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Kalakoutis M, Pollock RD, Lazarus NR, Atkinson RA, George M, Berber O, Woledge RC, Ochala J, Harridge SDR. Revisiting specific force loss in human permeabilised single skeletal muscle fibres obtained from older individuals. Am J Physiol Cell Physiol 2023. [PMID: 37212546 DOI: 10.1152/ajpcell.00525.2022] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Specific force (SF) has been shown to be reduced in some but not all studies of human ageing using chemically skinned single muscle fibres. This may be due in part to the health status/physical activity levels of different older cohorts, but also from methodological differences in studying skinned fibres. The aim of the present study was to compare SF in fibres from older hip fracture patients (HFP), healthy master cyclists (MC) and healthy non-trained young adults (YA) using two different activating solutions. Quadriceps muscle samples and 316 fibres were obtained from HFPs (74.6±4 years, n=5), MCs (74.8±1, n=5) and YA (25.5±2, n=6). Fibres were activated (pCa 4.5, 15oC) in solutions containing either 60 mM TES or 20 mM imidazole. SF was determined by normalising force to fibre CSA assuming either an elliptical or circular shape and to fibre myosin heavy chain content. Activation in TES resulted in significantly higher MHC-I SF in all groups and YA MHC-IIA fibres, irrespective of normalisation method. Whilst there were no differences in SF between the participant groups, the ratio of SF between the TES and imidazole solutions was lower in HFPs compared to YAs (MHC-I p<0.05; MHC-IIA p=0.055). Activating solution composition, as opposed to donor characteristics, had a more notable effect on single fibre SF. However, this two-solution approach revealed an age-related difference in sensitivity in HFPs which was not shown in MCs. This suggests further novel approaches may be required to probe age/activity-related differences in muscle contractile quality.
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Affiliation(s)
- Michaeljohn Kalakoutis
- Centre of Human and Applied Physiological Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Ross D Pollock
- Centre of Human and Applied Physiological Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Norman R Lazarus
- Centre of Human and Applied Physiological Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Institut de Pharmacologie et de Biologie Structurale, Institute of Pharmacology and Structural Biology, Toulouse, France
| | - Marc George
- Guy's and St Thomas' NHS Foundation Trust, United Kingdom
| | - Onur Berber
- Royal Free London NHS Foundation Trust, United Kingdom
| | - Roger C Woledge
- Centre of Human and Applied Physiological Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Julien Ochala
- Centre of Human and Applied Physiological Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen D R Harridge
- Centre of Human and Applied Physiological Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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2
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Crosas-Molist E, Graziani V, Maiques O, Pandya P, Monger J, Samain R, George SL, Malik S, Salise J, Morales V, Le Guennec A, Atkinson RA, Marti RM, Matias-Guiu X, Charras G, Conte MR, Elosegui-Artola A, Holt M, Sanz-Moreno V. AMPK is a mechano-metabolic sensor linking cell adhesion and mitochondrial dynamics to Myosin-dependent cell migration. Nat Commun 2023; 14:2740. [PMID: 37217519 PMCID: PMC10202939 DOI: 10.1038/s41467-023-38292-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 05/13/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Cell migration is crucial for cancer dissemination. We find that AMP-activated protein kinase (AMPK) controls cell migration by acting as an adhesion sensing molecular hub. In 3-dimensional matrices, fast-migrating amoeboid cancer cells exert low adhesion/low traction linked to low ATP/AMP, leading to AMPK activation. In turn, AMPK plays a dual role controlling mitochondrial dynamics and cytoskeletal remodelling. High AMPK activity in low adhering migratory cells, induces mitochondrial fission, resulting in lower oxidative phosphorylation and lower mitochondrial ATP. Concurrently, AMPK inactivates Myosin Phosphatase, increasing Myosin II-dependent amoeboid migration. Reducing adhesion or mitochondrial fusion or activating AMPK induces efficient rounded-amoeboid migration. AMPK inhibition suppresses metastatic potential of amoeboid cancer cells in vivo, while a mitochondrial/AMPK-driven switch is observed in regions of human tumours where amoeboid cells are disseminating. We unveil how mitochondrial dynamics control cell migration and suggest that AMPK is a mechano-metabolic sensor linking energetics and the cytoskeleton.
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Affiliation(s)
- Eva Crosas-Molist
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Vittoria Graziani
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Oscar Maiques
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Pahini Pandya
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Joanne Monger
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
| | - Remi Samain
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
| | - Samantha L George
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
| | - Saba Malik
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Jerrine Salise
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK
| | - Valle Morales
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
| | - Adrien Le Guennec
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR5089, CNRS-Université de Toulouse III-Paul Sabatier, BP 64182, 31077, Toulouse, Cedex 4, France
| | - Rosa M Marti
- Department of Dermatology, Hospital Universitari Arnau de Vilanova, University of Lleida, CIBERONC, IRB Lleida, Lleida, 25198, Spain
| | - Xavier Matias-Guiu
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova, University of Lleida, IRB Lleida, CIBERONC, Lleida, 25198, Spain
- Department of Pathology, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, CIBERONC, L'Hospitalet de Llobregat, Barcelona, 08907, Spain
| | - Guillaume Charras
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK
| | - Alberto Elosegui-Artola
- Cell and Tissue Mechanobiology Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Physics, King's College London, London, WC2R 2LS, UK
| | - Mark Holt
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
- School of Cardiovascular and Metabolic Medicine & Sciences, King's College London BHF Centre of Research Excellence, London, SE1 1UL, UK
| | - Victoria Sanz-Moreno
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK.
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK.
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3
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Hungnes IN, Al-Salemee F, Gawne PJ, Eykyn T, Atkinson RA, Terry SYA, Clarke F, Blower PJ, Pringle PG, Ma MT. One-step, kit-based radiopharmaceuticals for molecular SPECT imaging: a versatile diphosphine chelator for 99mTc radiolabelling of peptides. Dalton Trans 2021; 50:16156-16165. [PMID: 34704995 PMCID: PMC8594432 DOI: 10.1039/d1dt03177e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/15/2021] [Indexed: 11/21/2022]
Abstract
Radiotracers labelled with technetium-99m (99mTc) enable accessible diagnostic imaging of disease, provided that radiotracer preparation is simple. Whilst 99mTc radiopharmaceuticals for imaging perfusion are routinely prepared from kits, and regularly used in healthcare, there are no 99mTc-labelled receptor-targeted radiopharmaceuticals in widespread clinical use. This is in part due to the multistep radiosyntheses required for the latter. We demonstrate that the diphosphine, 2,3-bis(diphenylphosphino)maleic anhydride (BMA), is an excellent platform for preparation of kit-based, receptor-targeted 99mTc-labelled radiotracers: its conjugates are simple to prepare and can be easily labelled with 99mTc using one-step, kit-based protocols. Here, reaction of BMA with the αvβ3-integrin receptor targeted cyclic peptide, Arg-Gly-Asp-DPhe-Lys (RGD), provided the first diphosphine-peptide conjugate, DP-RGD. DP-RGD was incorporated into a "kit", and addition of a saline solution containing 99mTcO4- to this kit, followed by heating, furnished the radiotracer [99mTcO2(DP-RGD)2]+ in consistently high radiochemical yields (>90%). The analogous [ReO2(DP-RGD)2]+ compound was prepared and characterised, revealing that both [99mTcO2(DP-RGD)2]+ and [ReO2(DP-RGD)2]+ consist of a mixture of cis and trans geometric isomers. Finally, [99mTcO2(DP-RGD)2]+ exhibited high metabolic stability, and selectively targeted αvβ3-integrin receptors, enabling in vivo SPECT imaging of αvβ3-integrin receptor expression in mice.
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MESH Headings
- Animals
- Arthritis, Rheumatoid/diagnostic imaging
- Arthritis, Rheumatoid/metabolism
- Chelating Agents/administration & dosage
- Chelating Agents/chemistry
- Chelating Agents/pharmacokinetics
- Female
- Humans
- Integrin alphaVbeta3/chemistry
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Transgenic
- Peptides, Cyclic/administration & dosage
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/pharmacokinetics
- Phosphines/administration & dosage
- Phosphines/chemistry
- Phosphines/pharmacokinetics
- Radiopharmaceuticals/administration & dosage
- Radiopharmaceuticals/chemistry
- Radiopharmaceuticals/pharmacokinetics
- Technetium/administration & dosage
- Technetium/chemistry
- Technetium/pharmacokinetics
- Tomography, Emission-Computed, Single-Photon
- Mice
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Affiliation(s)
- Ingebjørg N Hungnes
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
| | - Fahad Al-Salemee
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
| | - Peter J Gawne
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
| | - Thomas Eykyn
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
| | - R Andrew Atkinson
- King's College London, Randall Centre for Cell and Molecular Biophysics, and Centre for Biomolecular Spectroscopy, London, UK
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, 31077 Toulouse, France
| | - Samantha Y A Terry
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
| | - Fiona Clarke
- King's College London, Centre for Inflammation Biology and Cancer Immunology, Faculty of Life Sciences and Medicine, London, UK
| | - Philip J Blower
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
| | - Paul G Pringle
- University of Bristol, School of Chemistry, Cantock's Close, Bristol, UK
| | - Michelle T Ma
- King's College London, School of Biomedical Engineering and Imaging Sciences, 4th Floor Lambeth Wing, St Thomas' Hospital, London, UK.
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4
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Young JD, Ma MT, Eykyn TR, Atkinson RA, Abbate V, Cilibrizzi A, Hider RC, Blower PJ. Dipeptide inhibitors of the prostate specific membrane antigen (PSMA): A comparison of urea and thiourea derivatives. Bioorg Med Chem Lett 2021; 42:128044. [PMID: 33865971 DOI: 10.1016/j.bmcl.2021.128044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/01/2021] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 11/22/2022]
Abstract
Glutamate carboxypeptidase II (GCP(II)), also known as the prostate-specific membrane antigen (PSMA), is a transmembrane zinc(II) metalloenzyme overexpressed in prostate cancer. Inhibitors of this receptor are used to target molecular imaging agents and molecular radiotherapy agents to prostate cancer and if the affinity of inhibitors for GCP(II)/PSMA could be improved, targeting might also improve. Compounds containing the dipeptide OH-Lys-C(O)-Glu-OH (compound 3), incorporating a urea motif, have high affinity for GCP(II)/PSMA. We hypothesized that substituting the zinc-coordinating urea group for a thiourea group, thus incorporating a sulfur atom, could facilitate stronger binding to zinc(II) within the active site, and thus improve affinity for GCP(II)/PSMA. A structurally analogous urea and thiourea pair (HO-Glu-C(O)-Glu-OH - compound 5 and HO-Glu-C(S)-Glu-OH - compound 6) were synthesized and the inhibitory concentration (IC50) of each compound measured with a cell-based assay, allowing us to refute the hypothesis: the thiourea analogue showed 100-fold weaker binding to PSMA than the urea analogue.
