1
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Zercher BP, Hong S, Roush AE, Feng Y, Bush MF. Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Anal Chem 2023; 95:9589-9597. [PMID: 37294019 PMCID: PMC10549206 DOI: 10.1021/acs.analchem.3c01222] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The structural stability of biomolecules in the gas phase remains an important topic in mass spectrometry applications for structural biology. Here, we evaluate the kinetic stability of native-like protein ions using time-dependent, tandem ion mobility (IM). In these tandem IM experiments, ions of interest are mobility-selected after a first dimension of IM and trapped for up to ∼14 s. Time-dependent, collision cross section distributions are then determined from separations in a second dimension of IM. In these experiments, monomeric protein ions exhibited structural changes specific to both protein and charge state, whereas large protein complexes did not undergo resolvable structural changes on the timescales of these experiments. We also performed energy-dependent experiments, i.e., collision-induced unfolding, as a comparison for time-dependent experiments to understand the extent of unfolding. Collision cross section values observed in energy-dependent experiments using high collision energies were significantly larger than those observed in time-dependent experiments, indicating that the structures observed in time-dependent experiments remain kinetically trapped and retain some memory of their solution-phase structure. Although structural evolution should be considered for highly charged, monomeric protein ions, these experiments demonstrate that higher-mass protein ions can have remarkable kinetic stability in the gas phase.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Seoyeon Hong
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Addison E. Roush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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2
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Su YC, Kadari M, Straw ML, Janoušková M, Jonsson S, Thofte O, Jalalvand F, Matuschek E, Sandblad L, Végvári Á, Zubarev RA, Riesbeck K. Non-typeable Haemophilus influenzae major outer membrane protein P5 contributes to bacterial membrane stability, and affects the membrane protein composition crucial for interactions with the human host. Front Cell Infect Microbiol 2023; 13:1085908. [PMID: 37305414 PMCID: PMC10250671 DOI: 10.3389/fcimb.2023.1085908] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/10/2023] [Indexed: 06/13/2023] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) is a Gram-negative human pathogen that causes a wide range of airway diseases. NTHi has a plethora of mechanisms to colonize while evading the host immune system for the establishment of infection. We previously showed that the outer membrane protein P5 contributes to bacterial serum resistance by the recruitment of complement regulators. Here, we report a novel role of P5 in maintaining bacterial outer membrane (OM) integrity and protein composition important for NTHi-host interactions. In silico analysis revealed a peptidoglycan-binding motif at the periplasmic C-terminal domain (CTD) of P5. In a peptidoglycan-binding assay, the CTD of P5 (P5CTD) formed a complex with peptidoglycan. Protein profiling analysis revealed that deletion of CTD or the entire P5 changed the membrane protein composition of the strains NTHi 3655Δp5CTD and NTHi 3655Δp5, respectively. Relative abundance of several membrane-associated virulence factors that are crucial for adherence to the airway mucosa, and serum resistance were altered. This was also supported by similar attenuated pathogenic phenotypes observed in both NTHi 3655Δp5 CTD and NTHi 3655Δp5. We found (i) a decreased adherence to airway epithelial cells and fibronectin, (ii) increased complement-mediated killing, and (iii) increased sensitivity to the β-lactam antibiotics in both mutants compared to NTHi 3655 wild-type. These mutants were also more sensitive to lysis at hyperosmotic conditions and hypervesiculated compared to the parent wild-type bacteria. In conclusion, our results suggest that P5 is important for bacterial OM stability, which ultimately affects the membrane proteome and NTHi pathogenesis.
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Affiliation(s)
- Yu-Ching Su
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Mahendar Kadari
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Megan L. Straw
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Martina Janoušková
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Sandra Jonsson
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Oskar Thofte
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Farshid Jalalvand
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Erika Matuschek
- European Committee on Antimicrobial Susceptibility Testing (EUCAST) Development Laboratory, c/o Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Linda Sandblad
- Department of Chemistry and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry & Biophysics (MBB), Proteomics Biomedicum, Karolinska Institute, Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Chemistry I, Department of Medical Biochemistry & Biophysics (MBB), Proteomics Biomedicum, Karolinska Institute, Stockholm, Sweden
| | - Kristian Riesbeck
- Department of Translational Medicine, Clinical Microbiology, Faculty of Medicine, Lund University, Malmö, Sweden
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3
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Cho THS, Wang J, Raivio TL. NlpE Is an OmpA-Associated Outer Membrane Sensor of the Cpx Envelope Stress Response. J Bacteriol 2023; 205:e0040722. [PMID: 37022159 PMCID: PMC10127795 DOI: 10.1128/jb.00407-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
Gram-negative bacteria utilize several envelope stress responses (ESRs) to sense and respond to diverse signals within a multilayered cell envelope. The CpxRA ESR responds to multiple stresses that perturb envelope protein homeostasis. Signaling in the Cpx response is regulated by auxiliary factors, such as the outer membrane (OM) lipoprotein NlpE, an activator of the response. NlpE communicates surface adhesion to the Cpx response; however, the mechanism by which NlpE accomplishes this remains unknown. In this study, we report a novel interaction between NlpE and the major OM protein OmpA. Both NlpE and OmpA are required to activate the Cpx response in surface-adhered cells. Furthermore, NlpE senses OmpA overexpression and the NlpE C-terminal domain transduces this signal to the Cpx response, revealing a novel signaling function for this domain. Mutation of OmpA peptidoglycan-binding residues abrogates signaling during OmpA overexpression, suggesting that NlpE signaling from the OM through the cell wall is coordinated via OmpA. Overall, these findings reveal NlpE to be a versatile envelope sensor that takes advantage of its structure, localization, and cooperation with other envelope proteins to initiate adaptation to diverse signals. IMPORTANCE The envelope is not only a barrier that protects bacteria from the environment but also a crucial site for the transduction of signals critical for colonization and pathogenesis. The discovery of novel complexes between NlpE and OmpA contributes to an emerging understanding of the key contribution of OM β-barrel protein and lipoprotein complexes to envelope stress signaling. Overall, our findings provide mechanistic insight into how the Cpx response senses signals relevant to surface adhesion and biofilm growth to facilitate bacterial adaptation.
