1
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McKenna S, Aylward F, Miliara X, Lau RJ, Huemer CB, Giblin SP, Huse KK, Liang M, Reeves L, Pearson M, Xu Y, Rouse SL, Pease JE, Sriskandan S, Kagawa TF, Cooney J, Matthews S. The protease associated (PA) domain in ScpA from Streptococcus pyogenes plays a role in substrate recruitment. Biochim Biophys Acta Proteins Proteom 2023; 1871:140946. [PMID: 37562488 DOI: 10.1016/j.bbapap.2023.140946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Annually, over 18 million disease cases and half a million deaths worldwide are estimated to be caused by Group A Streptococcus. ScpA (or C5a peptidase) is a well characterised member of the cell enveleope protease family, which possess a S8 subtilisin-like catalytic domain and a shared multi-domain architecture. ScpA cleaves complement factors C5a and C3a, impairing the function of these critical anaphylatoxins and disrupts complement-mediated innate immunity. Although the high resolution structure of ScpA is known, the details of how it recognises its substrate are only just emerging. Previous studies have identified a distant exosite on the 2nd fibronectin domain that plays an important role in recruitment via an interaction with the substrate core. Here, using a combination of solution NMR spectroscopy, mutagenesis with functional assays and computational approaches we identify a second exosite within the protease-associated (PA) domain. We propose a model in which the PA domain assists optimal delivery of the substrate's C terminus to the active site for cleavage.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Frances Aylward
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Xeni Miliara
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Rikin J Lau
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Camilla Berg Huemer
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sean P Giblin
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Mingyang Liang
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Lucy Reeves
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - James E Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Todd F Kagawa
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Jakki Cooney
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
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2
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Kumar A, Vadas O, Dos Santos Pacheco N, Zhang X, Chao K, Darvill N, Rasmussen HØ, Xu Y, Lin GMH, Stylianou FA, Pedersen JS, Rouse SL, Morgan ML, Soldati-Favre D, Matthews S. Structural and regulatory insights into the glideosome-associated connector from Toxoplasma gondii. eLife 2023; 12:e86049. [PMID: 37014051 PMCID: PMC10125020 DOI: 10.7554/elife.86049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
The phylum of Apicomplexa groups intracellular parasites that employ substrate-dependent gliding motility to invade host cells, egress from the infected cells, and cross biological barriers. The glideosome-associated connector (GAC) is a conserved protein essential to this process. GAC facilitates the association of actin filaments with surface transmembrane adhesins and the efficient transmission of the force generated by myosin translocation of actin to the cell surface substrate. Here, we present the crystal structure of Toxoplasma gondii GAC and reveal a unique, supercoiled armadillo repeat region that adopts a closed ring conformation. Characterisation of the solution properties together with membrane and F-actin binding interfaces suggests that GAC adopts several conformations from closed to open and extended. A multi-conformational model for assembly and regulation of GAC within the glideosome is proposed.
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Affiliation(s)
- Amit Kumar
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of GenevaGenevaSwitzerland
| | - Nicolas Dos Santos Pacheco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of GenevaGenevaSwitzerland
| | - Xu Zhang
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Kin Chao
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nicolas Darvill
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Helena Ø Rasmussen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus UniversityAarhusDenmark
| | - Yingqi Xu
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Gloria Meng-Hsuan Lin
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of GenevaGenevaSwitzerland
| | | | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus UniversityAarhusDenmark
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Marc L Morgan
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of GenevaGenevaSwitzerland
| | - Stephen Matthews
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
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3
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Hamburg S, Franks K, Rouse SL. Impact of bioscience DAOs on research and innovation. Biophys J 2023; 122:286a. [PMID: 36783419 DOI: 10.1016/j.bpj.2022.11.1623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Sarah Hamburg
- phas3, University College London, London, United Kingdom
| | | | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, London, United Kingdom
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4
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Miliara X, Tatsuta T, Eiyama A, Langer T, Rouse SL, Matthews S. An intermolecular hydrogen bonded network in the PRELID-TRIAP protein family plays a role in lipid sensing. Biochim Biophys Acta Proteins Proteom 2023; 1871:140867. [PMID: 36309326 DOI: 10.1016/j.bbapap.2022.140867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
The PRELID-TRIAP1 family of proteins is responsible for lipid transfer in mitochondria. Multiple structures have been resolved of apo and lipid substrate bound forms, allowing us to begin to piece together the molecular level details of the full lipid transfer cycle. Here, we used molecular dynamics simulations to demonstrate that the lipid binding is mediated by an extended, water-mediated hydrogen bonding network. A key mutation, R53E, was found to disrupt this network, causing lipid to be released from the complex. The X-ray crystal structure of R53E was captured in a fully closed and apo state. Lipid transfer assays and molecular simulations allow us to interpret the observed conformation in the context of the biological role. Together, our work provides further understanding of the mechanistic control of lipid transport by PRELID-TRIAP1 in mitochondria.