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Affiliation(s)
- Jennifer D Young
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom.
| | - Michelle T Ma
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom.
| | - Thomas R Eykyn
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom.
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.
| | - Vincenzo Abbate
- Institute of Pharmaceutical Science, King's College London, London, United Kingdom.
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, London, United Kingdom.
| | - Robert C Hider
- Institute of Pharmaceutical Science, King's College London, London, United Kingdom.
| | - Philip J Blower
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom.
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5
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Manzo G, Hind CK, Ferguson PM, Amison RT, Hodgson-Casson AC, Ciazynska KA, Weller BJ, Clarke M, Lam C, Man RCH, Shaughnessy BGO, Clifford M, Bui TT, Drake AF, Atkinson RA, Lam JKW, Pitchford SC, Page CP, Phoenix DA, Lorenz CD, Sutton JM, Mason AJ. A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy. Commun Biol 2020; 3:697. [PMID: 33247193 PMCID: PMC7699649 DOI: 10.1038/s42003-020-01420-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial peptides (AMPs) are a potential alternative to classical antibiotics that are yet to achieve a therapeutic breakthrough for treatment of systemic infections. The antibacterial potency of pleurocidin, an AMP from Winter Flounder, is linked to its ability to cross bacterial plasma membranes and seek intracellular targets while also causing membrane damage. Here we describe modification strategies that generate pleurocidin analogues with substantially improved, broad spectrum, antibacterial properties, which are effective in murine models of bacterial lung infection. Increasing peptide-lipid intermolecular hydrogen bonding capabilities enhances conformational flexibility, associated with membrane translocation, but also membrane damage and potency, most notably against Gram-positive bacteria. This negates their ability to metabolically adapt to the AMP threat. An analogue comprising D-amino acids was well tolerated at an intravenous dose of 15 mg/kg and similarly effective as vancomycin in reducing EMRSA-15 lung CFU. This highlights the therapeutic potential of systemically delivered, bactericidal AMPs.
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Affiliation(s)
- Giorgia Manzo
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Charlotte K Hind
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Philip M Ferguson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Richard T Amison
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Alice C Hodgson-Casson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Katarzyna A Ciazynska
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Bethany J Weller
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Maria Clarke
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Carolyn Lam
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Rico C H Man
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Blaze G O' Shaughnessy
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Melanie Clifford
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Tam T Bui
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, UK
| | - Alex F Drake
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, UK
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, UK
| | - Jenny K W Lam
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Simon C Pitchford
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Clive P Page
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - David A Phoenix
- School of Applied Science, London South Bank University, 103 Borough Road, London, SE1 0AA, UK
| | | | - J Mark Sutton
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK.
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
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6
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Cox IJ, Idilman R, Fagan A, Turan D, Ajayi L, Le Guennec AD, Taylor-Robinson SD, Karakaya F, Gavis E, Andrew Atkinson R, Williams R, Sikaroodi M, Nizam S, Gillevet PM, Bajaj JS. Metabolomics and microbial composition increase insight into the impact of dietary differences in cirrhosis. Liver Int 2020; 40:416-427. [PMID: 31544308 PMCID: PMC6980909 DOI: 10.1111/liv.14256] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/04/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Dietary changes can modulate gut microbiota and interact with cirrhosis. Our prior study demonstrated that microbial diversity was higher in cirrhotics from Turkish vs the USA, which was associated with lower risk of 90-day hospitalizations. We aimed to define gut microbial functional and metabolomic changes to increase insight into benefits of the Mediterranean compared to Western diets. METHODS In all, 139 Turkish (46 controls/50 compensated/43 decompensated) and 157 American subjects (48 controls/59 compensated/50 decompensated) were studied. Turkish subjects consumed a modified Mediterranean diet with daily fermented milk intake, whereas Americans consumed a Western diet. Predicted gut microbial functionalities and plasma metabolomics were compared between/within countries. Correlation network differences between microbiota and metabolites in cirrhotics from Turkey vs the USA were evaluated. RESULTS Predicted microbial function showed lower amino acid, bioenergetics and lipid pathways, with functions related to vitamin B, glycan, xenobiotic metabolism, DNA/RNA synthesis, in cirrhotics from Turkey compared to the USA. Plasma metabolomics demonstrated higher relative lactate levels in Turkey vs the USA. The metabolite changes in decompensated cirrhosis, compared to controls, showed similar trends in Turkey and the USA, with reduced lipids and phosphocholines. Phosphocholines were significantly lower in patients hospitalized in 90 days (P = .03). Correlation networks in cirrhotics demonstrated linkage differences between beneficial taxa, Blautia and Oscillispira, and lactate and unsaturated lipids, in Turkey compared to American patients. CONCLUSIONS A modified Mediterranean diet was associated with altered plasma metabolomics and beneficially alters microbiota functionality and correlations compared to Western diet in cirrhosis. These altered diet-microbial interactions could potentially affect the 90-day hospitalization risk.
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Affiliation(s)
- I Jane Cox
- Institute for Hepatology London, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College Hospital, London, UK
| | | | - Andrew Fagan
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | | | - Lola Ajayi
- Institute for Hepatology London, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College Hospital, London, UK
| | - Adrien D Le Guennec
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | | | | | - Edith Gavis
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
| | - R Andrew Atkinson
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | - Roger Williams
- Institute for Hepatology London, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College Hospital, London, UK
| | | | | | | | - Jasmohan S Bajaj
- Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, VA, USA
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7
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Bajaj JS, Salzman N, Acharya C, Takei H, Kakiyama G, Fagan A, White MB, Gavis EA, Holtz ML, Hayward M, Nittono H, Hylemon PB, Cox IJ, Williams R, Taylor-Robinson SD, Sterling RK, Matherly SC, Fuchs M, Lee H, Puri P, Stravitz RT, Sanyal AJ, Ajayi L, Le Guennec A, Atkinson RA, Siddiqui MS, Luketic V, Pandak WM, Sikaroodi M, Gillevet PM. Microbial functional change is linked with clinical outcomes after capsular fecal transplant in cirrhosis. JCI Insight 2019; 4:133410. [PMID: 31751317 PMCID: PMC6975263 DOI: 10.1172/jci.insight.133410] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUNDHepatic encephalopathy (HE) is associated with poor outcomes. A prior randomized, pilot trial demonstrated safety after oral capsular fecal microbial transplant (FMT) in HE, with favorable changes in microbial composition and cognition. However, microbial functional changes are unclear. The aim of this study was to determine the effect of FMT on the gut-brain axis compared with placebo, using microbial function based on bile acids (BAs), inflammation (serum IL-6, LPS-binding protein [LBP]), and their association with EncephalApp.METHODSTwenty cirrhotic patients were randomized 1:1 into groups that received 1-time FMT capsules from a donor enriched in Lachnospiraceae and Ruminococcaceae or placebo capsules, with 5-month follow-up for safety outcomes. Stool microbiota and BA; serum IL-6, BA, and LBP; and EncephalApp were analyzed at baseline and 4 weeks after FMT/placebo. Correlation networks among microbiota, BAs, EncephalApp, IL-6, and LBP were performed before/after FMT.RESULTSFMT-assigned participants had 1 HE recurrence and 2 unrelated infections. Six placebo-assigned participants developed negative outcomes. FMT, but not placebo, was associated with reduced serum IL-6 and LBP and improved EncephalApp. FMT-assigned participants demonstrated higher deconjugation and secondary BA formation in feces and serum compared with baseline. No change was seen in placebo. Correlation networks showed greater complexity after FMT compared with baseline. Beneficial taxa, such as Ruminococcaceae, Verrucomicrobiaceae, and Lachnospiraceae, were correlated with cognitive improvement and decrease in inflammation after FMT. Fecal/serum secondary/primary ratios and PiCRUST secondary BA pathways did not increase in participants who developed poor outcomes.CONCLUSIONGut microbial function in cirrhosis is beneficially affected by capsular FMT, with improved inflammation and cognition. Lower secondary BAs in FMT recipients could select for participants who develop negative outcomes.TRIAL REGISTRATIONClinicaltrials.gov NCT03152188.FUNDINGNational Center for Advancing Translational Sciences NIH grant R21TR002024, VA Merit Review grant 2I0CX001076, the United Kingdom National Institute for Health Research Biomedical Facility at Imperial College London, the British Heart Foundation, Wellcome Trust, and King's College London.
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Affiliation(s)
- Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Nita Salzman
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, Japan
| | - Genta Kakiyama
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Melanie B. White
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Edith A. Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Mary L. Holtz
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael Hayward
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - I. Jane Cox
- Institute for Hepatology London, Foundation for Liver Research, London, United Kingdom
| | - Roger Williams
- Institute for Hepatology London, Foundation for Liver Research, London, United Kingdom
| | | | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Scott C. Matherly
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Hannah Lee
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Puneet Puri
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - R. Todd Stravitz
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Arun J. Sanyal
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Lola Ajayi
- Institute for Hepatology London, Foundation for Liver Research, London, United Kingdom
| | - Adrien Le Guennec
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King’s College London, London, United Kingdom
| | - R. Andrew Atkinson
- Randall Centre for Cell & Molecular Biophysics and Centre for Biomolecular Spectroscopy, King’s College London, London, United Kingdom
| | - Mohammad S. Siddiqui
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Velimir Luketic
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - William M. Pandak
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
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8
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Abis G, Charles RL, Kopec J, Yue WW, Atkinson RA, Bui TTT, Lynham S, Popova S, Sun YB, Fraternali F, Eaton P, Conte MR. 15-deoxy-Δ 12,14-Prostaglandin J 2 inhibits human soluble epoxide hydrolase by a dual orthosteric and allosteric mechanism. Commun Biol 2019; 2:188. [PMID: 31123712 PMCID: PMC6525171 DOI: 10.1038/s42003-019-0426-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/12/2019] [Indexed: 01/01/2023] Open
Abstract
Human soluble epoxide hydrolase (hsEH) is an enzyme responsible for the inactivation of bioactive epoxy fatty acids, and its inhibition is emerging as a promising therapeutical strategy to target hypertension, cardiovascular disease, pain and insulin sensitivity. Here, we uncover the molecular bases of hsEH inhibition mediated by the endogenous 15-deoxy-Δ12,14-Prostaglandin J2 (15d-PGJ2). Our data reveal a dual inhibitory mechanism, whereby hsEH can be inhibited by reversible docking of 15d-PGJ2 in the catalytic pocket, as well as by covalent locking of the same compound onto cysteine residues C423 and C522, remote to the active site. Biophysical characterisations allied with in silico investigations indicate that the covalent modification of the reactive cysteines may be part of a hitherto undiscovered allosteric regulatory mechanism of the enzyme. This study provides insights into the molecular modes of inhibition of hsEH epoxy-hydrolytic activity and paves the way for the development of new allosteric inhibitors.