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Affiliation(s)
- Timothy H. S. Cho
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Junshu Wang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tracy L. Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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4
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Liao C, Santoscoy MC, Craft J, Anderson C, Soupir ML, Jarboe LR. Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution. PLoS One 2022; 17:e0276046. [PMID: 36227900 PMCID: PMC9560509 DOI: 10.1371/journal.pone.0276046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Miguel C. Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
| | - Julia Craft
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Chiron Anderson
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Laura R. Jarboe
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
- * E-mail:
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5
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Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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6
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Abstract
There is an increasing interest in phage therapy as an alternative to antibiotics for treating bacterial infections, especially using phages that select for evolutionary trade-offs between increased phage resistance and decreased fitness traits, such as virulence, in target bacteria. A vast repertoire of virulence factors allows the opportunistic bacterial pathogen Shigella flexneri to invade human gut epithelial cells, replicate intracellularly, and evade host immunity through intercellular spread. It has been previously shown that OmpA is necessary for the intercellular spread of S. flexneri. We hypothesized that a phage which uses OmpA as a receptor to infect S. flexneri should select for phage-resistant mutants with attenuated intercellular spread. Here, we show that phage A1-1 requires OmpA as a receptor and selects for reduced virulence in S. flexneri. We characterized five phage-resistant mutants by measuring phenotypic changes in various traits: cell-membrane permeability, total lipopolysaccharide (LPS), sensitivity to antibiotics, and susceptibility to other phages. The results separated the mutants into two groups: R1 and R2 phenotypically resembled ompA knockouts, whereas R3, R4, and R5 were similar to LPS-deficient strains. Whole-genome sequencing confirmed that R1 and R2 had mutations in ompA, while R3, R4, and R5 had mutations in the LPS inner-core biosynthesis genes gmhA and gmhC. Bacterial plaque assays confirmed that all the phage-resistant mutants were incapable of intercellular spread. We concluded that selection for S. flexneri resistance to phage A1-1 generally reduced virulence (i.e., intercellular spread), but this trade-off could be mediated by mutations either in ompA or in LPS-core genes that likely altered OmpA conformation. IMPORTANCEShigella flexneri is a facultative intracellular pathogen of humans and a leading cause of bacillary dysentery. With few effective treatments and rising antibiotic resistance in these bacteria, there is increasing interest in alternatives to classical infection management of S. flexneri infections. Phage therapy poses an attractive alternative, particularly if a therapeutic phage can be found that results in an evolutionary trade-off between phage resistance and bacterial virulence. Here, we isolate a novel lytic phage from water collected in Cuatro Cienegas, Mexico, which uses the OmpA porin of S. flexneri as a receptor. We use phenotypic assays and genome sequencing to show that phage A1-1 selects for phage-resistant mutants which can be grouped into two categories: OmpA-deficient mutants and LPS-deficient mutants. Despite these underlying mechanistic differences, we confirmed that naturally occurring phage A1-1 selected for evolved phage resistance which coincided with impaired intercellular spread of S. flexneri in a eukaryotic infection model.
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7
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Chavez JD, Wippel HH, Tang X, Keller A, Bruce JE. In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. Chem Rev 2021; 122:7647-7689. [PMID: 34232610 PMCID: PMC8966414 DOI: 10.1021/acs.chemrev.1c00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological systems have evolved to utilize proteins to accomplish nearly all functional roles needed to sustain life. A majority of biological functions occur within the crowded environment inside cells and subcellular compartments where proteins exist in a densely packed complex network of protein-protein interactions. The structural biology field has experienced a renaissance with recent advances in crystallography, NMR, and CryoEM that now produce stunning models of large and complex structures previously unimaginable. Nevertheless, measurements of such structural detail within cellular environments remain elusive. This review will highlight how advances in mass spectrometry, chemical labeling, and informatics capabilities are merging to provide structural insights on proteins, complexes, and networks that exist inside cells. Because of the molecular detection specificity provided by mass spectrometry and proteomics, these approaches provide systems-level information that not only benefits from conventional structural analysis, but also is highly complementary. Although far from comprehensive in their current form, these approaches are currently providing systems structural biology information that can uniquely reveal how conformations and interactions involving many proteins change inside cells with perturbations such as disease, drug treatment, or phenotypic differences. With continued advancements and more widespread adaptation, systems structural biology based on in-cell labeling and mass spectrometry will provide an even greater wealth of structural knowledge.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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8
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Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
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Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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9
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Pedebos C, Smith IPS, Boags A, Khalid S. The hitchhiker's guide to the periplasm: Unexpected molecular interactions of polymyxin B1 in E. coli. Structure 2021; 29:444-456.e2. [PMID: 33577754 DOI: 10.1016/j.str.2021.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/11/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022]
Abstract
The periplasm of Gram-negative bacteria is a complex, highly crowded molecular environment. Little is known about how antibiotics move across the periplasm and the interactions they experience. Here, atomistic molecular dynamics simulations are used to study the antibiotic polymyxin B1 within models of the periplasm, which are crowded to different extents. We show that PMB1 is likely to be able to "hitchhike" within the periplasm by binding to lipoprotein carriers-a previously unreported passive transport route. The simulations reveal that PMB1 forms both transient and long-lived interactions with proteins, osmolytes, lipids of the outer membrane, and the cell wall, and is rarely uncomplexed when in the periplasm. Furthermore, it can interfere in the conformational dynamics of native proteins. These are important considerations for interpreting its mechanism of action and are likely to also hold for other antibiotics that rely on diffusion to cross the periplasm.
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Affiliation(s)
- Conrado Pedebos
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Iain Peter Shand Smith
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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10
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Nielsen DW, Ricker N, Barbieri NL, Allen HK, Nolan LK, Logue CM. Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli. BMC Res Notes 2020; 13:51. [PMID: 32005127 PMCID: PMC6995065 DOI: 10.1186/s13104-020-4917-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/22/2020] [Indexed: 02/05/2023] Open
Abstract
Objective Extraintestinal Pathogenic E. coli (ExPEC), are responsible for host diseases such as Neonatal Meningitis Escherichia coli (NMEC), the second-leading cause of neonatal bacterial meningitis, Avian Pathogenic E. coli (APEC), a cause of extraintestinal disease in poultry, and Uropathogenic E. coli (UPEC), the most common cause of urinary tract infections. Virulence factors associated with NMEC include outer membrane protein A (OmpA) and type I fimbriae (FimH), which also occur in APEC and UPEC. OmpA contributes to NMEC’s ability to cross the blood–brain barrier, persist in the bloodstream and has been identified as a potential vaccine target for ExPEC, however the protein has amino acid variants, which may influence virulence of strains or alter vaccine efficacy. Although OmpA is present in virtually all E. coli, differences in its amino acid residues have yet to be surveyed in ExPEC. Results Here the ompA gene (n = 399) from ExPEC collections were sequenced and translated in silico. Twenty-five different OmpA polymorphism patterns were identified. Seven polymorphism patterns were significantly associated with an ExPEC subpathotype, but chromosomal history most likely accounts for most differences found. The differences in OmpA protein sequences suggest that OmpA may influence variation in virulence and host specificity within ExPEC subpathotypes.
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Affiliation(s)
- Daniel W Nielsen
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd, Ames, IA, 50011, USA.,Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA
| | - Nicole Ricker
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Nicolle L Barbieri
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA
| | - Lisa K Nolan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Catherine M Logue
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA.