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Affiliation(s)
- Xeni Miliara
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Takashi Tatsuta
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Akinori Eiyama
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), D-50931 Cologne, Germany
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK.
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5
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Rattu P, Glencross F, Mader SL, Skylaris CK, Matthews SJ, Rouse SL, Khalid S. Corrigendum to “Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing”. Comput Struct Biotechnol J 2022; 20:1027. [PMID: 35242292 PMCID: PMC8873219 DOI: 10.1016/j.csbj.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Punam Rattu
- School of Chemistry, University of Southampton, SO17 1BJ, United Kingdom
| | - Flo Glencross
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Sophie L. Mader
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
| | | | - Stephen J. Matthews
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Sarah L. Rouse
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, SO17 1BJ, United Kingdom
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
- Corresponding author.
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6
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Rattu P, Glencross F, Mader SL, Skylaris CK, Matthews SJ, Rouse SL, Khalid S. Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing. Comput Struct Biotechnol J 2021; 19:6417-6430. [PMID: 34938416 PMCID: PMC8649110 DOI: 10.1016/j.csbj.2021.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 12/01/2022] Open
Abstract
Two proteins of the Escherichia coli membrane protein complex, CsgG and CsgF, are studied as proteinaceous nanopores for DNA sequencing. It is highly desirable to control the DNA as it moves through the pores, this requires characterisation of DNA translocation and subsequent optimization of the pores. In order to inform protein engineering to improve the pores, we have conducted a series of molecular dynamics simulations to characterise the mechanical strength and conformational dynamics of CsgG and the CsgG-CsgF complex and how these impact ssDNA, water and ion movement. We find that the barrel of CsgG is more susceptible to damage from external electric fields compared to the protein vestibule. Furthermore, the presence of CsgF within the CsgG-CsgF complex enables the complex to withstand higher electric fields. We find that the eyelet loops of CsgG play a key role in both slowing the translocation rate of DNA and modulating the conductance of the pore. CsgF also impacts the DNA translocation rate, but to a lesser degree than CsgG.
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Affiliation(s)
- Punam Rattu
- School of Chemistry, University of Southampton, SO17 1BJ, United Kingdom
| | - Flo Glencross
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Sophie L Mader
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
| | | | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, SO17 1BJ, United Kingdom
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom
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7
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Matthews-Palmer TRS, Gonzalez-Rodriguez N, Calcraft T, Lagercrantz S, Zachs T, Yu XJ, Grabe GJ, Holden DW, Nans A, Rosenthal PB, Rouse SL, Beeby M. Structure of the cytoplasmic domain of SctV (SsaV) from the Salmonella SPI-2 injectisome and implications for a pH sensing mechanism. J Struct Biol 2021; 213:107729. [PMID: 33774138 PMCID: PMC8223533 DOI: 10.1016/j.jsb.2021.107729] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/22/2022]
Abstract
CryoEM of a full-length type III secretion system SctV resolves cytoplasmic but not transmembrane domains. MD simulations show SctV protomers flexibly hinge. Acidification expands the SctV ring by altering interprotomer interactions.