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Affiliation(s)
- Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Rebecca L. Charles
- School of Cardiovascular Medicine & Science, The Rayne Institute, Lambeth Wing, St Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Jolanta Kopec
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ UK
| | - Wyatt W. Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ UK
| | - R. Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
| | - Tam T. T. Bui
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, The James Black Centre, King’s College London, London, SE5 9NU UK
| | - Simona Popova
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Yin-Biao Sun
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
| | - Philip Eaton
- School of Cardiovascular Medicine & Science, The Rayne Institute, Lambeth Wing, St Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, SE1 1UL UK
- Centre for Biomolecular Spectroscopy, King’s College London, London, SE1 1UL UK
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9
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Cruz-Gallardo I, Martino L, Trotta R, De Tito S, Kelly G, Atkinson RA, Randazzo A, Conte MR. Resonance assignment of human LARP4A La module. Biomol NMR Assign 2019; 13:169-172. [PMID: 30632004 PMCID: PMC6439165 DOI: 10.1007/s12104-019-09871-4] [Citation(s) in RCA: 3] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
Human LARP4A belongs to a superfamily of RNA binding proteins called La-related proteins (LARPs). Whilst being a positive regulator of protein synthesis and a promoter of mRNA stability, LARP4A also controls cell morphology and motility in human breast and prostate cancer cells. All LARPs share a characteristic RNA binding unit named the La-module, which despite a high level of primary structure conservation exhibits a great versatility in RNA target selection. Human LARP4A La-module is the most divergent compared with other LARPs and its RNA recognition properties have only recently started to be revealed. Given the key role of LARP4A protein in cancer cell biology, we have initiated a complete NMR characterisation of its La-module and here we report the assignment of 1H, 15N and 13C resonances resulting from our studies.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Luigi Martino
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Roberta Trotta
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano De Tito
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK.
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK.
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10
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O'Brien KA, Atkinson RA, Richardson L, Koulman A, Murray AJ, Harridge SDR, Martin DS, Levett DZH, Mitchell K, Mythen MG, Montgomery HE, Grocott MPW, Griffin JL, Edwards LM. Metabolomic and lipidomic plasma profile changes in human participants ascending to Everest Base Camp. Sci Rep 2019; 9:2297. [PMID: 30783167 PMCID: PMC6381113 DOI: 10.1038/s41598-019-38832-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 06/01/2018] [Accepted: 01/10/2019] [Indexed: 12/19/2022] Open
Abstract
At high altitude oxygen delivery to the tissues is impaired leading to oxygen insufficiency (hypoxia). Acclimatisation requires adjustment to tissue metabolism, the details of which remain incompletely understood. Here, metabolic responses to progressive environmental hypoxia were assessed through metabolomic and lipidomic profiling of human plasma taken from 198 human participants before and during an ascent to Everest Base Camp (5,300 m). Aqueous and lipid fractions of plasma were separated and analysed using proton (1H)-nuclear magnetic resonance spectroscopy and direct infusion mass spectrometry, respectively. Bayesian robust hierarchical regression revealed decreasing isoleucine with ascent alongside increasing lactate and decreasing glucose, which may point towards increased glycolytic rate. Changes in the lipid profile with ascent included a decrease in triglycerides (48-50 carbons) associated with de novo lipogenesis, alongside increases in circulating levels of the most abundant free fatty acids (palmitic, linoleic and oleic acids). Together, this may be indicative of fat store mobilisation. This study provides the first broad metabolomic account of progressive exposure to environmental hypobaric hypoxia in healthy humans. Decreased isoleucine is of particular interest as a potential contributor to muscle catabolism observed with exposure to hypoxia at altitude. Substantial changes in lipid metabolism may represent important metabolic responses to sub-acute exposure to environmental hypoxia.
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Affiliation(s)
- Katie A O'Brien
- Centre for Human and Applied Physiological Sciences, King's College London, London, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK.
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics King's College London Guy's Campus London, London, UK
| | - Larissa Richardson
- NIHR BRC Nutritional Biomarker Laboratory, University of Cambridge, Pathology building level 4, Addenbrooke's Hospital, Cambridge, UK
| | - Albert Koulman
- NIHR BRC Nutritional Biomarker Laboratory, University of Cambridge, Pathology building level 4, Addenbrooke's Hospital, Cambridge, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK
| | - Stephen D R Harridge
- Centre for Human and Applied Physiological Sciences, King's College London, London, UK
| | - Daniel S Martin
- University College London Centre for Altitude Space and Extreme Environment Medicine, UCLH NIHR Biomedical Research Centre, Institute of Sport and Exercise Health, First Floor, 170 Tottenham Court Road, London, W1T 7HA, UK
- Critical Care Unit, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Denny Z H Levett
- Southampton NIHR Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Integrative Physiological and Critical Illness Group, Division of Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Kay Mitchell
- Southampton NIHR Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Integrative Physiological and Critical Illness Group, Division of Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Monty G Mythen
- University College London Hospitals National Institute of Health Research Biomedical Research Centre, London, UK
| | - Hugh E Montgomery
- University College London Centre for Altitude Space and Extreme Environment Medicine, UCLH NIHR Biomedical Research Centre, Institute of Sport and Exercise Health, First Floor, 170 Tottenham Court Road, London, W1T 7HA, UK
- Centre for Human Health and Performance, Department of Medicine, University College London, London, UK
| | - Michael P W Grocott
- Southampton NIHR Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Integrative Physiological and Critical Illness Group, Division of Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Lindsay M Edwards
- Centre for Human and Applied Physiological Sciences, King's College London, London, UK.
- Respiratory Data Sciences Group, Respiratory TAU, GlaxoSmithKline Medicines Research, Stevenage, UK.
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11
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Manzo G, Ferguson PM, Gustilo VB, Hind CK, Clifford M, Bui TT, Drake AF, Atkinson RA, Sutton JM, Batoni G, Lorenz CD, Phoenix DA, Mason AJ. Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity. Sci Rep 2019; 9:1385. [PMID: 30718667 PMCID: PMC6362004 DOI: 10.1038/s41598-018-37630-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 07/06/2018] [Accepted: 12/10/2018] [Indexed: 11/08/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a potential source of new molecules to counter the increase in antimicrobial resistant infections but a better understanding of their properties is required to understand their native function and for effective translation as therapeutics. Details of the mechanism of their interaction with the bacterial plasma membrane are desired since damage or penetration of this structure is considered essential for AMPs activity. Relatively modest modifications to AMPs primary sequence can induce substantial changes in potency and/or spectrum of activity but, hitherto, have not been predicted to substantially alter the mechanism of interaction with the bacterial plasma membrane. Here we use a combination of molecular dynamics simulations, circular dichroism, solid-state NMR and patch clamp to investigate the extent to which temporin B and its analogues can be distinguished both in vitro and in silico on the basis of their interactions with model membranes. Enhancing the hydrophobicity of the N-terminus and cationicity of the C-terminus in temporin B improves its membrane activity and potency against both Gram-negative and Gram-positive bacteria. In contrast, enhancing the cationicity of the N-terminus abrogates its ability to trigger channel conductance and renders it ineffective against Gram-positive bacteria while nevertheless enhancing its potency against Escherichia coli. Our findings suggest even closely related AMPs may target the same bacterium with fundamentally differing mechanisms of action.
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Affiliation(s)
- Giorgia Manzo
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom
| | - Philip M Ferguson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom
| | - V Benjamin Gustilo
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom
| | - Charlotte K Hind
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Melanie Clifford
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Tam T Bui
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, United Kingdom
| | - Alex F Drake
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, United Kingdom
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London, SE1 1UL, United Kingdom
| | - J Mark Sutton
- Technology Development Group, National Infection Service, Public Health England, Salisbury, UK
| | - Giovanna Batoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Christian D Lorenz
- Department of Physics, King's College London, London, WC2R 2LS, United Kingdom
| | - David A Phoenix
- School of Applied Science, London South Bank University, 103 Borough Road, London, SE1 0AA, United Kingdom
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, United Kingdom.
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12
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Martínez-Lumbreras S, Alfano C, Evans NJ, Collins KM, Flanagan KA, Atkinson RA, Krysztofinska EM, Vydyanath A, Jackter J, Fixon-Owoo S, Camp AH, Isaacson RL. Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB. Structure 2018; 26:640-648.e5. [PMID: 29526435 PMCID: PMC5890618 DOI: 10.1016/j.str.2018.02.007] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/17/2017] [Accepted: 02/06/2018] [Indexed: 11/23/2022]
Abstract
Global changes in bacterial gene expression can be orchestrated by the coordinated activation/deactivation of alternative sigma (σ) factor subunits of RNA polymerase. Sigma factors themselves are regulated in myriad ways, including via anti-sigma factors. Here, we have determined the solution structure of anti-sigma factor CsfB, responsible for inhibition of two alternative sigma factors, σG and σE, during spore formation by Bacillus subtilis. CsfB assembles into a symmetrical homodimer, with each monomer bound to a single Zn2+ ion via a treble-clef zinc finger fold. Directed mutagenesis indicates that dimer formation is critical for CsfB-mediated inhibition of both σG and σE, and we have characterized these interactions in vitro. This work represents an advance in our understanding of how CsfB mediates inhibition of two alternative sigma factors to drive developmental gene expression in a bacterium.