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11
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Outer membrane protein A (OmpA) as a potential therapeutic target for Acinetobacter baumannii infection. J Biomed Sci 2020; 27:26. [PMID: 31954394 PMCID: PMC6969976 DOI: 10.1186/s12929-020-0617-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/14/2020] [Indexed: 01/12/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is an important opportunistic pathogen causing serious nosocomial infections, which is considered as the most threatening Gram-negative bacteria (GNB). Outer membrane protein A (OmpA), a major component of outer membrane proteins (OMPs) in GNB, is a key virulence factor which mediates bacterial biofilm formation, eukaryotic cell infection, antibiotic resistance and immunomodulation. The characteristics of OmpA in Escherichia coli (E. coli) have been extensively studied since 1974, but only in recent years researchers started to clarify the functions of OmpA in A. baumannii. In this review, we summarized the structure and functions of OmpA in A. baumannii (AbOmpA), collected novel therapeutic strategies against it for treating A. baumannii infection, and emphasized the feasibility of using AbOmpA as a potential therapeutic target.
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12
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The Mutation of Conservative Asp268 Residue in the Peptidoglycan-Associated Domain of the OmpA Protein Affects Multiple Acinetobacter baumannii Virulence Characteristics. Molecules 2019; 24:molecules24101972. [PMID: 31121924 PMCID: PMC6572160 DOI: 10.3390/molecules24101972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/07/2019] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Acinetobacter baumannii is a nosocomial human pathogen of increasing concern due to its multidrug resistance profile. The outer membrane protein A (OmpA) is an abundant bacterial cell surface component involved in A. baumannii pathogenesis. It has been shown that the C-terminal domain of OmpA is located in the periplasm and non-covalently associates with the peptidoglycan layer via two conserved amino acids, thereby anchoring OmpA to the cell wall. Here, we investigated the role of one of the respective residues, D268 in OmpA of A. baumannii clinical strain Ab169, on its virulence characteristics by complementing the ΔompA mutant with the plasmid-borne ompAD268A allele. We show that while restoring the impaired biofilm formation of the ΔompA strain, the Ab169ompAD268A mutant tended to form bacterial filaments, indicating the abnormalities in cell division. Moreover, the Ab169 OmpA D268-mediated association to peptidoglycan was required for the manifestation of twitching motility, desiccation resistance, serum-induced killing, adhesion to epithelial cells and virulence in a nematode infection model, although it was dispensable for the uptake of β-lactam antibiotics by outer membrane vesicles. Overall, the results of this study demonstrate that the OmpA C-terminal domain-mediated association to peptidoglycan is critical for a number of virulent properties displayed by A. baumannii outside and within the host.
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13
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Shearer J, Jefferies D, Khalid S. Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints. J Chem Theory Comput 2019; 15:2608-2619. [PMID: 30848905 DOI: 10.1021/acs.jctc.8b01059] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.
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Affiliation(s)
- Jonathan Shearer
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Damien Jefferies
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Syma Khalid
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
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14
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Binding from Both Sides: TolR and Full-Length OmpA Bind and Maintain the Local Structure of the E. coli Cell Wall. Structure 2019; 27:713-724.e2. [PMID: 30713026 DOI: 10.1016/j.str.2019.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/12/2018] [Accepted: 12/31/2018] [Indexed: 12/23/2022]
Abstract
We present a molecular modeling and simulation study of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane, in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed binds peptidoglycan largely through electrostatic interactions. Non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides, respectively, maintain the position of the cell wall even in the absence of Braun's lipoprotein. The charged residues that mediate the cell-wall interactions of TolR in our simulations are conserved across a number of species of gram-negative bacteria.
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15
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Khalid S, Piggot TJ, Samsudin F. Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned? Acc Chem Res 2019; 52:180-188. [PMID: 30562009 DOI: 10.1021/acs.accounts.8b00377] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bacterial membranes, and those of Gram-negative bacteria in particular, are some of the most biochemically diverse membranes known. They incorporate a wide range of lipid types and proteins of varying sizes, architectures, and functions. While simpler biological membranes have been the focus of myriad simulation studies over the years that have yielded invaluable details to complement, and often to direct, ongoing experimental studies, simulations of complex bacterial membranes have been slower to emerge. However, the past few years have seen tremendous activity in this area, leading to advances such as the development of atomistic and coarse-grain models of the lipopolysaccharide (LPS) component of the outer membrane that are compatible with widely used simulation codes. In this Account, we review our contributions to the field of molecular simulations of the bacterial cell envelope, including the development of models of both membranes and the cell wall of Gram-negative bacteria, with a predominant focus on E. coli. At the atomistic level, simulations of chemically accurate models of both membranes have revealed the tightly cross-linked nature of the LPS headgroups and have shown that penetration of solutes through these regions is not as straightforward as the route through phospholipids. The energetic differences between the two routes have been calculated. Simulations of native outer membrane proteins in LPS-containing membranes have shown that the conformational dynamics of the proteins is not only slower in LPS but also different compared to in simpler models of phospholipid bilayers. These chemically more complex and consequently biologically more relevant models are leading to details of conformational dynamics that were previously inaccessible from simulations. Coarse-grain models have enabled simulations of multiprotein systems on time scales of microseconds, leading to insights not only into the rates of protein and lipid diffusion but also into the trends in their respective directions of flow. We find that the motions of LPS molecules are highly correlated with each other but also with outer membrane proteins embedded within the membrane. We have shown that the two leaflets of the outer membrane exhibit communication, whereby regions of low disorder in one leaflet correspond to regions of high disorder in the other. The cell wall remains a comparatively neglected component, although models of the E. coli peptidoglycan are now emerging, particularly at the atomistic level. Our simulations of Braun's lipoprotein have shown that bending and tilting of this protein afford a degree of variability in the gap between the cell wall and the OM. The noncovalent interactions with the cell wall of proteins such as OmpA can further influence the width of this gap by extension or contraction of their linker domains. Overall we have shown that the dynamics of proteins, lipids, and other molecular species within the outer membrane cannot be approximated using simpler phospholipid bilayers, if one is addressing questions regarding the in vivo behavior of Gram-negative bacteria. These membranes have their own unique chemical characteristics that cannot be decoupled from their biological functions.
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Affiliation(s)
- Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
- Chemical Biological and Radiological Sciences, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, U.K
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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16
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Huber RG, Carpenter TS, Dube N, Holdbrook DA, Ingólfsson HI, Irvine WA, Marzinek JK, Samsudin F, Allison JR, Khalid S, Bond PJ. Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions. Methods Mol Biol 2019; 2003:1-30. [PMID: 31218611 DOI: 10.1007/978-1-4939-9512-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lipid membranes play a crucial role in living systems by compartmentalizing biological processes and forming a barrier between these processes and the environment. Naturally, a large apparatus of biomolecules is responsible for construction, maintenance, transport, and degradation of these lipid barriers. Additional classes of biomolecules are tasked with transport of specific substances or transduction of signals from the environment across lipid membranes. In this article, we intend to describe a set of techniques that enable one to build accurate models of lipid systems and their associated proteins, and to simulate their dynamics over a variety of time and length scales. We discuss the methods and challenges that allow us to derive structural, mechanistic, and thermodynamic information from these models. We also show how these models have recently been applied in research to study some of the most complex lipid-protein systems to date, including bacterial and viral envelopes, neuronal membranes, and mammalian signaling systems.