Bacterial type III secretion systems assemble the axial structures of both injectisomes and flagella. Injectisome type III secretion systems subsequently secrete effector proteins through their hollow needle into a host, requiring co-ordination. In the Salmonella enterica serovar Typhimurium SPI-2 injectisome, this switch is triggered by sensing the neutral pH of the host cytoplasm. Central to specificity switching is a nonameric SctV protein with an N-terminal transmembrane domain and a toroidal C-terminal cytoplasmic domain. A ‘gatekeeper’ complex interacts with the SctV cytoplasmic domain in a pH dependent manner, facilitating translocon secretion while repressing effector secretion through a poorly understood mechanism. To better understand the role of SctV in SPI-2 translocon-effector specificity switching, we purified full-length SctV and determined its toroidal cytoplasmic region’s structure using cryo-EM. Structural comparisons and molecular dynamics simulations revealed that the cytoplasmic torus is stabilized by its core subdomain 3, about which subdomains 2 and 4 hinge, varying the flexible outside cleft implicated in gatekeeper and substrate binding. In light of patterns of surface conservation, deprotonation, and structural motion, the location of previously identified critical residues suggest that gatekeeper binds a cleft buried between neighboring subdomain 4s. Simulations suggest that a local pH change from 5 to 7.2 stabilizes the subdomain 3 hinge and narrows the central aperture of the nonameric torus. Our results are consistent with a model of local pH sensing at SctV, where pH-dependent dynamics of SctV cytoplasmic domain affect binding of gatekeeper complex.
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Affiliation(s)
| | | | - Thomas Calcraft
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Signe Lagercrantz
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tobias Zachs
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiu-Jun Yu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Grzegorz J Grabe
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - David W Holden
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
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8
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Murphy P, Xu Y, Rouse SL, Jaffray EG, Plechanovová A, Matthews SJ, Carlos Penedo J, Hay RT. Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer. Nat Commun 2020; 11:3807. [PMID: 32733036 PMCID: PMC7393505 DOI: 10.1038/s41467-020-17647-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
The human genome contains an estimated 600 ubiquitin E3 ligases, many of which are single-subunit E3s (ssE3s) that can bind to both substrate and ubiquitin-loaded E2 (E2~Ub). Within ssE3s structural disorder tends to be located in substrate binding and domain linking regions. RNF4 is a ssE3 ligase with a C-terminal RING domain and disordered N-terminal region containing SUMO Interactions Motifs (SIMs) required to bind SUMO modified substrates. Here we show that, although the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global architecture primed for SUMO interaction. Segregated charged regions within the RNF4 N-terminus promote compaction, juxtaposing RING domain and SIMs to facilitate substrate ubiquitination. Mutations that induce a more extended shape reduce ubiquitination activity. Our result offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function.
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Affiliation(s)
- Paul Murphy
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Yingqi Xu
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - Sarah L Rouse
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - Ellis G Jaffray
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Anna Plechanovová
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Steve J Matthews
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - J Carlos Penedo
- Centre of Biophotonics, School of Physics and Astronomy, University of St. Andrews, KY16 9SS, St. Andrews, UK
- Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, KY16 9ST, St. Andrews, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK.
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9
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Chorev DS, Tang H, Rouse SL, Bolla JR, von Kügelgen A, Baker LA, Wu D, Gault J, Grünewald K, Bharat TAM, Matthews SJ, Robinson CV. The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes. Nat Protoc 2020; 15:1690-1706. [PMID: 32238951 PMCID: PMC7305028 DOI: 10.1038/s41596-020-0303-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/23/2020] [Indexed: 12/28/2022]
Abstract
Recent applications of mass spectrometry (MS) to study membrane protein complexes are yielding valuable insights into the binding of lipids and their structural and functional roles. To date, most native MS experiments with membrane proteins are based on detergent solubilization. Many insights into the structure and function of membrane proteins have been obtained using detergents; however, these can promote local lipid rearrangement and can cause fluctuations in the oligomeric state of protein complexes. To overcome these problems, we developed a method that does not use detergents or other chemicals. Here we report a detailed protocol that enables direct ejection of protein complexes from membranes for analysis by native MS. Briefly, lipid vesicles are prepared directly from membranes of different sources and subjected to sonication pulses. The resulting destabilized vesicles are concentrated, introduced into a mass spectrometer and ionized. The mass of the observed protein complexes is determined and this information, in conjunction with 'omics'-based strategies, is used to determine subunit stoichiometry as well as cofactor and lipid binding. Within this protocol, we expand the applications of the method to include peripheral membrane proteins of the S-layer and amyloid protein export machineries overexpressed in membranes from which the most abundant components have been removed. The described experimental procedure takes approximately 3 d from preparation to MS. The time required for data analysis depends on the complexity of the protein assemblies embedded in the membrane under investigation.