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MESH Headings
- Amino Acid Sequence
- Bacillus subtilis/chemistry
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Binding Sites
- Cations, Divalent
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Multimerization
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Repressor Proteins/chemistry
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sigma Factor/antagonists & inhibitors
- Sigma Factor/chemistry
- Sigma Factor/genetics
- Sigma Factor/metabolism
- Spores, Bacterial/chemistry
- Spores, Bacterial/genetics
- Spores, Bacterial/metabolism
- Zinc/chemistry
- Zinc/metabolism
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Affiliation(s)
| | - Caterina Alfano
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Structural Biology and Biophysics Unit, Fondazione Ri.MED, Via Bandiera, 11, 90133 Palermo, Italy
| | - Nicola J Evans
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katherine M Collins
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Kelly A Flanagan
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Ewelina M Krysztofinska
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Anupama Vydyanath
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Jacquelin Jackter
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Sarah Fixon-Owoo
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Amy H Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
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13
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Zervou S, Yin X, Nabeebaccus AA, O’Brien BA, Cross RL, McAndrew DJ, Atkinson RA, Eykyn TR, Mayr M, Neubauer S, Lygate CA. Proteomic and metabolomic changes driven by elevating myocardial creatine suggest novel metabolic feedback mechanisms. Amino Acids 2016; 48:1969-81. [PMID: 27143170 PMCID: PMC4974297 DOI: 10.1007/s00726-016-2236-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/11/2016] [Indexed: 01/04/2023]
Abstract
Mice over-expressing the creatine transporter have elevated myocardial creatine levels [Cr] and are protected against ischaemia/reperfusion injury via improved energy reserve. However, mice with very high [Cr] develop cardiac hypertrophy and dysfunction. To investigate these contrasting effects, we applied a non-biased hypothesis-generating approach to quantify global protein and metabolite changes in the LV of mice stratified for [Cr] levels: wildtype, moderately elevated, and high [Cr] (65-85; 100-135; 160-250 nmol/mg protein, respectively). Male mice received an echocardiogram at 7 weeks of age with tissue harvested at 8 weeks. RV was used for [Cr] quantification by HPLC to select LV tissue for subsequent analysis. Two-dimensional difference in-gel electrophoresis identified differentially expressed proteins, which were manually picked and trypsin digested for nano-LC-MS/MS. Principal component analysis (PCA) showed efficient group separation (ANOVA P ≤ 0.05) and peptide sequences were identified by mouse database (UniProt 201203) using Mascot. A total of 27 unique proteins were found to be differentially expressed between normal and high [Cr], with proteins showing [Cr]-dependent differential expression, chosen for confirmation, e.g. α-crystallin B, a heat shock protein implicated in cardio-protection and myozenin-2, which could contribute to the hypertrophic phenotype. Nuclear magnetic resonance (¹H-NMR at 700 MHz) identified multiple strong correlations between [Cr] and key cardiac metabolites. For example, positive correlations with α-glucose (r² = 0.45; P = 0.002), acetyl-carnitine (r² = 0.50; P = 0.001), glutamine (r² = 0.59; P = 0.0002); and negative correlations with taurine (r² = 0.74; P < 0.0001), fumarate (r² = 0.45; P = 0.003), aspartate (r² = 0.59; P = 0.0002), alanine (r² = 0.66; P < 0.0001) and phosphocholine (r² = 0.60; P = 0.0002). These findings suggest wide-ranging and hitherto unexpected adaptations in substrate utilisation and energy metabolism with a general pattern of impaired energy generating pathways in mice with very high creatine levels.
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Affiliation(s)
- Sevasti Zervou
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, and the BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Xiaoke Yin
- King’s British Heart Foundation Centre, King’s College London, London, UK
| | | | - Brett A. O’Brien
- Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, UK
| | - Rebecca L. Cross
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, and the BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Debra J. McAndrew
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, and the BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - R. Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, and the BHF Centre of Research Excellence, Centre for Biomolecular Spectroscopy, King’s College London, London, UK
| | - Thomas R. Eykyn
- Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, UK
| | - Manuel Mayr
- King’s British Heart Foundation Centre, King’s College London, London, UK
| | - Stefan Neubauer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, and the BHF Centre of Research Excellence, University of Oxford, Oxford, UK
| | - Craig A. Lygate
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, and the BHF Centre of Research Excellence, University of Oxford, Oxford, UK
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Davies BM, Atkinson RA, Ludwinski F, Freemont AJ, Hoyland JA, Gnanalingham KK. Qualitative grading of disc degeneration by magnetic resonance in the lumbar and cervical spine: lack of correlation with histology in surgical cases. Br J Neurosurg 2016; 30:414-21. [PMID: 26999322 DOI: 10.3109/02688697.2016.1161174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Clinically, magnetic resonance (MR) imaging is the most effective non-invasive tool for assessing IVD degeneration. Histological examination of the IVD provides a more detailed assessment of the pathological changes at a tissue level. However, very few reports have studied the relationship between these techniques. Identifying a relationship may allow more detailed staging of IVD degeneration, of importance in targeting future regenerative therapies. OBJECTIVES To investigate the relationship between MR and histological grading of IVD degeneration in the cervical and lumbar spine in patients undergoing discectomy. METHODS Lumbar (N = 99) and cervical (N = 106) IVD samples were obtained from adult patients undergoing discectomy surgery for symptomatic IVD herniation and graded to ascertain a histological grade of degeneration. The pre-operative MR images from these patients were graded for the degree of IVD (MR grade) and vertebral end-plate degeneration (Modic Changes, MC). The relationship between histological and MR grades of degeneration were studied. RESULTS In lumbar and cervical IVD the majority of samples (93%) exhibited moderate levels of degeneration (ie MR grades 3-4) on pre-operative MR scans. Histologically, most specimens displayed moderate to severe grades of degeneration in lumbar (99%) and cervical spine (93%). MR grade was weakly correlated with patient age in lumbar and cervical study groups. MR and histological grades of IVD degeneration did not correlate in lumbar or cervical study groups. MC were more common in the lumbar than cervical spine (e.g. 39 versus 20% grade 2 changes; p < 0.05), but failed to correlate with MR or histological grades for degeneration. CONCLUSIONS In this surgical series, the resected IVD tissue displayed moderate to severe degeneration, but there is no correlation between MR and histological grades using a qualitative classification system. There remains a need for a quantitative, non-invasive, pre-clinical measure of IVD degeneration that correlates with histological changes seen in the IVD.
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Affiliation(s)
- B M Davies
- a Department of Neurosurgery , Greater Manchester Neurosciences Centre (GMNC), Salford Royal NHS Foundation Trust , Manchester , UK
| | - R A Atkinson
- a Department of Neurosurgery , Greater Manchester Neurosciences Centre (GMNC), Salford Royal NHS Foundation Trust , Manchester , UK ;,b Regenerative Medicine , Institute of Inflammation and Repair, University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - F Ludwinski
- b Regenerative Medicine , Institute of Inflammation and Repair, University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - A J Freemont
- b Regenerative Medicine , Institute of Inflammation and Repair, University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - J A Hoyland
- b Regenerative Medicine , Institute of Inflammation and Repair, University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
| | - K K Gnanalingham
- a Department of Neurosurgery , Greater Manchester Neurosciences Centre (GMNC), Salford Royal NHS Foundation Trust , Manchester , UK ;,b Regenerative Medicine , Institute of Inflammation and Repair, University of Manchester, Manchester Academic Health Science Centre , Manchester , UK
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15
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Atkinson RA, Fikrey L, Vail A, Patel HC. Silver-impregnated external-ventricular-drain-related cerebrospinal fluid infections: a meta-analysis. J Hosp Infect 2015; 92:263-72. [PMID: 26601606 DOI: 10.1016/j.jhin.2015.09.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/16/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND Cerebrospinal fluid (CSF) infection is the primary complication associated with placement of an external ventricular drain (EVD). The use of silver-impregnated EVD catheters has become commonplace in many neurosurgical centres. AIM To assess the effect of silver-impregnated EVD catheter usage on catheter-related CSF infections. METHODS A meta-analysis was performed by systematically searching Medline, Embase and the Cochrane Library. All randomized controlled trials (RCTs) and non-RCTs comparing silver-impregnated and plain EVD catheters were identified and analysed. FINDINGS Six non-RCTs were included. The crude infection rate was 10.8% for plain catheters and 8.9% for silver-impregnated catheters [pooled odds ratio (OR) 0.71, 95% confidence interval (CI) 0.46-1.08; P = 0.11]. In a microbiological spectrum analysis, silver-impregnated catheters demonstrated a significantly lower rate of CSF infections caused by Gram-positive organisms (2.0% vs 6.7% in the silver-impregnated and plain catheter groups, respectively; pooled OR 0.27, 95% CI 0.11-0.63; P = 0.002). CONCLUSION The antimicrobial effects of silver-impregnated EVD catheters may be selective, and may need to be evaluated further in a prospective, controlled manner.
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Affiliation(s)
- R A Atkinson
- Greater Manchester Neurosciences Centre, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre, Salford, UK; Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - L Fikrey
- Leiden University Medical Centre, Leiden, The Netherlands
| | - A Vail
- Centre for Biostatistics, The University of Manchester, Manchester Academic Health Science Centre, Salford Royal NHS Foundation Trust, Salford, UK
| | - H C Patel
- Greater Manchester Neurosciences Centre, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre, Salford, UK; Vascular and Stroke Centre, Institute of Cardiovascular Sciences, The University of Manchester, Manchester Academic Health Science Centre, Salford Royal NHS Foundation Trust, Salford, UK.
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16
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Martino L, Salisbury NJH, Brown P, Kelly G, Atkinson RA, Conte MR. (1)H, (15)N and (13)C chemical shift assignments of the La motif and RRM1 from human LARP6. Biomol NMR Assign 2015; 9:337-40. [PMID: 25896032 PMCID: PMC4568005 DOI: 10.1007/s12104-015-9605-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
We report here the nearly complete (1)H, (15)N and (13)C resonance assignment of the La motif and RNA recognition motif 1 of human LARP6, an RNA binding protein involved in regulating collagen synthesis.
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Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Nicholas J H Salisbury
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Paul Brown
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.
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Ramírez J, Recht R, Charbonnier S, Ennifar E, Atkinson RA, Travé G, Nominé Y, Kieffer B. Disorder-to-order transition of MAGI-1 PDZ1 C-terminal extension upon peptide binding: thermodynamic and dynamic insights. Biochemistry 2015; 54:1327-37. [PMID: 25590897 DOI: 10.1021/bi500845j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PDZ domains are highly abundant protein-protein interaction modules commonly found in multidomain scaffold proteins. The PDZ1 domain of MAGI-1, a protein present at cellular tight junctions that contains six PDZ domains, is targeted by the E6 oncoprotein of the high-risk human papilloma virus. Thermodynamic and dynamic studies using complementary isothermal titration calorimetry and nuclear magnetic resonance (NMR) (15)N heteronuclear relaxation measurements were conducted at different temperatures to decipher the molecular mechanism of this interaction. Binding of E6 peptides to the MAGI-1 PDZ1 domain is accompanied by an unusually large and negative change in heat capacity (ΔC(p)) that is attributed to a disorder-to-order transition of the C-terminal extension of the PDZ1 domain upon E6 binding. Analysis of temperature-dependent thermodynamic parameters and (15)N NMR relaxation data of a PDZ1 mutant in which this disorder-to-order transition was abolished allows the unusual thermodynamic signature of E6 binding to be correlated to local folding of the PDZ1 C-terminal extension. Comparison of the exchange contributions observed for wild-type and mutant proteins explains how variation in the solvent-exposed area may compensate for the loss of conformational entropy and further designates a distinct set of a few residues that mediate this local folding phenomena.