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Affiliation(s)
- Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Namita Dube
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Daniel A Holdbrook
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - William A Irvine
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Jane R Allison
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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17
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Chorev DS, Baker LA, Wu D, Beilsten-Edmands V, Rouse SL, Zeev-Ben-Mordehai T, Jiko C, Samsudin F, Gerle C, Khalid S, Stewart AG, Matthews SJ, Grünewald K, Robinson CV. Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry. Science 2018; 362:829-834. [PMID: 30442809 PMCID: PMC6522346 DOI: 10.1126/science.aau0976] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 10/08/2018] [Indexed: 12/25/2022]
Abstract
Membrane proteins reside in lipid bilayers and are typically extracted from this environment for study, which often compromises their integrity. In this work, we ejected intact assemblies from membranes, without chemical disruption, and used mass spectrometry to define their composition. From Escherichia coli outer membranes, we identified a chaperone-porin association and lipid interactions in the β-barrel assembly machinery. We observed efflux pumps bridging inner and outer membranes, and from inner membranes we identified a pentameric pore of TonB, as well as the protein-conducting channel SecYEG in association with F1FO adenosine triphosphate (ATP) synthase. Intact mitochondrial membranes from Bos taurus yielded respiratory complexes and fatty acid-bound dimers of the ADP (adenosine diphosphate)/ATP translocase (ANT-1). These results highlight the importance of native membrane environments for retaining small-molecule binding, subunit interactions, and associated chaperones of the membrane proteome.
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Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Lindsay A Baker
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Victoria Beilsten-Edmands
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College, London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Chimari Jiko
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Christoph Gerle
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- Core Research for Evolutional Science and Technology, Japan and Science and Technology Agency, Kawaguchi, Japan
| | - Syma Khalid
- School of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- Faculty of Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College, London, South Kensington Campus, London SW7 2AZ, UK
| | - Kay Grünewald
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Centre of Structural Systems Biology (CSSB), Notkestr. 85, D-22607, Heinrich-Pette Institute/University of Hamburg, Hamburg, Germany
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
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18
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Yanagisawa N, Ueshiba H, Abe Y, Kato H, Higuchi T, Yagi J. Outer Membrane Protein of Gut Commensal Microorganism Induces Autoantibody Production and Extra-Intestinal Gland Inflammation in Mice. Int J Mol Sci 2018; 19:ijms19103241. [PMID: 30347705 PMCID: PMC6214128 DOI: 10.3390/ijms19103241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/25/2018] [Accepted: 10/15/2018] [Indexed: 02/08/2023] Open
Abstract
Gut commensal microorganisms have been linked with chronic inflammation at the extra-intestinal niche of the body. The object of the study was to investigate on the chronic effects of a gut commensal Escherichia coli on extra-intestinal glands. The presence of autoimmune response was diagnosed by autoantibody levels and histological methods. Repeated injection of E. coli induced mononuclear cell inflammation in the Harderian and submandibular salivary glands of female C57BL/6 mice. Inflammation was reproduced by adoptive transfer of splenocytes to immune-deficient Rag2 knockout mice and CD4+ T cells to mature T cell-deficient TCRβ-TCRδ knockout mice. MALDI TOF mass spectrometry of the protein to which sera of E. coli-treated mice reacted was determined as the outer membrane protein A (OmpA) of E. coli. Multiple genera of the Enterobacteriaceae possessed OmpA with high amino-acid sequence similarities. Repeated injection of recombinant OmpA reproduced mononuclear cell inflammation of the Harderian and salivary glands in mice and elevation of autoantibodies against Sjögren’s-syndrome-related antigens SSA/Ro and SSB/La. The results indicated the possibility of chronic stimuli from commensal bacteria-originated components as a pathogenic factor to elicit extra-intestinal autoimmunity.
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Affiliation(s)
- Naoko Yanagisawa
- Microbiology and Immunology, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
| | - Hidehiro Ueshiba
- Microbiology and Immunology, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
| | - Yoshihiro Abe
- Microbiology and Immunology, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
| | - Hidehito Kato
- Microbiology and Immunology, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
| | - Tomoaki Higuchi
- Microbiology and Immunology, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
| | - Junji Yagi
- Microbiology and Immunology, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
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19
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Calabrese AN, Radford SE. Mass spectrometry-enabled structural biology of membrane proteins. Methods 2018; 147:187-205. [DOI: 10.1016/j.ymeth.2018.02.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 01/01/2023] Open
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20
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Thoma J, Sapra KT, Müller DJ. Single-Molecule Force Spectroscopy of Transmembrane β-Barrel Proteins. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:375-395. [PMID: 29894225 DOI: 10.1146/annurev-anchem-061417-010055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule force spectroscopy (SMFS) has been widely applied to study the mechanical unfolding and folding of transmembrane proteins. Here, we review the recent progress in characterizing bacterial and human transmembrane β-barrel proteins by SMFS. First, we describe the mechanical unfolding of transmembrane β-barrels, which follows a general mechanism dictated by the sequential unfolding and extraction of individual β-strands and β-hairpins from membranes. Upon force relaxation, the unfolded polypeptide can insert stepwise into the membrane as single β-strands or β-hairpins to fold as the native β-barrel. The refolding can be followed at a high spatial and temporal resolution, showing that small β-barrels are able to fold without assistance, whereas large and complex β-barrels require chaperone cofactors. Applied in the dynamic mode, SMFS can quantify the kinetic and mechanical properties of single β-hairpins and reveal complementary insight into the membrane protein structure and function relationship. We further outline the challenges that SMFS experiments must overcome for a comprehensive understanding of the folding and function of transmembrane β-barrel proteins.
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Affiliation(s)
- Johannes Thoma
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
| | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
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21
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Liew CW, Hynson RM, Ganuelas LA, Shah-Mohammadi N, Duff AP, Kojima S, Homma M, Lee LK. Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering. Biochem Biophys Res Commun 2017; 495:1614-1619. [PMID: 29197577 DOI: 10.1016/j.bbrc.2017.11.194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/18/2023]
Abstract
The bacterial flagellar motor drives the rotation of helical flagellar filaments to propel bacteria through viscous media. It consists of a dynamic population of mechanosensitive stators that are embedded in the inner membrane and activate in response to external load. This entails assembly around the rotor, anchoring to the peptidoglycan layer to counteract torque from the rotor and opening of a cation channel to facilitate an influx of cations, which is converted into mechanical rotation. Stator complexes are comprised of four copies of an integral membrane A subunit and two copies of a B subunit. Each B subunit includes a C-terminal OmpA-like peptidoglycan-binding (PGB) domain. This is thought to be linked to a single N-terminal transmembrane helix by a long unstructured peptide, which allows the PGB domain to bind to the peptidoglycan layer during stator anchoring. The high-resolution crystal structures of flagellar motor PGB domains from Salmonella enterica (MotBC2) and Vibrio alginolyticus (PomBC5) have previously been elucidated. Here, we use small-angle X-ray scattering (SAXS). We show that unlike MotBC2, the dimeric conformation of the PomBC5 in solution differs to its crystal structure, and explore the functional relevance by characterising gain-of-function mutants as well as wild-type constructs of various lengths. These provide new insight into the conformational diversity of flagellar motor PGB domains and experimental verification of their overall topology.