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Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Haiping Tang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, London, UK
| | - Jani Reddy Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Microscopy Imaging Centre, Oxford, UK
| | - Lindsay A Baker
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Kay Grünewald
- Division of Structural Biology, University of Oxford, Oxford, UK
- Heinrich Pette Institute, Leibniz-Institut für Experimentelle Virologie, Centre for Structural Systems Biology, c/o DESY, Hamburg, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Microscopy Imaging Centre, Oxford, UK
| | | | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
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10
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Khalid S, Rouse SL. Simulation of subcellular structures. Curr Opin Struct Biol 2020; 61:167-172. [DOI: 10.1016/j.sbi.2019.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/18/2019] [Accepted: 12/26/2019] [Indexed: 12/21/2022]
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11
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McKenna S, Malito E, Rouse SL, Abate F, Bensi G, Chiarot E, Micoli F, Mancini F, Gomes Moriel D, Grandi G, Mossakowska D, Pearson M, Xu Y, Pease J, Sriskandan S, Margarit I, Bottomley MJ, Matthews S. Structure, dynamics and immunogenicity of a catalytically inactive C XC chemokine-degrading protease SpyCEP from Streptococcus pyogenes. Comput Struct Biotechnol J 2020; 18:650-660. [PMID: 32257048 PMCID: PMC7113628 DOI: 10.1016/j.csbj.2020.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
Over 18 million disease cases and half a million deaths worldwide are estimated to be caused annually by Group A Streptococcus. A vaccine to prevent GAS disease is urgently needed. SpyCEP (Streptococcus pyogenes Cell-Envelope Proteinase) is a surface-exposed serine protease that inactivates chemokines, impairing neutrophil recruitment and bacterial clearance, and has shown promising immunogenicity in preclinical models. Although SpyCEP structure has been partially characterized, a more complete and higher resolution understanding of its antigenic features would be desirable prior to large scale manufacturing. To address these gaps and facilitate development of this globally important vaccine, we performed immunogenicity studies with a safety-engineered SpyCEP mutant, and comprehensively characterized its structure by combining X-ray crystallography, NMR spectroscopy and molecular dynamics simulations. We found that the catalytically-inactive SpyCEP antigen conferred protection similar to wild-type SpyCEP in a mouse infection model. Further, a new higher-resolution crystal structure of the inactive SpyCEP mutant provided new insights into this large chemokine protease comprising nine domains derived from two non-covalently linked fragments. NMR spectroscopy and molecular simulation analyses revealed conformational flexibility that is likely important for optimal substrate recognition and overall function. These combined immunogenicity and structural data demonstrate that the full-length SpyCEP inactive mutant is a strong candidate human vaccine antigen. These findings show how a multi-disciplinary study was used to overcome obstacles in the development of a GAS vaccine, an approach applicable to other future vaccine programs. Moreover, the information provided may also facilitate the structure-based discovery of small-molecule therapeutics targeting SpyCEP protease inhibition.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | - Enrico Malito
- GlaxoSmithKline, 14200 Shady Grove Road, Rockville, MD 20850, United States
| | - Sarah L. Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | | | | | | | - Francesca Micoli
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Francesca Mancini
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Danilo Gomes Moriel
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Danuta Mossakowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University Krakow, Gronostajowa 7a Str, 30-387 Krakow, Poland
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | - James Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | | | | | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, UK
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12
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Miliara X, Tatsuta T, Berry JL, Rouse SL, Solak K, Chorev DS, Wu D, Robinson CV, Matthews S, Langer T. Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins. Nat Commun 2019; 10:1130. [PMID: 30850607 PMCID: PMC6408443 DOI: 10.1038/s41467-019-09089-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
Conserved lipid transfer proteins of the Ups/PRELI family regulate lipid accumulation in mitochondria by shuttling phospholipids in a lipid-specific manner across the intermembrane space. Here, we combine structural analysis, unbiased genetic approaches in yeast and molecular dynamics simulations to unravel determinants of lipid specificity within the conserved Ups/PRELI family. We present structures of human PRELID1-TRIAP1 and PRELID3b-TRIAP1 complexes, which exert lipid transfer activity for phosphatidic acid and phosphatidylserine, respectively. Reverse yeast genetic screens identify critical amino acid exchanges that broaden and swap their lipid specificities. We find that amino acids involved in head group recognition and the hydrophobicity of flexible loops regulate lipid entry into the binding cavity. Molecular dynamics simulations reveal different membrane orientations of PRELID1 and PRELID3b during the stepwise release of lipids. Our experiments thus define the structural determinants of lipid specificity and the dynamics of lipid interactions by Ups/PRELI proteins.
