narrow hydrophobic channel that contains a bound n-dodecyl-N,N-dimethylamine-N-oxide detergent molecule. Single channel conductance experiments show that OmpW functions as an ion channel in planar lipid bilayers. The channel activity can be blocked by the addition of n-dodecyl-N,N-dimethylamine-N-oxide. Taken together, the data suggest that members of the OmpW family could be involved in the transport of small hydrophobic molecules across the bacterial outer membrane.
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Affiliation(s)
- Heedeok Hong
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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43
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Law RJ, Capener C, Baaden M, Bond PJ, Campbell J, Patargias G, Arinaminpathy Y, Sansom MSP. Membrane protein structure quality in molecular dynamics simulation. J Mol Graph Model 2006; 24:157-65. [PMID: 16102990 DOI: 10.1016/j.jmgm.2005.05.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2005] [Indexed: 10/25/2022]
Abstract
Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure-function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined.
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Affiliation(s)
- Richard J Law
- Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK.
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44
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Gumbart J, Wang Y, Aksimentiev A, Tajkhorshid E, Schulten K. Molecular dynamics simulations of proteins in lipid bilayers. Curr Opin Struct Biol 2005; 15:423-31. [PMID: 16043343 PMCID: PMC2474857 DOI: 10.1016/j.sbi.2005.07.007] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 06/14/2005] [Accepted: 07/13/2005] [Indexed: 11/19/2022]
Abstract
With recent advances in X-ray crystallography of membrane proteins promising many new high-resolution structures, molecular dynamics simulations will become increasingly valuable for understanding membrane protein function, as they can reveal the dynamic behavior concealed in the static structures. Dramatic increases in computational power, in synergy with more efficient computational methodologies, now allow us to carry out molecular dynamics simulations of any structurally known membrane protein in its native environment, covering timescales of up to 0.1 micros. At the frontiers of membrane protein simulations are ion channels, aquaporins, passive and active transporters, and bioenergetic proteins.
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Affiliation(s)
- James Gumbart
- Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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45
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Abstract
Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.
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46
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Ash WL, Zlomislic MR, Oloo EO, Tieleman DP. Computer simulations of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:158-89. [PMID: 15519314 DOI: 10.1016/j.bbamem.2004.04.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.
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Affiliation(s)
- Walter L Ash
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB, Canada T2N 1N4
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47
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Saladino AC, Xu Y, Tang P. Homology modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor. Biophys J 2004; 88:1009-17. [PMID: 15574706 PMCID: PMC1305108 DOI: 10.1529/biophysj.104.053421] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A three-dimensional model of the transmembrane domain of a neuronal-type nicotinic acetylcholine receptor (nAChR), (alpha4)2(beta2)3, was constructed from a homology structure of the muscle-type nAChR recently determined by cryo-electron microscopy. The neuronal channel model was embedded in a fully hydrated DMPC lipid bilayer, and molecular-dynamics simulations were performed for 5 ns. A comparative analysis of the neuronal- versus muscle-type nAChR models revealed many conserved pore-lining residues, but an important difference was found near the periplasmic mouth of the pore. A flickering salt-bridge of alpha4-E266 with its adjacent beta2-K260 was observed in the neuronal-type channel during the course of the molecular-dynamics simulations. The narrowest region, with a pore radius of approximately 2 A formed by the salt-bridges, does not seem to be the restriction site for a continuous water passage. Instead, two hydrophobic rings, formed by alpha4-V259, alpha4-L263, and the homologous residues in the beta2-subunits, act as the gates for water flow, even though the region has a slightly larger pore radius. The model offers new insight into the water transport across the (alpha4)2(beta2)3 nAChR channel, and may lead to a better understanding of the structures, dynamics, and functions of this family of ion channels.