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Affiliation(s)
- C W Liew
- School of Medical Sciences, The University of New South Wales, Australia
| | - R M Hynson
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - L A Ganuelas
- School of Medical Sciences, The University of New South Wales, Australia
| | - N Shah-Mohammadi
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - A P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - S Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - M Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - L K Lee
- School of Medical Sciences, The University of New South Wales, Australia; Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.
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22
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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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23
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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24
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Hsu PC, Samsudin F, Shearer J, Khalid S. It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli. J Phys Chem Lett 2017; 8:5513-5518. [PMID: 29053278 DOI: 10.1021/acs.jpclett.7b02432] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The cell envelope of Gram-negative bacteria is composed of two membranes separated by a soluble region. Here, we report microsecond time scale coarse-grained molecular dynamics simulations of models of the Escherichia coli cell envelope that incorporate both membranes and various native membrane proteins. Our results predict that both the inner and outer membranes curve in a manner dependent on the size of the embedded proteins. The tightly cross-linked lipopolysaccharide molecules (LPS) of the outer membrane cause a strong coupling between the movement of proteins and lipids. While the flow of phospholipids is more random, their diffusion is nevertheless influenced by nearby proteins. Our results reveal protein-induced lipid sorting, whereby cardiolipin is significantly enriched within the vicinity of the water channel AqpZ and the multidrug efflux pump AcrBZ. In summary, our results provide unprecedented details of the intricate relationship between both membranes of E. coli and the proteins embedded within them.
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Affiliation(s)
- Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
| | - Jonathan Shearer
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
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25
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Kar UK, Simonian M, Whitelegge JP. Integral membrane proteins: bottom-up, top-down and structural proteomics. Expert Rev Proteomics 2017; 14:715-723. [PMID: 28737967 DOI: 10.1080/14789450.2017.1359545] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information. Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.
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Affiliation(s)
- Upendra K Kar
- a Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Margaret Simonian
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
| | - Julian P Whitelegge
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
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26
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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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27
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Tan K, Deatherage Kaiser BL, Wu R, Cuff M, Fan Y, Bigelow L, Jedrzejczak RP, Adkins JN, Cort JR, Babnigg G, Joachimiak A. Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi. Protein Sci 2017; 26:1738-1748. [PMID: 28580643 DOI: 10.1002/pro.3209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 11/10/2022]
Abstract
Salmonella enterica serovar Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded β-barrel transmembrane domain and a C-terminal domain (OmpACTD ). The OmpACTD and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the OM. Here we present the first crystal structures of the OmpACTD from two pathogens: S. typhimurium (STOmpACTD ) in open and closed forms and causative agent of Lyme Disease Borrelia burgdorferi (BbOmpACTD ), in closed form. In the open form of STOmpACTD , an aspartate residue from a long β2-α3 loop points into the binding pocket, suggesting that an anion group such as a carboxylate group from PG is favored at the binding site. In the closed form of STOmpACTD and in the structure of BbOmpACTD , a sulfate group from the crystallization buffer is tightly bound at the binding site. The differences between the closed and open forms of STOmpACTD , suggest a large conformational change that includes an extension of α3 helix by ordering a part of β2-α3 loop. We propose that the sulfate anion observed in these structures mimics the carboxylate group of PG when bound to STOmpACTD suggesting PG-anchoring mechanism. In addition, the binding of PG or a ligand mimic may enhance dimerization of STOmpACTD , or possibly that of full length STOmpA.
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Affiliation(s)
- Kemin Tan
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
| | | | - Ruiying Wu
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Marianne Cuff
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Yao Fan
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Robert P Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637
| | - Joshua N Adkins
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
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28
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Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. J Phys Chem Lett 2017; 8:2513-2518. [PMID: 28467715 DOI: 10.1021/acs.jpclett.7b00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative. In addition, conserved molecular patterns associated with the bacterial envelope are recognized by receptors as part of the mammalian defensive response to infection, and an improved understanding of bacteria-host interactions would facilitate the search for novel immunotherapeutics. This Perspective introduces an emerging area of computational biology: multiscale molecular dynamics simulations of chemically complex models of bacterial lipids and membranes. We discuss progress to date, and identify areas for future development that will enable the study of aspects of the membrane components that are as yet unexplored by computational methods.
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Affiliation(s)
- Alister Boags
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Matrix 07-01, 30 Biopolis Street, 138671 Singapore
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, 117543 Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton, United Kingdom , SO17 1BJ
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29
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Liao C, Liang X, Yang F, Soupir ML, Howe AC, Thompson ML, Jarboe LR. Allelic Variation in Outer Membrane Protein A and Its Influence on Attachment of Escherichia coli to Corn Stover. Front Microbiol 2017; 8:708. [PMID: 28515712 PMCID: PMC5413513 DOI: 10.3389/fmicb.2017.00708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 04/05/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the genetic factors that govern microbe-sediment interactions in aquatic environments is important for water quality management and reduction of waterborne disease outbreaks. Although chemical properties of bacteria have been identified that contribute to initiation of attachment, the outer membrane proteins that contribute to these chemical properties still remain unclear. In this study we explored the attachment of 78 Escherichia coli environmental isolates to corn stover, a representative agricultural residue. Outer membrane proteome analysis led to the observation of amino acid variations, some of which had not been previously described, in outer membrane protein A (OmpA) at 10 distinct locations, including each of the four extracellular loops, three of the eight transmembrane segments, the proline-rich linker and the dimerization domain. Some of the polymorphisms within loops 1, 2, and 3 were found to significantly co-occur. Grouping of sequences according to the outer loop polymorphisms revealed five distinct patterns that each occur in at least 5% of our isolates. The two most common patterns, I and II, are encoded by 33.3 and 20.5% of these isolates and differ at each of the four loops. Statistically significant differences in attachment to corn stover were observed among isolates expressing different versions of OmpA and when different versions of OmpA were expressed in the same genetic background. Most notable was the increased corn stover attachment associated with a loop 3 sequence of SNFDGKN relative to the standard SNVYGKN sequence. These results provide further insight into the allelic variation of OmpA and implicate OmpA in contributing to attachment to corn stover.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA
| | - Xiao Liang
- Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Michelle L Soupir
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Adina C Howe
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | | | - Laura R Jarboe
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Chemical and Biological Engineering, Iowa State UniversityAmes, IA, USA
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30
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Jahangiri A, Rasooli I, Owlia P, Fooladi AAI, Salimian J. In silico design of an immunogen against Acinetobacter baumannii based on a novel model for native structure of Outer membrane protein A. Microb Pathog 2017; 105:201-210. [DOI: 10.1016/j.micpath.2017.02.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/05/2017] [Accepted: 02/20/2017] [Indexed: 11/17/2022]
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31
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Native Mass Spectrometry for the Characterization of Structure and Interactions of Membrane Proteins. Methods Mol Biol 2017; 1635:205-232. [PMID: 28755371 DOI: 10.1007/978-1-4939-7151-0_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past years, native mass spectrometry and ion mobility have grown into techniques that are widely applicable to the study of aspects of protein structure. More recently, it has become apparent that this approach provides a very promising avenue for the investigation of integral membrane proteins in lipid or detergent environments.In this chapter, we discuss applications of native mass spectrometry and ion mobility in membrane protein research-what is important to take into consideration when working with membrane proteins, and what the requirements are for sample preparation for native mass spectrometry. Furthermore, we will discuss the types of information provided by the measurements, including the oligomeric state, subunit composition and stoichiometry, interactions with detergents or lipids, conformational transitions, and the binding and structural effect of ligands and drugs.