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Affiliation(s)
- Xeni Miliara
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK
| | - Takashi Tatsuta
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK
| | - Kübra Solak
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK.
| | - Thomas Langer
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany.
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13
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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: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Rouse SL, Stylianou F, Wu HYG, Berry JL, Sewell L, Morgan RML, Sauerwein AC, Matthews S. The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil. J Mol Biol 2018; 430:3863-3871. [PMID: 29886016 PMCID: PMC6173795 DOI: 10.1016/j.jmb.2018.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/09/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022]
Abstract
Gram-negative bacteria possess specialized biogenesis machineries that facilitate the export of amyloid subunits, the fibers of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialized outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8-Å resolution. This domain forms a novel asymmetric trimeric coiled coil that possesses a single buried tyrosine residue as well as an extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - H Y Grace Wu
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Lee Sewell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andrea C Sauerwein
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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15
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Abstract
Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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16
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Darvill N, Dubois DJ, Rouse SL, Hammoudi PM, Blake T, Benjamin S, Liu B, Soldati-Favre D, Matthews S. Structural Basis of Phosphatidic Acid Sensing by APH in Apicomplexan Parasites. Structure 2018; 26:1059-1071.e6. [PMID: 29910186 PMCID: PMC6084407 DOI: 10.1016/j.str.2018.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 10/29/2022]
Abstract
Plasmodium falciparum and Toxoplasma gondii are obligate intracellular parasites that belong to the phylum of Apicomplexa and cause major human diseases. Their access to an intracellular lifestyle is reliant on the coordinated release of proteins from the specialized apical organelles called micronemes and rhoptries. A specific phosphatidic acid effector, the acylated pleckstrin homology domain-containing protein (APH) plays a central role in microneme exocytosis and thus is essential for motility, cell entry, and egress. TgAPH is acylated on the surface of the micronemes and recruited to phosphatidic acid (PA)-enriched membranes. Here, we dissect the atomic details of APH PA-sensing hub and its functional interaction with phospholipid membranes. We unravel the key determinant of PA recognition for the first time and show that APH inserts into and clusters multiple phosphate head-groups at the bilayer binding surface.
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Affiliation(s)
- Nick Darvill
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - David J Dubois
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, 1 Rue Michel-Servet, 1211 Geneva, Switzerland
| | - Sarah L Rouse
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Pierre-Mehdi Hammoudi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, 1 Rue Michel-Servet, 1211 Geneva, Switzerland
| | - Tom Blake
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Stefi Benjamin
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Bing Liu
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK; BioBank, First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, 1 Rue Michel-Servet, 1211 Geneva, Switzerland.
| | - Steve Matthews
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK; BioBank, First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, 710049, P. R. China.