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Affiliation(s)
- Juan Ramírez
- Equipe Oncoprotéines, Ecole Supérieure de Biotechnologie de Strasbourg, Biotechnologie et Signalisation Cellulaire, UMR 7242, CNRS, Université de Strasbourg , Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch cedex, France
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18
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Martino L, Pennell S, Kelly G, Busi B, Brown P, Atkinson RA, Salisbury NJH, Ooi ZH, See KW, Smerdon SJ, Alfano C, Bui TTT, Conte MR. Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module. Nucleic Acids Res 2015; 43:645-60. [PMID: 25488812 PMCID: PMC4288179 DOI: 10.1093/nar/gku1287] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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: 08/18/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023] Open
Abstract
The La-related proteins (LARPs) form a diverse group of RNA-binding proteins characterized by the possession of a composite RNA binding unit, the La module. The La module comprises two domains, the La motif (LaM) and the RRM1, which together recognize and bind to a wide array of RNA substrates. Structural information regarding the La module is at present restricted to the prototypic La protein, which acts as an RNA chaperone binding to 3' UUUOH sequences of nascent RNA polymerase III transcripts. In contrast, LARP6 is implicated in the regulation of collagen synthesis and interacts with a specific stem-loop within the 5' UTR of the collagen mRNA. Here, we present the structure of the LaM and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. A mutagenic study guided by the structures revealed that RNA recognition requires synergy between the LaM and RRM1 as well as the participation of the interdomain linker, probably in realizing tandem domain configurations and dynamics required for substrate selectivity. Our study highlights a considerable complexity and plasticity in the architecture of the La module within LARPs.
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Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Simon Pennell
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Baptiste Busi
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biology, École Normale Supérieure de Lyon, CEDEX 07, France
| | - Paul Brown
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Nicholas J H Salisbury
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Zi-Hao Ooi
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Kang-Wei See
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Stephen J Smerdon
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Caterina Alfano
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Tam T T Bui
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
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Lu Z, Bergeron JRC, Atkinson RA, Schaller T, Veselkov DA, Oregioni A, Yang Y, Matthews SJ, Malim MH, Sanderson MR. Insight into the HIV-1 Vif SOCS-box-ElonginBC interaction. Open Biol 2013; 3:130100. [PMID: 24225024 PMCID: PMC3843819 DOI: 10.1098/rsob.130100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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] [Indexed: 12/02/2022] Open
Abstract
The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.
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Affiliation(s)
- Zhisheng Lu
- Randall Division of Cell and Molecular Biophysics, King's College London, 3rd Floor, New Hunt's House, Guy's Campus, London Bridge, London SE1 1UL, UK
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20
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DeNicola GF, Martin ED, Chaikuad A, Bassi R, Clark J, Martino L, Verma S, Sicard P, Tata R, Atkinson RA, Knapp S, Conte MR, Marber MS. Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1. Nat Struct Mol Biol 2013; 20:1182-90. [PMID: 24037507 PMCID: PMC3822283 DOI: 10.1038/nsmb.2668] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 08/02/2013] [Indexed: 11/09/2022]
Abstract
p38α Mitogen-activated Protein Kinase (p38α) is activated by a variety of mechanisms, including autophosphorylation initiated by TGFβ-activated kinase 1 binding protein 1 (TAB1) during myocardial ischemia and other stresses. Chemical genetic approaches and co-expression in mammalian, bacterial and cell-free systems revealed that mouse p38α autophosphorylation occurs in cis by direct interaction with TAB1(371-416). In isolated rat cardiac myocytes and perfused mouse hearts TAT-TAB1(371-416) rapidly activates p38 and profoundly perturbs function. Crystal structures and characterization in solution revealed a bipartite docking site for TAB1 in the p38α C-terminal kinase lobe. TAB1 binding stabilizes active p38α and induces rearrangements within the activation segment by helical extension of the Thr-Gly-Tyr motif that allows auto-phosphorylation in cis. Interference with p38α recognition by TAB1 abolishes its cardiac toxicity. Potentially, such intervention could circumvent the drawbacks seen when pharmacological inhibitors of p38 catalytic activity are used clinically.
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Affiliation(s)
- Gian Felice DeNicola
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK.,Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Eva Denise Martin
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Apirat Chaikuad
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford OX3 7LD, UK
| | - Rekha Bassi
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - James Clark
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Sharwari Verma
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Pierre Sicard
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Renée Tata
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford OX3 7LD, UK.,Department of Biochemistry and Molecular Biology, George Washington University, Washington, DC 20037, USA.,University of Oxford, Nuffield Department of Clinical Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Michael S Marber
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
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Takacs M, Petoukhov MV, Atkinson RA, Roblin P, Ogi FX, Demeler B, Potier N, Chebaro Y, Dejaegere A, Svergun DI, Moras D, Billas IML. The asymmetric binding of PGC-1α to the ERRα and ERRγ nuclear receptor homodimers involves a similar recognition mechanism. PLoS One 2013; 8:e67810. [PMID: 23874451 PMCID: PMC3706463 DOI: 10.1371/journal.pone.0067810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 03/12/2013] [Accepted: 05/22/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND PGC-1α is a crucial regulator of cellular metabolism and energy homeostasis that functionally acts together with the estrogen-related receptors (ERRα and ERRγ) in the regulation of mitochondrial and metabolic gene networks. Dimerization of the ERRs is a pre-requisite for interactions with PGC-1α and other coactivators, eventually leading to transactivation. It was suggested recently (Devarakonda et al) that PGC-1α binds in a strikingly different manner to ERRγ ligand-binding domains (LBDs) compared to its mode of binding to ERRα and other nuclear receptors (NRs), where it interacts directly with the two ERRγ homodimer subunits. METHODS/PRINCIPAL FINDINGS Here, we show that PGC-1α receptor interacting domain (RID) binds in an almost identical manner to ERRα and ERRγ homodimers. Microscale thermophoresis demonstrated that the interactions between PGC-1α RID and ERR LBDs involve a single receptor subunit through high-affinity, ERR-specific L3 and low-affinity L2 interactions. NMR studies further defined the limits of PGC-1α RID that interacts with ERRs. Consistent with these findings, the solution structures of PGC-1α/ERRα LBDs and PGC-1α/ERRγ LBDs complexes share an identical architecture with an asymmetric binding of PGC-1α to homodimeric ERR. CONCLUSIONS/SIGNIFICANCE These studies provide the molecular determinants for the specificity of interactions between PGC-1α and the ERRs, whereby negative cooperativity prevails in the binding of the coactivators to these receptors. Our work indicates that allosteric regulation may be a general mechanism controlling the binding of the coactivators to homodimers.
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Affiliation(s)
- Maria Takacs
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Maxim V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL DESY, Hamburg, Germany
| | - R. Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Pierre Roblin
- SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, France
- INRA-URBIA, Nantes, France
| | | | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Noelle Potier
- Institut de Chimie LC3, Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), UMR 7177, Strasbourg, France
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL DESY, Hamburg, Germany
| | - Dino Moras
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
| | - Isabelle M. L. Billas
- Department of Integrative Structural Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Université de Strasbourg (UdS), Illkirch, France
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Vermeer LS, Lan Y, Abbate V, Ruh E, Bui TT, Wilkinson LJ, Kanno T, Jumagulova E, Kozlowska J, Patel J, McIntyre CA, Yam WC, Siu G, Atkinson RA, Lam JKW, Bansal SS, Drake AF, Mitchell GH, Mason AJ. Conformational flexibility determines selectivity and antibacterial, antiplasmodial, and anticancer potency of cationic α-helical peptides. J Biol Chem 2012; 287:34120-33. [PMID: 22869378 PMCID: PMC3464521 DOI: 10.1074/jbc.m112.359067] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [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: 12/18/2022] Open
Abstract
We used a combination of fluorescence, circular dichroism (CD), and NMR spectroscopies in conjunction with size exclusion chromatography to help rationalize the relative antibacterial, antiplasmodial, and cytotoxic activities of a series of proline-free and proline-containing model antimicrobial peptides (AMPs) in terms of their structural properties. When compared with proline-free analogs, proline-containing peptides had greater activity against Gram-negative bacteria, two mammalian cancer cell lines, and intraerythrocytic Plasmodium falciparum, which they were capable of killing without causing hemolysis. In contrast, incorporation of proline did not have a consistent effect on peptide activity against Mycobacterium tuberculosis. In membrane-mimicking environments, structures with high α-helix content were adopted by both proline-free and proline-containing peptides. In solution, AMPs generally adopted disordered structures unless their sequences comprised more hydrophobic amino acids or until coordinating phosphate ions were added. Proline-containing peptides resisted ordering induced by either method. The roles of the angle subtended by positively charged amino acids and the positioning of the proline residues were also investigated. Careful positioning of proline residues in AMP sequences is required to enable the peptide to resist ordering and maintain optimal antibacterial activity, whereas varying the angle subtended by positively charged amino acids can attenuate hemolytic potential albeit with a modest reduction in potency. Maintaining conformational flexibility improves AMP potency and selectivity toward bacterial, plasmodial, and cancerous cells while enabling the targeting of intracellular pathogens.
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Affiliation(s)
- Louic S Vermeer
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
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23
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Kappo MA, Ab E, Hassem F, Atkinson RA, Faro A, Muleya V, Mulaudzi T, Poole JO, McKenzie JM, Chibi M, Moolman-Smook JC, Rees DJG, Pugh DJR. Solution structure of RING finger-like domain of retinoblastoma-binding protein-6 (RBBP6) suggests it functions as a U-box. J Biol Chem 2011; 287:7146-58. [PMID: 22130672 DOI: 10.1074/jbc.m110.217059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Retinoblastoma-binding protein-6 (RBBP6) plays a facilitating role, through its RING finger-like domain, in the ubiquitination of p53 by Hdm2 that is suggestive of E4-like activity. Although the presence of eight conserved cysteine residues makes it highly probable that the RING finger-like domain coordinates two zinc ions, analysis of the primary sequence suggests an alternative classification as a member of the U-box family, the members of which do not bind zinc ions. We show here that despite binding two zinc ions, the domain adopts a homodimeric structure highly similar to those of a number of U-boxes. Zinc ions could be replaced by cadmium ions without significantly disrupting the structure or the stability of the domain, although the rate of substitution was an order of magnitude slower than any previous measurement, suggesting that the structure is particularly stable, a conclusion supported by the high thermal stability of the domain. A hallmark of U-box-containing proteins is their association with chaperones, with which they cooperate in eliminating irretrievably unfolded proteins by tagging them for degradation by the proteasome. Using a yeast two-hybrid screen, we show that RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. Taken together with the structural similarities to U-box-containing proteins, our data suggest that RBBP6 plays a role in chaperone-mediated ubiquitination and possibly in protein quality control.