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32
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Samsudin F, Ortiz-Suarez ML, Piggot TJ, Bond PJ, Khalid S. OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment. Structure 2016; 24:2227-2235. [PMID: 27866852 DOI: 10.1016/j.str.2016.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/16/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022]
Abstract
The envelope of Gram-negative bacteria is highly complex, containing separate outer and inner membranes and an intervening periplasmic space encompassing a peptidoglycan (PGN) cell wall. The PGN scaffold is anchored non-covalently to the outer membrane via globular OmpA-like domains of various proteins. We report atomically detailed simulations of PGN bound to OmpA in three different states, including the isolated C-terminal domain (CTD), the full-length monomer, or the complete full-length dimeric form. Comparative analysis of dynamics of OmpA CTD from different bacteria helped to identify a conserved PGN-binding mode. The dynamics of full-length OmpA, embedded within a realistic representation of the outer membrane containing full-rough (Ra) lipopolysaccharide, phospholipids, and cardiolipin, suggested how the protein may provide flexible mechanical support to the cell wall. An accurate model of the heterogeneous bacterial cell envelope should facilitate future efforts to develop antibacterial agents.
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Affiliation(s)
- Firdaus Samsudin
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Maite L Ortiz-Suarez
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Peter J Bond
- Bioinformatics Institute (A(∗)STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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33
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Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, Singh PK, Manoil C, Bruce JE. In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Nat Commun 2016; 7:13414. [PMID: 27834373 PMCID: PMC5114622 DOI: 10.1038/ncomms13414] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 09/30/2016] [Indexed: 12/13/2022] Open
Abstract
The nosocomial pathogen Acinetobacter baumannii is a frequent cause of hospital-acquired infections worldwide and is a challenge for treatment due to its evolved resistance to antibiotics, including carbapenems. Here, to gain insight on A. baumannii antibiotic resistance mechanisms, we analyse the protein interaction network of a multidrug-resistant A. baumannii clinical strain (AB5075). Using in vivo chemical cross-linking and mass spectrometry, we identify 2,068 non-redundant cross-linked peptide pairs containing 245 intra- and 398 inter-molecular interactions. Outer membrane proteins OmpA and YiaD, and carbapenemase Oxa-23 are hubs of the identified interaction network. Eighteen novel interactors of Oxa-23 are identified. Interactions of Oxa-23 with outer membrane porins OmpA and CarO are verified with co-immunoprecipitation analysis. Furthermore, transposon mutagenesis of oxa-23 or interactors of Oxa-23 demonstrates changes in meropenem or imipenem sensitivity in strain AB5075. These results provide a view of porin-localized antibiotic inactivation and increase understanding of bacterial antibiotic resistance mechanisms.
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Affiliation(s)
- Xia Wu
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Devin K. Schweppe
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Chunxiang Zheng
- Department of Chemistry, University of Washington, Seattle, Washington 98109, USA
| | - Chad R. Weisbrod
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Ananya Murali
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Samuel A. Lee
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Elizabeth Ramage
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - Larry A. Gallagher
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | | | - Mauna E. Edrozo
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
| | | | | | - Samuel I. Miller
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Pradeep K. Singh
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, 850 Republican Street, Brotman Building Room 154, Seattle, Washington 98109, USA
- Department of Chemistry, University of Washington, Seattle, Washington 98109, USA
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34
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Terral G, Beck A, Cianférani S. Insights from native mass spectrometry and ion mobility-mass spectrometry for antibody and antibody-based product characterization. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1032:79-90. [DOI: 10.1016/j.jchromb.2016.03.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
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35
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Scribano D, Damico R, Ambrosi C, Superti F, Marazzato M, Conte MP, Longhi C, Palamara AT, Zagaglia C, Nicoletti M. The Shigella flexneri OmpA amino acid residues 188EVQ 190 are essential for the interaction with the virulence factor PhoN2. Biochem Biophys Rep 2016; 8:168-173. [PMID: 28955953 PMCID: PMC5613738 DOI: 10.1016/j.bbrep.2016.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/27/2016] [Accepted: 08/01/2016] [Indexed: 01/07/2023] Open
Abstract
Shigella flexneri is an intracellular pathogen that deploys an arsenal of virulence factors promoting host cell invasion, intracellular multiplication and intra- and inter-cellular dissemination. We have previously reported that the interaction between apyrase (PhoN2), a periplasmic ATP-diphosphohydrolase, and the C-terminal domain of the outer membrane (OM) protein OmpA is likely required for proper IcsA exposition at the old bacterial pole and thus for full virulence expression of Shigella flexneri (Scribano et al., 2014). OmpA, that is the major OM protein of Gram-negative bacteria, is a multifaceted protein that plays many different roles both in the OM structural integrity and in the virulence of several pathogens. Here, by using yeast two-hybrid technology and by constructing an in silico 3D model of OmpA from S. flexneri 5a strain M90T, we observed that the OmpA residues 188EVQ190 are likely essential for PhoN2-OmpA interaction. The 188EVQ190 amino acids are located within a flexible region of the OmpA protein that could represent a scaffold for protein-protein interaction.