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MESH Headings
- Amino Acid Sequence
- Computer Simulation
- Diffusion
- Dimyristoylphosphatidylcholine/chemistry
- Lipid Bilayers/chemistry
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Motion
- Muscle, Skeletal/chemistry
- Muscle, Skeletal/metabolism
- Neurons/chemistry
- Neurons/metabolism
- Porosity
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Nicotinic/analysis
- Receptors, Nicotinic/chemistry
- Receptors, Nicotinic/ultrastructure
- Sequence Analysis, Protein/methods
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
- Water/chemistry
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Affiliation(s)
- Alexander C Saladino
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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48
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Saiz L, Klein ML. The transmembrane domain of the acetylcholine receptor: insights from simulations on synthetic peptide models. Biophys J 2004; 88:959-70. [PMID: 15556982 PMCID: PMC1305168 DOI: 10.1529/biophysj.104.049726] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the structure and properties of a bundle of alpha-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle of five transmembrane deltaM2 segments constitutes the model for the pore region of the nicotinic acetylcholine receptor, which is the neurotransmitter-gated ion-channel responsible for the fast propagation of electrical signals between cells at the nerve-muscle synapse. The deltaM2 segments were shown to oligomerize in biomembranes resulting in ion-channel activity with characteristics similar to the native protein, and the structure of the isolated peptides was studied in 1,2-dimyristoyl-3-phosphatidylcholine bilayers and micelles by NMR experiments (Opella, S. J., et al. 1999. Nat. Struct. Biol. 6:374-379). Our analyses indicate that the structure, helix tilt, and the overall shape of the channel are in good agreement with the NMR experiments and the proposed model for the channel, which we show is formed by rings of functional residues. The studied geometry resulted in a closed pore state, where the channel is partially dehydrated at the hydrophobic extracellular half and the extracellular mouth of the channel blocked by the hydrocarbon chains of Arg+ residues. The arginine amino acids form intermolecular salt-bridges with the C-terminus, which contribute as well to the bundle stabilization.
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Affiliation(s)
- Leonor Saiz
- Center for Molecular Modeling, Chemistry Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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49
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Deol SS, Bond PJ, Domene C, Sansom MSP. Lipid-protein interactions of integral membrane proteins: a comparative simulation study. Biophys J 2004; 87:3737-49. [PMID: 15465855 PMCID: PMC1304887 DOI: 10.1529/biophysj.104.048397] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interactions between membrane proteins and their lipid bilayer environment play important roles in the stability and function of such proteins. Extended (15-20 ns) molecular dynamics simulations have been used to explore the interactions of two membrane proteins with phosphatidylcholine bilayers. One protein (KcsA) is an alpha-helix bundle and embedded in a palmitoyl oleoyl phosphatidylcholine bilayer; the other (OmpA) is a beta-barrel outer-membrane protein and is in a dimyristoyl phosphatidylcholine bilayer. The simulations enable analysis in detail of a number of aspects of lipid-protein interactions. In particular, the interactions of aromatic amphipathic side chains (i.e., Trp, Tyr) with lipid headgroups, and "snorkeling" interactions of basic side chains (i.e., Lys, Arg) with phosphate groups are explored. Analysis of the number of contacts and of H-bonds reveal fluctuations on an approximately 1- to 5-ns timescale. There are two clear bands of interacting residues on the surface of KcsA, whereas there are three such bands on OmpA. A large number of Arg-phosphate interactions are seen for KcsA; for OmpA, the number of basic-phosphate interactions is smaller and shows more marked fluctuations with respect to time. Both classes of interaction occur in clearly defined interfacial regions of width approximately 1 nm. Analysis of lateral diffusion of lipid molecules reveals that "boundary" lipid molecules diffuse at about half the rate of bulk lipid. Overall, these simulations present a dynamic picture of lipid-protein interactions: there are a number of more specific interactions but even these fluctuate on an approximately 1- to 5-ns timescale.
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Affiliation(s)
- Sundeep S Deol
- Department of Biochemistry, and Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
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50
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Dupont M, Dé E, Chollet R, Chevalier J, Pagès JM. Enterobacter aerogenes OmpX, a cation-selective channel mar- and osmo-regulated. FEBS Lett 2004; 569:27-30. [PMID: 15225603 DOI: 10.1016/j.febslet.2004.05.047] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 05/05/2004] [Accepted: 05/12/2004] [Indexed: 11/15/2022]
Abstract
The ompX gene of Enterobacter aerogenes was cloned. Its overexpression induced a decrease in the major porin Omp36 production and consequently a beta-lactam resistance was noted. Purified outer membrane protein X (OmpX) was reconstituted into artificial membranes and formed ion channels with a conductance of 20 pS in 1 M NaCl and a cationic selectivity. Both MarA expression and high osmolarity induced a noticeable increase of the OmpX synthesis in the E. aerogenes ATCC 13048 strain. In addition, OmpX synthesis increased under conditions in which the expression of the E. aerogenes major non-specific porins, Omp36 and Omp35, decreased.
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Affiliation(s)
- Myrielle Dupont
- EA2197, IFR48, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France
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