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Affiliation(s)
- Mautin A Kappo
- Biotechnology Department, University of the Western Cape, Bellville 7535, South Africa
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24
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Charbonnier S, Stier G, Orfanoudakis G, Kieffer B, Atkinson RA, Travé G. Defining the minimal interacting regions of the tight junction protein MAGI-1 and HPV16 E6 oncoprotein for solution structure studies. Protein Expr Purif 2008; 60:64-73. [DOI: 10.1016/j.pep.2008.03.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 03/17/2008] [Accepted: 03/19/2008] [Indexed: 11/30/2022]
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25
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Wasielewski E, Tzou DL, Dillmann B, Czaplicki J, Abdallah MA, Atkinson RA, Kieffer B. Multiple Conformations of the Metal-Bound Pyoverdine PvdI, a Siderophore of Pseudomonas aeruginosa: A Nuclear Magnetic Resonance Study,. Biochemistry 2008; 47:3397-406. [DOI: 10.1021/bi702214s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emeric Wasielewski
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
| | - Der-Lii Tzou
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
| | - Baudoin Dillmann
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
| | - Jerzy Czaplicki
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
| | - Mohamed A. Abdallah
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
| | - R. Andrew Atkinson
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
| | - Bruno Kieffer
- Laboratoire de Biologie et de Génomique Structurales, Biomolecular NMR group, IGBMC UMR 7104 CNRS, ESBS, bd Sébastien Brandt BP 10413, 67404 Illkirch Cedex, France, Institute of Chemistry, Academia Sinica, 128 Yen-Chiu-Yuan Road,Sec. 2, Nankang, Taipei 115, Taiwan, Republic of China, Université Paul Sabatier/Institut de Pharmacologie et de Biologie Structurale CNRS, 205, route de Narbonne, 31077 Toulouse, France, and Département Récepteurs et Protéines Membranaires, UMR 7175 École Supérieure de
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Vitorino M, Coin F, Zlobinskaya O, Atkinson RA, Moras D, Egly JM, Poterszman A, Kieffer B. Solution Structure and Self-association Properties of the p8 TFIIH Subunit Responsible for Trichothiodystrophy. J Mol Biol 2007; 368:473-80. [PMID: 17350038 DOI: 10.1016/j.jmb.2007.02.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 02/02/2007] [Accepted: 02/06/2007] [Indexed: 11/24/2022]
Abstract
Trichothiodystrophy (TTD) is a rare hereditary multi-system disorder associated with defects in nucleotide excision repair (NER) and transcription as consequences of mutations in XPB, XPD and p8/TTD-A subunits of transcription factor IIH (TFIIH). Here, we report the solution structure of the p8/TTD-A protein, a small alpha/beta protein built around an antiparallel beta-sheet that forms a homodimer with an extended interface. In order to characterize the dimer interface, we have introduced a mutation at position 44, which destabilizes the dimeric form of the protein. We have shown that this mutation has no effect on the intrinsic ability of p8/TTD-A to stimulate NER in vitro, but affects the capacity of p8/TTD-A to restore TFIIH concentration in TTD-A fibroblasts. Point mutations found in TTD-A patients are discussed on the basis of the present structure.
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Affiliation(s)
- Marc Vitorino
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
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27
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Aukrust I, Evensen L, Hollås H, Berven F, Atkinson RA, Travé G, Flatmark T, Vedeler A. Engineering, Biophysical Characterisation and Binding Properties of a Soluble Mutant form of Annexin A2 Domain IV that Adopts a Partially Folded Conformation. J Mol Biol 2006; 363:469-81. [PMID: 16963080 DOI: 10.1016/j.jmb.2006.08.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Revised: 08/15/2006] [Accepted: 08/16/2006] [Indexed: 11/15/2022]
Abstract
The four approximately 75-residue domains (repeats) that constitute the annexin core structure all possess an identical five-alpha-helix bundle topology, but the physico-chemical properties of the isolated domains are different. Domain IV of the annexins has previously been expressed only as inclusion bodies, resistant to solubilisation. Analysis of the conserved, exposed hydrophobic residues of the four annexin domains reveals that domain IV contains the largest number of hydrophobic residues involved in interfacial contacts with the other domains. We designed five constructs of domain IV of annexin A2 in which several interfacial hydrophobic residues were substituted by hydrophilic residues. The mutant domain, in which all fully exposed hydrophobic interfacial residues were substituted, was isolated as a soluble protein. Circular dichroism measurements indicate that it harbours a high content of alpha-helical secondary structure and some tertiary structure. The CD-monitored (lambda=222 nm) thermal melting profile suggests a weak cooperative transition. Nuclear magnetic resonance (1H-15N) correlation spectroscopy reveals heterogeneous line broadening and an intermediate spectral dispersion. These properties are indicative of a partially folded protein in which some residues are in a fairly structured conformation, whereas others are in an unfolded state. This conclusion is corroborated by 1-anilinonaphthalene-8-sulfonate fluorescence (ANS) analyses. Surface plasmon resonance measurements also indicate that this domain binds heparin, a known ligand of domain IV in the full-length annexin A2, although with lower affinity.
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Affiliation(s)
- Ingvild Aukrust
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
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28
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Oblak M, Grdadolnik SG, Kotnik M, Poterszman A, Atkinson RA, Nierengarten H, Desplancq D, Moras D, Solmajer T. Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase. Biochem Biophys Res Commun 2006; 349:1206-13. [PMID: 16979583 DOI: 10.1016/j.bbrc.2006.08.172] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 08/21/2006] [Indexed: 11/27/2022]
Abstract
Fighting bacterial resistance is a challenging task in the field of medicinal chemistry. DNA gyrase represents a validated antibacterial target and has drawn much interest in recent years. By a structure-based approach we have previously discovered compound 1, an indolinone derivative, possessing inhibitory activity against DNA gyrase. In the present paper, a detailed biophysical characterization of this inhibitor is described. Using mass spectrometry, NMR spectroscopy, and fluorescence experiments we have demonstrated that compound 1 binds reversibly to the ATP-binding site of the 24 kDa N-terminal fragment of DNA gyrase B from Escherichia coli (GyrB24) with low micromolar affinity. Based on these data, a plausible molecular model of compound 1 in the active site of GyrB24 was constructed. The predicted binding mode explains the competitive inhibitory mechanism with respect to ATP and forms a useful basis for further development of potent DNA gyrase inhibitors.
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Affiliation(s)
- Marko Oblak
- Laboratory of Molecular Modeling and NMR Spectroscopy, National Institute of Chemistry, POB660, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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29
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Charbonnier S, Coutouly MA, Kieffer B, Travé G, Atkinson RA. 13C, 15N and 1H resonance assignment of the PDZ1 domain of MAGI-1 using QUASI. J Biomol NMR 2006; 36 Suppl 1:33. [PMID: 16636753 DOI: 10.1007/s10858-006-0017-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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30
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Schons V, Atkinson RA, Dugave C, Graff R, Mislin GLA, Rochet L, Hennard C, Kieffer B, Abdallah MA, Schalk IJ. The Structure−Activity Relationship of Ferric Pyoverdine Bound to Its Outer Membrane Transporter: Implications for the Mechanism of Iron Uptake. Biochemistry 2005; 44:14069-79. [PMID: 16245923 DOI: 10.1021/bi051155s] [Citation(s) in RCA: 20] [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: 11/28/2022]
Abstract
Under iron limitation, Pseudomonas aeruginosa ATCC 15692 secretes a major siderophore, pyoverdine I (PvdI). This molecule chelates iron in the extracellular medium and shuttles it into the cells via a specific outer membrane transporter, FpvAI. PvdI consists of a fluorescent chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline and containing one of the bidentate groups involved in iron chelation, linked to a peptide moiety containing the two other bidentate groups required for binding to Fe(3+). Kinetic studies, based on the fluorescence properties of this siderophore, showed that pH 8.0 was optimal for the binding of PvdI and PvdI-Fe to FpvAI. We investigated the mechanism of interaction of PvdI and PvdI-Fe with FpvAI, by synthesizing various analogues of this siderophore, determining their affinity for FpvAI in vitro and in vivo and their ability to transport iron, and interpreting the results obtained in light of the structure of FpvAI-PvdI. Our findings demonstrate that the succinyl moiety linked to the chromophore of PvdI and the first amino acid of the peptide moiety can be sterically hindered with no effect on binding or the iron uptake properties of PvdI-Fe. Moreover, the sequence and the structure of the peptide moiety of PvdI seems to be more important for the iron uptake step than for the binding of the siderophore to FpvAI. Finally, the efficiency of iron uptake and of recycling of the various PvdI analogues after iron release suggests that iron dissociates from PvdI on FpvAI or in the periplasm. All these data have serious implications for the specificity and mechanism of PvdI-mediated iron transport in P. aeruginosa.
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Affiliation(s)
- V Schons
- UMR7100 CNRS, ESBS, Bld Sébastien Brant, F-67 412 Illkirch, Strasbourg, France
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31
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Houben K, Wasielewski E, Dominguez C, Kellenberger E, Atkinson RA, Timmers HTM, Kieffer B, Boelens R. Dynamics and Metal Exchange Properties of C4C4 RING Domains from CNOT4 and the p44 Subunit of TFIIH. J Mol Biol 2005; 349:621-37. [PMID: 15890366 DOI: 10.1016/j.jmb.2005.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Revised: 03/30/2005] [Accepted: 04/05/2005] [Indexed: 10/25/2022]
Abstract
Zinc fingers are small structured protein domains that require the coordination of zinc for a stable tertiary fold. Together with FYVE and PHD, the RING domain forms a distinct class of zinc-binding domains, where two zinc ions are ligated in a cross-braced manner, with the first and third pairs of ligands coordinating one zinc ion, while the second and fourth pairs ligate the other zinc ion. To investigate the relationship between the stability and dynamic behaviour of the domains and the stability of the metal-binding site, we studied metal exchange for the C4C4 RING domains of CNOT4 and the p44 subunit of TFIIH. We found that Zn(2+)-Cd(2+) exchange is different between the two metal-binding sites in the C4C4 RING domains of the two proteins. In order to understand the origins of these distinct exchange rates, we studied the backbone dynamics of both domains in the presence of zinc and of cadmium by NMR spectroscopy. The differential stability of the two metal-binding sites in the RING domains, as reflected by the different metal exchange rates, can be explained by a combination of accessibility and an electrostatic ion interaction model. A greater backbone flexibility for the p44 RING domain as compared to CNOT4 may be related to the distinct types of protein-protein interactions in which the two C4C4 RING domains are involved.
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Affiliation(s)
- Klaartje Houben
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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32
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Nominé Y, Charbonnier S, Miguet L, Potier N, Van Dorsselaer A, Atkinson RA, Travé G, Kieffer B. 1H and 15N resonance assignment, secondary structure and dynamic behaviour of the C-terminal domain of human papillomavirus oncoprotein E6. J Biomol NMR 2005; 31:129-141. [PMID: 15772752 DOI: 10.1007/s10858-004-7802-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 12/10/2004] [Indexed: 05/24/2023]
Abstract
E6 is a viral oncoprotein implicated in cervical cancers, produced by human papillomaviruses (HPVs). E6 contains two putative zinc-binding domains of about 75 residues each. The difficulty in producing recombinant E6 has long hindered the obtention of structural data. Recently, we described the expression and purification of E6-C 4C/4S, a stable, folded mutant of the C-terminal domain of HPV16 E6. Here, we have produced 15N-labelled samples of E6-C 4C/4S for structural studies by NMR. We have assigned most 1H and 15N resonances and identified the elements of secondary structure of the domain. The domain displays an original alpha/beta topology with roughly equal proportions of alpha-helix and beta-sheet. The PDZ-binding region of E6, located at the extreme C-terminus of the domain, is in a random conformation. Mass spectrometry demonstrated the presence of one zinc ion per protein molecule. Kinetics of replacement of zinc by cadmium followed by 1H,15N-HSQC experiments revealed specific frequency changes for the zinc-binding cysteines and their immediate neighbours. NMR spectra were affected by severe line-broadening effects which seriously hindered the assignment work. Investigation of these effects by 15N relaxation experiments showed that they are due to heterogeneous dynamic behaviour with mus-ms time scale motions occurring in localised regions of the monomeric domain.