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Affiliation(s)
- Daniela Scribano
- Dip. Scienze Mediche, Orali e Biotecnologiche, Università "G. D'Annunzio" di Chieti, Chieti, Italy.,Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Rosanna Damico
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Cecilia Ambrosi
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Fabiana Superti
- Reparto Patologia Infettiva Ultrastrutturale, Dipartimento di Tecnologie e Salute, Istituto Superiore di Sanità, Rome, Italy
| | - Massimiliano Marazzato
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Maria Pia Conte
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Catia Longhi
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Anna Teresa Palamara
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Carlo Zagaglia
- Dip. di Sanità Pubblica e Malattie Infettive, Università "Sapienza" di Roma, Rome, Italy
| | - Mauro Nicoletti
- Dip. Scienze Mediche, Orali e Biotecnologiche, Università "G. D'Annunzio" di Chieti, Chieti, Italy
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36
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Bosák J, Micenková L, Doležalová M, Šmajs D. Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1. Int J Med Microbiol 2016; 306:486-494. [PMID: 27510856 DOI: 10.1016/j.ijmm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 01/04/2023] Open
Abstract
Interactions of colicins U and Y with the OmpA (Outer membrane protein A) receptor molecule were studied using site-directed mutagenesis and colicin binding assay. A systematic mutagenesis of the colicin-susceptible OmpA sequence from Escherichia coli (OmpAEC) to the colicin-resistant OmpA sequence from Serratia marcescens (OmpASM) was performed in regions corresponding to extracellular OmpA loops 1-4. Susceptibility to colicins U and Y was significantly affected by the OmpA mutation in loop 1. As with functional analysis, a decrease in binding capacity of His-tagged colicin U was found for recombinant OmpA with a mutated segment in loop 1 compared to control OmpAEC. To verify the importance of the identified amino acid residues in OmpA loop 1, we introduced loop 1 from OmpAEC into OmpASM, which resulted in the substantial increase of susceptibility to colicins U and Y. In addition, colicins U and Y were tested against a panel of 118 bacteriocin non-producing strains of four Escherichia species, including E. coli (39 strains), E. fergusonii (10 strains), E. hermannii (42 strains), and E. vulneris (27 strains). A majority (82%) of E. coli strains was susceptible to colicins U and Y. Interestingly, colicins U and Y also inhibited all of the 30 tested multidrug-resistant E. coli O25b-ST131 isolates. These findings, together with the fact that OmpA loop 1 is important for bacterial virulence and is evolutionary conserved, offer the potential of using colicins U and Y as specific anti-OmpA loop 1 directed antibacterial proteins.
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Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Magda Doležalová
- Department of Environment Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, T. G. Masaryk square 275, Zlín, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
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37
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Horne JE, Radford SE. A growing toolbox of techniques for studying β-barrel outer membrane protein folding and biogenesis. Biochem Soc Trans 2016; 44:802-9. [PMID: 27284045 PMCID: PMC4900752 DOI: 10.1042/bst20160020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/21/2023]
Abstract
Great strides into understanding protein folding have been made since the seminal work of Anfinsen over 40 years ago, but progress in the study of membrane protein folding has lagged behind that of their water soluble counterparts. Researchers in these fields continue to turn to more advanced techniques such as NMR, mass spectrometry, molecular dynamics (MD) and single molecule methods to interrogate how proteins fold. Our understanding of β-barrel outer membrane protein (OMP) folding has benefited from these advances in the last decade. This class of proteins must traverse the periplasm and then insert into an asymmetric lipid membrane in the absence of a chemical energy source. In this review we discuss old, new and emerging techniques used to examine the process of OMP folding and biogenesis in vitro and describe some of the insights and new questions these techniques have revealed.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K.
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38
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In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality. Int J Mol Sci 2016; 17:ijms17040599. [PMID: 27110766 PMCID: PMC4849052 DOI: 10.3390/ijms17040599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 12/18/2022] Open
Abstract
Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms.
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39
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Watkinson TG, Calabrese AN, Giusti F, Zoonens M, Radford SE, Ashcroft AE. Systematic analysis of the use of amphipathic polymers for studies of outer membrane proteins using mass spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 391:54-61. [PMID: 26869850 PMCID: PMC4708066 DOI: 10.1016/j.ijms.2015.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/19/2015] [Accepted: 06/26/2015] [Indexed: 05/10/2023]
Abstract
Membrane proteins (MPs) are essential for numerous important biological processes. Recently, mass spectrometry (MS), coupled with an array of related techniques, has been used to probe the structural properties of MPs and their complexes. Typically, detergent micelles have been employed for delivering MPs into the gas-phase, but these complexes have intrinsic properties that can limit the utility of structural studies of MPs using MS methods. Amphipols (APols) have advantages over detergent micelles and have been shown to be capable of delivering native MPs into the gas-phase. Comparing six different APols which vary in mass and charge, and the detergent n-dodecyl-β-d-maltopyranoside, we aimed to determine which APols are most efficient for delivery of native outer membrane proteins (OMPs) into the gas-phase. We show that maintaining the solution-phase folding and global structures of three different OMPs (PagP, OmpT and tOmpA) are independent of the APol used, but differences in OMP activity can result from the different APol:OMP complexes. ESI-IMS-MS analysis of OMP:APol complexes shows that the A8-35 APol is most proficient at liberating all three OMPs into the gas-phase, without altering their gas-phase conformations.
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Affiliation(s)
- Thomas G. Watkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fabrice Giusti
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
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40
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Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE. Host-Microbe Protein Interactions during Bacterial Infection. ACTA ACUST UNITED AC 2015; 22:1521-1530. [PMID: 26548613 DOI: 10.1016/j.chembiol.2015.09.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 12/24/2022]
Abstract
Interspecies protein-protein interactions are essential mediators of infection. While bacterial proteins required for host cell invasion and infection can be identified through bacterial mutant library screens, information about host target proteins and interspecies complex structures has been more difficult to acquire. Using an unbiased chemical crosslinking/mass spectrometry approach, we identified interspecies protein-protein interactions in human lung epithelial cells infected with Acinetobacter baumannii. These efforts resulted in identification of 3,076 crosslinked peptide pairs and 46 interspecies protein-protein interactions. Most notably, the key A. baumannii virulence factor, OmpA, was identified as crosslinked to host proteins involved in desmosomes, specialized structures that mediate host cell-to-cell adhesion. Co-immunoprecipitation and transposon mutant experiments were used to verify these interactions and demonstrate relevance for host cell invasion and acute murine lung infection. These results shed new light on A. baumannii-host protein interactions and their structural features, and the presented approach is generally applicable to other systems.
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Affiliation(s)
- Devin K Schweppe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher Harding
- Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Xia Wu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth Ramage
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Pradeep K Singh
- Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Colin Manoil
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, 850 Republican Street, Brotman Building, Room 154, Seattle, WA 98109, USA.
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41
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Marcoux J, Cianférani S. Towards integrative structural mass spectrometry: Benefits from hybrid approaches. Methods 2015; 89:4-12. [DOI: 10.1016/j.ymeth.2015.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/06/2015] [Accepted: 05/25/2015] [Indexed: 01/10/2023] Open
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42
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Wang H, Li Q, Fang Y, Yu S, Tang B, Na L, Yu B, Zou Q, Mao X, Gu J. Biochemical and functional characterization of the periplasmic domain of the outer membrane protein A from enterohemorrhagic Escherichia coli. Microbiol Res 2015; 182:109-15. [PMID: 26686619 DOI: 10.1016/j.micres.2015.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/01/2015] [Accepted: 10/10/2015] [Indexed: 11/25/2022]
Abstract
Outer membrane protein A (OmpA) plays multiple roles in the physiology and pathogenesis of the zoonotic pathogen enterohemorrhagic Escherichia coli (EHEC). The N-terminus of OmpA forms a transmembrane domain (OmpA™), and the roles of this domain in bacterial pathogenesis have been well studied. However, how its C-terminal domain (OmpAper), which is located at the periplasmic space in the bacterial membrane, contributes to virulence remains unclear. Herein, we report that OmpAper forms a dimer and binds to peptidoglycan in vitro. Furthermore, OmpAper is responsible for bacterial resistance to acidic conditions, high osmotic pressure and high SDS environments. In addition, OmpAper contributes to the adhesion of bacteria to HeLa cells in vitro and ex vivo. These results provide an additional understanding of the role of OmpA in EHEC physiology and pathogenesis.