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17
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Rouse SL, Hawthorne WJ, Berry JL, Chorev DS, Ionescu SA, Lambert S, Stylianou F, Ewert W, Mackie U, Morgan RML, Otzen D, Herbst FA, Nielsen PH, Dueholm M, Bayley H, Robinson CV, Hare S, Matthews S. A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Nat Commun 2017; 8:263. [PMID: 28811582 PMCID: PMC5557850 DOI: 10.1038/s41467-017-00361-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/23/2017] [Indexed: 11/25/2022] Open
Abstract
Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits for construction of a biofilm matrix. The secretion of bacterial functional amyloid requires a bespoke outer-membrane protein channel through which unfolded amyloid substrates are translocated. Here, we combine X-ray crystallography, native mass spectrometry, single-channel electrical recording, molecular simulations and circular dichroism measurements to provide high-resolution structural insight into the functional amyloid transporter from Pseudomonas, FapF. FapF forms a trimer of gated β-barrel channels in which opening is regulated by a helical plug connected to an extended coil-coiled platform spanning the bacterial periplasm. Although FapF represents a unique type of secretion system, it shares mechanistic features with a diverse range of peptide translocation systems. Our findings highlight alternative strategies for handling and export of amyloid protein sequences. Gram-negative bacteria assemble biofilms from amyloid fibres, which translocate across the outer membrane as unfolded amyloid precursors through a secretion system. Here, the authors characterise the structural details of the amyloid transporter FapF in Pseudomonas.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - William J Hawthorne
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Dror S Chorev
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sebastian Lambert
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Wiebke Ewert
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Uma Mackie
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.,Walthamstow School for Girls, London, E17 9RZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Stephen Hare
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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18
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Rouse SL, Hawthorne W, Berry J, Matthews S. Structural and Mechanistic Insights into Transport of Functional Amyloid Subunits across the Pseudomonas Outer Membrane. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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19
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Rouse SL, Hawthorne WJ, Lambert S, Morgan ML, Hare SA, Matthews S. Purification, crystallization and characterization of the Pseudomonas outer membrane protein FapF, a functional amyloid transporter. Acta Crystallogr F Struct Biol Commun 2016; 72:892-896. [PMID: 27917837 PMCID: PMC5137466 DOI: 10.1107/s2053230x16017921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 11/12/2023] Open
Abstract
Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon. Initial attempts at crystallizing full-length and N-terminally truncated constructs by refolding techniques were not successful; however, after preparing FapF106-430 from the membrane fraction, reproducible crystals were obtained using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.5 Å resolution. These crystals belonged to the monoclinic space group C121, with unit-cell parameters a = 143.4, b = 124.6, c = 80.4 Å, α = γ = 90, β = 96.32° and three monomers in the asymmetric unit. It was found that the switch to complete detergent exchange into C8E4 was crucial for forming well diffracting crystals, and it is suggested that this combined with limited proteolysis is a potentially useful protocol for membrane β-barrel protein crystallography. The three-dimensional structure of FapF will provide invaluable information on the mechanistic differences of biogenesis between the curli and Fap functional amyloid systems.
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Affiliation(s)
- Sarah L. Rouse
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Wlliam J. Hawthorne
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Sebastian Lambert
- Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Marc L. Morgan
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Stephen A. Hare
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Stephen Matthews
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
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20
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Hedger G, Rouse SL, Domański J, Chavent M, Koldsø H, Sansom MSP. Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes. Biochemistry 2016; 55:6238-6249. [PMID: 27786441 PMCID: PMC5120876 DOI: 10.1021/acs.biochem.6b00751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
The exchange of ADP
and ATP across the inner mitochondrial membrane
is a fundamental cellular process. This exchange is facilitated by
the adenine nucleotide translocase, the structure and function of
which are critically dependent on the signature phospholipid of mitochondria,
cardiolipin (CL). Here we employ multiscale molecular dynamics simulations
to investigate CL interactions within a membrane environment. Using
simulations at both coarse-grained and atomistic resolutions, we identify
three CL binding sites on the translocase, in agreement with those
seen in crystal structures and inferred from nuclear magnetic resonance
measurements. Characterization of the free energy landscape for lateral
lipid interaction via potential of mean force calculations demonstrates
the strength of interaction compared to those of binding sites on
other mitochondrial membrane proteins, as well as their selectivity
for CL over other phospholipids. Extending the analysis to other members
of the family, yeast Aac2p and mouse uncoupling protein 2, suggests
a degree of conservation. Simulation of large patches of a model mitochondrial
membrane containing multiple copies of the translocase shows that
CL interactions persist in the presence of protein–protein
interactions and suggests CL may mediate interactions between translocases.
This study provides a key example of how computational microscopy
may be used to shed light on regulatory lipid–protein interactions.