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Affiliation(s)
- Yves Nominé
- Laboratoire d'Immunotechnologie, CNRS UMR 7100, Ecole Supérieure de Biotechnologie de Strasbourg, 67400 Illkirch, France
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33
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Klein FAC, Atkinson RA, Potier N, Moras D, Cavarelli J. Biochemical and NMR Mapping of the Interface between CREB-binding Protein and Ligand Binding Domains of Nuclear Receptor. J Biol Chem 2005; 280:5682-92. [PMID: 15542861 DOI: 10.1074/jbc.m411697200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 11/06/2022] Open
Abstract
CBP, cAMP-response element-binding protein (CREB)-binding protein, plays an important role as a general cointegrator of various signaling pathways and interacts with a large number of transcription factors. Interactions of CBP with ligand binding domains (LBDs) of nuclear receptors are mediated by LXXLL motifs, as are those of p160 proteins, although the number, distribution, and precise sequences of the motifs differ. We used a large N-terminal fragment of murine CBP to map by biochemical methods and NMR spectroscopy the interaction domain of CBP with the LBDs of several nuclear receptors. We show that distinct zones of that fragment are involved in the interactions: a 20-residue segment containing the LXXLL motif (residues 61-80) is implicated in the interaction with all three domains tested (peroxisome proliferator-activated receptor gamma-LBD, retinoid X receptor alpha-LBD, and estrogen-related receptor gamma-LBD), whereas a second N-terminal well conserved block of around 25 residues centered on a consensus L(40)PDEL(44) motif constitutes a secondary motif of interaction with peroxisome proliferator-activated receptor gamma-LBD. Sequence analysis reveals that both zones are well conserved in all vertebrate p300/CBP proteins, suggesting their functional importance. Interactions of p300/CBP coactivators with the LBDs of nuclear receptors are not limited to the canonical LXXLL motifs, involving both a longer contiguous segment around the motif and, for certain domains, an additional zone.
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Affiliation(s)
- Fabrice A C Klein
- Département de Biologie et Génomique Structurales, UMR 7104, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP Strasbourg, 1 rue Laurent Fries Illkirch 67404, France
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34
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Tzou DL, Wasielewski E, Abdallah MA, Kieffer B, Atkinson RA. A low-temperature heteronuclear NMR study of two exchanging conformations of metal-bound pyoverdin PaA fromPseudomonas aeruginosa. Biopolymers 2005; 79:139-49. [PMID: 16078193 DOI: 10.1002/bip.20343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [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: 11/11/2022]
Abstract
Under iron-deficient conditions, the Gram-negative bacterium Pseudomonas aeruginosa ATCC 15692 secretes a peptidic siderophore, pyoverdin PaA, composed of an aromatic chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline and a partially cyclized octapeptide, D-Ser-L-Arg-D-Ser-L-FoOHOrn-(L-Lys-L-FoOHOrn-L-Thr-L-Thr) (FoOHOrn: delta N-formyl-delta N-hydroxyornithine), in which the C-terminal carboxyl group forms a peptidic bond with the primary amine of the L-Lys side chain. Ferric iron is chelated by the catechol group on the chromophore and the two hydroxyornithine side chains. In aqueous solution, the (1)H-NMR spectrum of pyoverdin PaA-Ga(III), in which Ga(III) is used instead of Fe(III) for spectroscopic purposes, showed clear evidence of exchange broadening, preventing further structural characterization. The use of cryo-solvents allowed measurements to be made at temperatures as low as 253 K where two distinct conformations with roughly equivalent populations could be observed. (13)C and (15)N labeling of pyoverdin PaA enabled complete assignment of both forms of pyoverdin PaA-Ga(III) at 253 and 267 K, using triple-resonance multidimensional NMR experiments commonly applied to doubly labeled proteins.
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Affiliation(s)
- Der-Lii Tzou
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan, Republic of China
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35
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Au Y, Atkinson RA, Guerrini R, Kelly G, Joseph C, Martin SR, Muskett FW, Pallavicini A, Faulkner G, Pastore A. Solution structure of ZASP PDZ domain; implications for sarcomere ultrastructure and enigma family redundancy. Structure 2004; 12:611-22. [PMID: 15062084 DOI: 10.1016/j.str.2004.02.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [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: 11/18/2003] [Revised: 12/30/2003] [Accepted: 01/08/2004] [Indexed: 11/26/2022]
Abstract
Z band alternately spliced PDZ-containing protein (ZASP) is a sarcomere Z disk protein expressed in human cardiac and skeletal muscle that is thought to be involved in a dominant familial dilated cardiomyopathy. The N-terminal PDZ domain of ZASP interacts with the C terminus of alpha-actinin-2, the major component of the Z disk, probably by forming a ternary complex with titin Z repeats. We have determined the structure of ZASP PDZ by NMR and showed that it is a classical class 1 PDZ domain that recognizes the carboxy-terminal sequence of an alpha-actinin-2 calmodulin-like domain with micromolar affinity. We also characterized the role of each component in the ternary complex ZASP/alpha-actinin-2/titin, showing that the alpha-actinin-2/ZASP PDZ interaction involves a binding surface distinct from that recognized by the titin Z repeats. ZASP PDZ structure was used to model other members of the enigma family by homology and to predict their abilities to bind alpha-actinin-2.
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Affiliation(s)
- Yunghan Au
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
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36
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Jawhari A, Boussert S, Lamour V, Atkinson RA, Kieffer B, Poch O, Potier N, van Dorsselaer A, Moras D, Poterszman A. Domain Architecture of the p62 Subunit from the Human Transcription/Repair Factor TFIIH Deduced by Limited Proteolysis and Mass Spectrometry Analysis. Biochemistry 2004; 43:14420-30. [PMID: 15533047 DOI: 10.1021/bi048884c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [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: 11/30/2022]
Abstract
TFIIH is a multiprotein complex that plays a central role in both transcription and DNA repair. The subunit p62 is a structural component of the TFIIH core that is known to interact with VP16, p53, Eralpha, and E2F1 in the context of activated transcription, as well as with the endonuclease XPG in DNA repair. We used limited proteolysis experiments coupled to mass spectrometry to define structural domains within the conserved N-terminal part of the molecule. The first domain identified resulted from spontaneous proteolysis and corresponds to residues 1-108. The second domain encompasses residues 186-240, and biophysical characterization by fluorescence studies and NMR analysis indicated that it is at least partially folded and thus may correspond to a structural entity. This module contains a region of high sequence conservation with an invariant FWxxPhiPhi motif (Phi representing either tyrosine or phenylalanine), which was also found in other protein families and could play a key role as a protein-protein recognition module within TFIIH. The approach used in this study is general and can be straightforwardly applied to other multidomain proteins and/or multiprotein assemblies.
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Affiliation(s)
- Anass Jawhari
- Laboratoire de Biologie et Génomique Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, BP 163, 67404 Illkirch Cedex, France
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37
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Wasielewski E, Atkinson RA, Abdallah MA, Kieffer B. The three-dimensional structure of the gallium complex of azoverdin, a siderophore of Azomonas macrocytogenes ATCC 12334, determined by NMR using residual dipolar coupling constants. Biochemistry 2002; 41:12488-97. [PMID: 12369840 DOI: 10.1021/bi025990a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [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: 11/28/2022]
Abstract
In iron-deficient conditions, Azomonas macrocytogenes ATCC 12334 excretes a fluorescent siderophore called azoverdin, which is composed of a six-amino-acid peptide chain linked to a chromophore. Azoverdin chelates iron(III) very strongly, solubilizing it and transporting it back into the cells using an outer-membrane receptor. This compound is related to the pyoverdins, the peptidic siderophores of Pseudomonas, but differs in the site on the chromophore at which the peptide is covalently linked. This feature identifies azoverdin as a member of a new class of pyoverdins: the isopyoverdins. We report the three-dimensional structure of azoverdin-Ga(III) in solution. The use of orientational constraints obtained from the measurement of residual dipolar couplings using samples dissolved in a liquid crystalline medium allowed us to define the absolute configuration of the metal complex, which is Delta. The structure is characterized by a U-shape adopted by the peptide chain, with the N(delta)-acetyl-N(delta)-hydroxyornithine side chains adopting extended conformations in order to chelate the gallium ion. This conformation leaves a large open space permitting access to the gallium ion. The structural consequences of the particular isopyoverdin chemical structure are discussed in the context of the three-dimensional structures of other pyoverdins.
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Affiliation(s)
- Emeric Wasielewski
- Laboratoire de Biologie et de Génomique Structurales, Groupe de RMN, UMR 7104 CNRS, ESBS, bd Sébastien Brant, 67400 Illkirch, France
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38
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Ramboarina S, Srividya N, Atkinson RA, Morellet N, Roques BP, Lefèvre JF, Mély Y, Kieffer B. Effects of temperature on the dynamic behaviour of the HIV-1 nucleocapsid NCp7 and its DNA complex. J Mol Biol 2002; 316:611-27. [PMID: 11866521 DOI: 10.1006/jmbi.2001.5379] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [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: 11/22/2022]
Abstract
The nucleocapsid protein NCp7 of human immunodeficiency virus type 1 (HIV-1) contains two highly conserved CCHC zinc fingers and is involved in many crucial steps of the virus life-cycle. A large number of physiological rôles of NCp7 involve its binding to single-stranded nucleic acid chains. Several solution structures of NCp7 and its complex with single-stranded RNA or DNA have been reported. We have investigated the changes in the dynamic behaviour experienced by the (12-53)NCp7 peptide upon DNA binding using (15)N heteronuclear relaxation measurements at 293 K and 308 K, and fluorescence spectroscopy. The relaxation data were interpreted using the reduced spectral density approach, which allowed the high-frequency motion, overall tumbling rates and the conformational exchange contributions to be characterized for various states of the peptide without using a specific motional model. Analysis of the temperature-dependent correlation times derived from both NMR and fluorescence data indicated a co-operative change of the molecular shape of apo (12-53)NCp7 around 303 K, leading to an increased hydrodynamic radius at higher temperatures. The binding of (12-53)NCp7 to a single-stranded d(ACGCC) pentanucleotide DNA led to a reduction of the conformational flexibility that characterized the apo peptide. Translational diffusion experiments as well as rotational correlation times indicated that the (12-53)NCp7/d(ACGCC) complex tumbles as a rigid object. The amplitudes of high-frequency motions were restrained in the complex and the occurrence of conformational exchange was displaced from the second zinc finger to the linker residue Ala30.