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Affiliation(s)
- Haiguang Wang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Qian Li
- Department of Clinical Microbiology and Immunology, Southwest Hospital & College of Medical Laboratory Science, Third Military Medical University, Chongqing, People's Republic of China
| | - Yao Fang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Shu Yu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Bin Tang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Li Na
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Bo Yu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Xuhu Mao
- Department of Clinical Microbiology and Immunology, Southwest Hospital & College of Medical Laboratory Science, Third Military Medical University, Chongqing, People's Republic of China.
| | - Jiang Gu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, People's Republic of China.
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43
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Anand A, LeDoyt M, Karanian C, Luthra A, Koszelak-Rosenblum M, Malkowski MG, Puthenveetil R, Vinogradova O, Radolf JD. Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL β-BARREL DOMAIN. J Biol Chem 2015; 290:12313-31. [PMID: 25805501 PMCID: PMC4424362 DOI: 10.1074/jbc.m114.629188] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 03/20/2015] [Indexed: 11/06/2022] Open
Abstract
We previously identified Treponema pallidum repeat proteins TprC/D, TprF, and TprI as candidate outer membrane proteins (OMPs) and subsequently demonstrated that TprC is not only a rare OMP but also forms trimers and has porin activity. We also reported that TprC contains N- and C-terminal domains (TprC(N) and TprC(C)) orthologous to regions in the major outer sheath protein (MOSP(N) and MOSP(C)) of Treponema denticola and that TprC(C) is solely responsible for β-barrel formation, trimerization, and porin function by the full-length protein. Herein, we show that TprI also possesses bipartite architecture, trimeric structure, and porin function and that the MOSP(C)-like domains of native TprC and TprI are surface-exposed in T. pallidum, whereas their MOSP(N)-like domains are tethered within the periplasm. TprF, which does not contain a MOSP(C)-like domain, lacks amphiphilicity and porin activity, adopts an extended inflexible structure, and, in T. pallidum, is tightly bound to the protoplasmic cylinder. By thermal denaturation, the MOSP(N) and MOSP(C)-like domains of TprC and TprI are highly thermostable, endowing the full-length proteins with impressive conformational stability. When expressed in Escherichia coli with PelB signal sequences, TprC and TprI localize to the outer membrane, adopting bipartite topologies, whereas TprF is periplasmic. We propose that the MOSP(N)-like domains enhance the structural integrity of the cell envelope by anchoring the β-barrels within the periplasm. In addition to being bona fide T. pallidum rare outer membrane proteins, TprC/D and TprI represent a new class of dual function, bipartite bacterial OMP.
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Affiliation(s)
| | | | | | | | | | - Michael G Malkowski
- the Hauptman-Woodward Medical Research Institute and Department of Structural Biology, State University of New York, Buffalo, New York 14203, and
| | | | - Olga Vinogradova
- Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Justin D Radolf
- From the Departments of Medicine, Pediatrics, Molecular Biology and Biophysics, Genetics and Genomic Science, and Immunology, University of Connecticut Health Center, Farmington, Connecticut 06030,
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44
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Mehmood S, Allison TM, Robinson CV. Mass Spectrometry of Protein Complexes: From Origins to Applications. Annu Rev Phys Chem 2015; 66:453-74. [DOI: 10.1146/annurev-physchem-040214-121732] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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45
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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46
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Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry. Structure 2015; 23:762-73. [PMID: 25800553 DOI: 10.1016/j.str.2015.01.022] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/13/2015] [Accepted: 01/23/2015] [Indexed: 11/22/2022]
Abstract
In pathogenic Gram-negative bacteria, interactions among membrane proteins are key mediators of host cell attachment, invasion, pathogenesis, and antibiotic resistance. Membrane protein interactions are highly dependent upon local properties and environment, warranting direct measurements on native protein complex structures as they exist in cells. Here we apply in vivo chemical cross-linking mass spectrometry, to reveal the first large-scale protein interaction network in Pseudomonas aeruginosa, an opportunistic human pathogen, by covalently linking interacting protein partners, thereby fixing protein complexes in vivo. A total of 626 cross-linked peptide pairs, including previously unknown interactions of many membrane proteins, are reported. These pairs not only define the existence of these interactions in cells but also provide linkage constraints for complex structure predictions. Structures of three membrane proteins, namely, SecD-SecF, OprF, and OprI are predicted using in vivo cross-linked sites. These findings improve understanding of membrane protein interactions and structures in cells.
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47
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Gupta A, Iyer BR, Chaturvedi D, Maurya SR, Mahalakshmi R. Thermodynamic, structural and functional properties of membrane protein inclusion bodies are analogous to purified counterparts: case study from bacteria and humans. RSC Adv 2015. [DOI: 10.1039/c4ra11207e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purification-free transmembrane protein inclusion body preparations for rapid and cost-effective biophysical, functional and structural studies.
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Affiliation(s)
- Ankit Gupta
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Deepti Chaturvedi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Svetlana Rajkumar Maurya
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal
- India
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48
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Calabrese AN, Watkinson TG, Henderson PJF, Radford SE, Ashcroft AE. Amphipols outperform dodecylmaltoside micelles in stabilizing membrane protein structure in the gas phase. Anal Chem 2014; 87:1118-26. [PMID: 25495802 PMCID: PMC4636139 DOI: 10.1021/ac5037022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied.
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Affiliation(s)
- Antonio N Calabrese
- School of Molecular and Cellular Biology and ‡School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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49
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Mehmood S, Marcoux J, Hopper JTS, Allison TM, Liko I, Borysik AJ, Robinson CV. Charge reduction stabilizes intact membrane protein complexes for mass spectrometry. J Am Chem Soc 2014; 136:17010-2. [PMID: 25402655 DOI: 10.1021/ja510283g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The study of intact soluble protein assemblies by means of mass spectrometry is providing invaluable contributions to structural biology and biochemistry. A recent breakthrough has enabled similar study of membrane protein complexes, following their release from detergent micelles in the gas phase. Careful optimization of mass spectrometry conditions, particularly with respect to energy regimes, is essential for maintaining compact folded states as detergent is removed. However, many of the saccharide detergents widely employed in structural biology can cause unfolding of membrane proteins in the gas phase. Here, we investigate the potential of charge reduction by introducing three membrane protein complexes from saccharide detergents and show how reducing their overall charge enables generation of compact states, as evidenced by ion mobility mass spectrometry. We find that charge reduction stabilizes the oligomeric state and enhances the stability of lipid-bound complexes. This finding is significant since maintaining native-like membrane proteins enables ligand binding to be assessed from a range of detergents that retain solubility while protecting the overall fold.
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Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford , Oxford, U.K
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50
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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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