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Affiliation(s)
- George Hedger
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Sarah L Rouse
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - Jan Domański
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,D. E. Shaw Research , 120 West 45th Street, 39th Floor, New York, New York 10036, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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21
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Abstract
![]()
Structural
studies of membrane proteins have highlighted the likely
influence of membrane mimetic environments (i.e., lipid bilayers versus
detergent micelles) on the conformation and dynamics of small α-helical
membrane proteins. We have used molecular dynamics simulations to
compare the conformational dynamics of BM2 (a small α-helical
protein from the membrane of influenza B) in a model phospholipid
bilayer environment with its behavior in protein–detergent
complexes with either the zwitterionic detergent dihexanoylphosphatidylcholine
(DHPC) or the nonionic detergent dodecylmaltoside (DDM). We find that
DDM more closely resembles the lipid bilayer in terms of its interaction
with the protein, while the short-tailed DHPC molecule forms “nonphysiological”
interactions with the protein termini. We find that the intrinsic
micelle properties of each detergent are conserved upon formation
of the protein–detergent complex. This implies that simulations
of detergent micelles may be used to help select optimal conditions
for experimental studies of membrane proteins.
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Affiliation(s)
- Sarah L Rouse
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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22
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Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MSP, Caffrey M. A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa. Acta Crystallogr D Biol Crystallogr 2014; 70:2054-68. [PMID: 25084326 PMCID: PMC4118822 DOI: 10.1107/s1399004714001850] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/26/2014] [Indexed: 11/11/2022]
Abstract
The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gate (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.
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Affiliation(s)
- Jingquan Tan
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Dianfan Li
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Valerie E. Pye
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Lutz Vogeley
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Alette R. Brinth
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Toufic El Arnaout
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - John C. Whitney
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Martin Caffrey
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
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23
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Lonsdale R, Rouse SL, Sansom MSP, Mulholland AJ. A multiscale approach to modelling drug metabolism by membrane-bound cytochrome P450 enzymes. PLoS Comput Biol 2014; 10:e1003714. [PMID: 25033460 PMCID: PMC4102395 DOI: 10.1371/journal.pcbi.1003714] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/28/2014] [Indexed: 01/30/2023] Open
Abstract
Cytochrome P450 enzymes are found in all life forms. P450s play an important role in drug metabolism, and have potential uses as biocatalysts. Human P450s are membrane-bound proteins. However, the interactions between P450s and their membrane environment are not well-understood. To date, all P450 crystal structures have been obtained from engineered proteins, from which the transmembrane helix was absent. A significant number of computational studies have been performed on P450s, but the majority of these have been performed on the solubilised forms of P450s. Here we present a multiscale approach for modelling P450s, spanning from coarse-grained and atomistic molecular dynamics simulations to reaction modelling using hybrid quantum mechanics/molecular mechanics (QM/MM) methods. To our knowledge, this is the first application of such an integrated multiscale approach to modelling of a membrane-bound enzyme. We have applied this protocol to a key human P450 involved in drug metabolism: CYP3A4. A biologically realistic model of CYP3A4, complete with its transmembrane helix and a membrane, has been constructed and characterised. The dynamics of this complex have been studied, and the oxidation of the anticoagulant R-warfarin has been modelled in the active site. Calculations have also been performed on the soluble form of the enzyme in aqueous solution. Important differences are observed between the membrane and solution systems, most notably for the gating residues and channels that control access to the active site. The protocol that we describe here is applicable to other membrane-bound enzymes.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (MSPS); (AJM)
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
- * E-mail: (MSPS); (AJM)
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Rouse SL, Marcoux J, Robinson CV, Sansom MSP. Dodecyl maltoside protects membrane proteins in vacuo. Biophys J 2014; 105:648-56. [PMID: 23931313 DOI: 10.1016/j.bpj.2013.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 05/14/2013] [Accepted: 06/17/2013] [Indexed: 11/26/2022] Open
Abstract
Molecular dynamics simulations have been used to characterize the effects of transfer from aqueous solution to a vacuum to inform our understanding of mass spectrometry of membrane-protein-detergent complexes. We compared two membrane protein architectures (an α-helical bundle versus a β-barrel) and two different detergent types (phosphocholines versus an alkyl sugar) with respect to protein stability and detergent packing. The β-barrel membrane protein remained stable as a protein-detergent complex in vacuum. Zwitterionic detergents formed conformationally destabilizing interactions with an α-helical membrane protein after detergent micelle inversion driven by dehydration in vacuum. In contrast, a nonionic alkyl sugar detergent resisted micelle inversion, maintaining the solution-phase conformation of the protein. This helps to explain the relative stability of membrane proteins in the presence of alkyl sugar detergents such as dodecyl maltoside.
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Affiliation(s)
- Sarah L Rouse
- Department of Biochemistry, University of Oxford, United Kingdom
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Rouse SL, Sansom MS. Molecular Dynamics Simulations of the BM2 Proton Channel: Interactions with Lipids and Detergents. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Rouse SL, Carpenter T, Stansfeld PJ, Sansom MSP. Simulations of the BM2 proton channel transmembrane domain from influenza virus B. Biochemistry 2009; 48:9949-51. [PMID: 19780586 DOI: 10.1021/bi901166n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BM2 is a small integral membrane protein from influenza B virus which forms proton-permeable channels. Coarse-grained (CG) molecular dynamics simulations have been used to produce a model of the BM2 channel by self-assembly of a tetrameric bundle of BM2 transmembrane helices in a lipid bilayer. The BM2 channel model is conformationally stable on a 5 mus time scale. This CG model was converted to atomistic resolution to refine interhelix and channel-water interactions. Atomistic molecular dynamics simulations indicate that the BM2 channel is closed when no more than two of the four His19 residues are protonated. Protonating a third His19 side chain initiates a conformational change that opens the channel. In summary, our simulations suggest a common mechanism for BM2 and A/M2, whereby changes in helix packing play a functional role in channel gating.
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Affiliation(s)
- Sarah L Rouse
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Towt J, Tsai SC, Hernandez MR, Klimov AD, Kravec CV, Rouse SL, Subuhi HS, Twarowska B, Salamone SJ. ONTRAK TESTCUP: a novel, on-site, multi-analyte screen for the detection of abused drugs. J Anal Toxicol 1995; 19:504-10. [PMID: 8926746 DOI: 10.1093/jat/19.6.504] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We developed a rapid, sensitive, and simple-to-use multi-analyte diagnostic device for the detection of drugs of abuse in urine: the ONTRAK TESTCUP. No sample or reagent handling is necessary with this device, and the device also serves as the sample collection cup. The TESTCUP contains immunochromatographic reagents that qualitatively and simultaneously detect the presence of benzoylecgonine, morphine, and cannabinoids (delta9-tetrahydrocannabinol [THC] in urine. It is based on the principle of competition between the drug in the sample and membrane- immobilized drug conjugate for antidrug antibodies coated on blue-dyed microparticles. Each drug assay has its own strip, which contains an antibody specific to benzoylecgonine, morphine, or THC. A sample is collected in the TESTCUP, a lid is placed on it, and a chamber at the top of the cup is filled with urine by inverting the cup for 5 s. Urine proceeds down immunochromatographic strips, and the assays are developed. In approximately 3-5 min, the Test Valid bars appear, a decal is removed from the detection window, and the results are interpreted. The appearance of a colored bar at the detection window for each drug indicates a negative result. The absence of color in any specific drug detection window indicates a positive result for that drug. If a positive result is obtained, the same device (cup) can be used for gas chromatographic-mass spectrometric (GC-MS) confirmation. When the precision of the TESTCUP was evaluated, the results obtained were as follows: for urine controls containing drug at 50% of its cutoff concentration, the results were greater than or equal to 96, 98, and 96% negative for benzoylecgonine, morphine, and THC, respectively; for urine controls containing drug at 120% of its cutoff concentration, the results were greater than or equal to 97, 100, and 98% positive for benzoylecgonine, morphine, and THC, respectively. The correlations of clinical sample results using the TESTCUP versus results by GC-MS and the ONTRAK and OnLine assays were assessed. There was 100% agreement between samples prescreened positive by GC-MS and positive by TESTCUP for all three assays. There was 100% agreement between TESTCUP and ONTRAK results and between TESTCUP and OnLine results when testing clinical samples positive and negative for cocaine (benzoylecgonine) or THC. Greater than 99% agreement was observed between TESTCUP and ONTRAK results and between TESTCUP and OnLine results when testing clinical samples positive and negative for morphine. The cross-reactivity of the TESTCUP assay to related drugs and drug metabolites was also determined, and the results were similar to those of the ONTRAK and OnLine assays.
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Affiliation(s)
- J Towt
- International Drug Monitoring Business Unit, Roche Diagnostic Systems, Inc., Somerville, NJ 08876, USA
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