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Affiliation(s)
- Stéphanie Ramboarina
- Laboratoire de Génomique Structurale, CNRS UPR 9004 ESBS, Bd Sébastien Brant, Illkirch, France
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39
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Abstract
Assignment of the resonances in nuclear magnetic resonance spectra is considered a pre-requisite for the interpretation of spectra that yield structural information. The determination of the three-dimensional structure of a biological macromolecule may, however, be achieved directly without spectral assignment, using the same set of heteronuclear scalar and dipolar coupling experiments as normally used. A cross-peak in any of the spectra may be interpreted as a distance between atoms, yielding a set of distances between unassigned atoms that serves to define the tertiary structure of the molecule. The principle is illustrated using the 76 amino acid protein ubiquitin.
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Affiliation(s)
- R Andrew Atkinson
- UPR 9004 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400 Illkirch, France.
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40
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Hölscher C, Atkinson RA, Arendse B, Brown N, Myburgh E, Alber G, Brombacher F. A protective and agonistic function of IL-12p40 in mycobacterial infection. J Immunol 2001; 167:6957-66. [PMID: 11739515 DOI: 10.4049/jimmunol.167.12.6957] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
IL-12p35(-/-)p40(-/-) mice are highly susceptible to Mycobacterium bovis bacillus Calmette-Guérin (BCG) or Mycobacterium tuberculosis infection. In this study IL-12p35(-/-) mice, which are able to produce endogenous IL-12p40, cleared M. bovis BCG and showed reduced susceptibility to pulmonary M. tuberculosis infection, which was in striking contrast to the outcome of mycobacterial infection in IL-12p35(-/-)p40(-/-) mice. Resistance in wild-type and IL-12p35(-/-) mice was accompanied by protective granuloma formation and Ag-specific delayed-type hypersensitivity responses, which were impaired in susceptible IL-12p35(-/- )p40(-/-) mice. Furthermore, IL-12p35(-/-) mice, but not IL-12p35(-/-)p40(-/-) mice, mounted Ag-specific Th1 and cytotoxic T cell responses. In vivo therapy with rIL-12p40 homodimer restored the impaired delayed-type hypersensitivity responses in M. bovis BCG-infected IL-12p35(-/-)p40(-/-) mice and reverted them to a more resistant phenotype. Together, these results show evidence for a protective and agonistic role of endogenous and exogenous IL-12p40 in mycobacterial infection, which is independent of IL-12p70.
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MESH Headings
- Animals
- Antigens, Bacterial/immunology
- Cells, Cultured
- Colony Count, Microbial
- Granuloma/immunology
- Granuloma/microbiology
- Granuloma/pathology
- Hypersensitivity, Delayed/immunology
- Interleukin-12/genetics
- Interleukin-12/pharmacology
- Interleukin-12/physiology
- Interleukin-23
- Interleukin-23 Subunit p19
- Interleukins/biosynthesis
- Lymphocyte Activation
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mycobacterium bovis/growth & development
- Mycobacterium bovis/immunology
- Mycobacterium tuberculosis/growth & development
- Mycobacterium tuberculosis/immunology
- Protein Subunits
- Survival Rate
- T-Lymphocytes, Cytotoxic/immunology
- Th1 Cells/immunology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/immunology
- Tuberculosis, Pulmonary/pathology
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Affiliation(s)
- C Hölscher
- Medical Research Council Unit Immunology in Infectious Diseases, Department of Immunology, University of Cape Town, Cape Town, South Africa
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41
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Atkinson RA, Joseph C, Kelly G, Muskett FW, Frenkiel TA, Nietlispach D, Pastore A. Ca2+-independent binding of an EF-hand domain to a novel motif in the alpha-actinin-titin complex. Nat Struct Biol 2001; 8:853-7. [PMID: 11573089 DOI: 10.1038/nsb1001-853] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The interaction between alpha-actinin and titin, two modular muscle proteins, is essential for sarcomere assembly. We have solved the solution structure of a complex between the calcium-insensitive C-terminal EF-hand domain of alpha-actinin-2 and the seventh Z-repeat of titin. The structure of the complex is in a semi-open conformation and closely resembles that of myosin light chains in their complexes with heavy chain IQ motifs. However, no IQ motif is present in the Z-repeat, suggesting that the semi-open conformation is a general structural solution for calcium-independent recognition of EF-hand domains.
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Affiliation(s)
- R A Atkinson
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA UK
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42
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Joseph C, Stier G, O'Brien R, Politou AS, Atkinson RA, Bianco A, Ladbury JE, Martin SR, Pastore A. A structural characterization of the interactions between titin Z-repeats and the alpha-actinin C-terminal domain. Biochemistry 2001; 40:4957-65. [PMID: 11305911 DOI: 10.1021/bi002739r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [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] [Indexed: 11/28/2022]
Abstract
Titin and alpha-actinin, two modular muscle proteins, are with actin the major components of the Z-band in vertebrate striated muscles where they serve to organize the antiparallel actin filament arrays in adjacent sarcomeres and to transmit tension between sarcomeres during activation. Interactions between titin and alpha-actinin have been mainly localized in a 45-amino acid multiple motif (Z-repeat) in the N-terminal region of titin and the C-terminal region of alpha-actinin. In this study, we provide the first quantitative characterization of alpha-actinin-Z-repeat recognition and dissect the interaction to its minimal units. Different complementary techniques, such as circular dichroism, calorimetry, and nuclear magnetic spectroscopy, were used. Two overlapping alpha-actinin constructs (Act-EF34 and Act-EF1234) containing two and four EF-hand motifs, respectively, were produced, and their folding properties were examined. Complex formation of Act-EF34 and Act-EF1234 with single- and double-Z-repeat constructs was studied. Act-EF34 was shown quantitatively to be necessary and sufficient for binding to Z-repeats, excluding the presence of additional high-affinity binding sites in the remaining part of the domain. The binding affinities of the different Z-repeats for Act-EF34 range from micromolar to millimolar values. The strongest of these interactions are comparable to those observed in troponin C-troponin I complexes. The binding affinities for Act-EF34 are maximal for Zr1 and Zr7, the two highly homologous sequences present in all muscle isoforms. No cooperative or additional contributions to the interaction were observed for Z-repeat double constructs. These findings have direct relevance for evaluating current models of Z-disk assembly.
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Affiliation(s)
- C Joseph
- NIMR, The Ridgeway, London NW7 1AA, UK
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43
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Abstract
In order to isolate genes coding for antigens of Neospora caninum which are recognised by the host immune system during a chronic murine infection, a cDNA library was immunoscreened with pooled sera from mice which survived three independent infections by N. caninum. Two new genes from N. caninum were isolated and expressed in Escherichia coli. The genes identified include one homologous to GRA1 of Toxoplasma gondii, plus another (NCP20) previously unknown in any taxon. Both genes encode small polypeptides which induced an IgG response in the mouse and were also recognised by IgG from a cow chronically infected with N. caninum. These results are consistent with the hypothesis that the polypeptides encoded by these genes are a target for the host immune system during chronic infections of N. caninum.
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Affiliation(s)
- R A Atkinson
- Molecular Parasitology Unit, Department of Cell and Molecular Biology, University of Technology, Sydney, Westbourne St., NSW 2065, Gore Hill, Australia
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44
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Abstract
Titin is an exceptionally large protein (M.Wt. approximately 3 MDa) that spans half the sarcomere in muscle, from the Z-disk to the M-line. In the Z-disk, it interacts with alpha-actinin homodimers that are a principal component of the Z-filaments linking actin filaments. The interaction between titin and alpha-actinin involves repeating approximately 45 amino acid sequences (Z-repeats) near the N-terminus of titin and the C-lobe of the C-terminal calmodulin-like domain of alpha-actinin. The conformation of Z-repeat 7 (ZR7) of titin when complexed with the 73-amino acid C-terminal portion of alpha-actinin (EF34) was studied by heteronuclear NMR spectroscopy using (15)N-labeling of ZR7 and found to be helical over a stretch of 18 residues. Complex formation resulted in the protection of one site of preferential cleavage of EF34 at Phe14-Leu17, as determined by limited proteolysis experiments coupled to mass spectrometry measurements. Intermolecular NOEs show Val16 of ZR7 to be positioned close in space to the backbone of EF34 around Phe14. These observations suggest that the mode of binding of ZR7 to EF34 is similar to that of troponin I to troponin C and of peptide C20W to calmodulin. These complexes would appear to represent a general alternative binding mode of calmodulin-like domains to target peptides.
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Affiliation(s)
- R A Atkinson
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
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45
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Atkinson RA, Kieffer B, Dejaegere A, Sirockin F, Lefèvre JF. Structural and dynamic characterization of omega-conotoxin MVIIA: the binding loop exhibits slow conformational exchange. Biochemistry 2000; 39:3908-19. [PMID: 10747778 DOI: 10.1021/bi992651h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [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: 11/29/2022]
Abstract
omega-Conotoxin MVIIA is a 25-residue, disulfide-bridged polypeptide from the venom of the sea snail Conus magus that binds to neuronal N-type calcium channels. It forms a compact folded structure, presenting a loop between Cys8 and Cys15 that contains a set of residues critical for its binding. The loop does not have a unique defined structure, nor is it intrinsically flexible. Broadening of a subset of resonances in the NMR spectrum at low temperature, anomalous temperature dependence of the chemical shifts of some resonances, and exchange contributions to J(0) from (13)C relaxation measurements reveal that conformational exchange affects the residues in this loop. The effects of this exchange on the calculated structure of omega-conotoxin MVIIA are discussed. The exchange appears to be associated with a change in the conformation of the disulfide bridge Cys8-Cys20. The implications for the use of the omega-conotoxins as a scaffold for carrying other functions is discussed.
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Affiliation(s)
- R A Atkinson
- UPR 9003 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Bld. Sébastien Brant, 67400 Illkirch, France.
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46
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Atkinson RA, Cook RW, Reddacliff LA, Rothwell J, Broady KW, Harper P, Ellis JT. Seroprevalence of Neospora caninum infection following an abortion outbreak in a dairy cattle herd. Aust Vet J 2000; 78:262-6. [PMID: 10840574 DOI: 10.1111/j.1751-0813.2000.tb11752.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [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: 11/29/2022]
Abstract
OBJECTIVE To investigate the seroprevalence of Neospora caninum infection in a commercial dairy cattle herd, 15 months after detection of an abortion outbreak. PROCEDURE Sera from the whole herd (n = 266) were examined for N caninum antibodies by indirect fluorescent antibody test (IFAT) and immunoblot analysis. Herd records were reviewed to collate serological results with abortion history, proximity to calving, and pedigree data. RESULTS The seroprevalence of N caninum infection was 24% (63/266) for IFAT titre > or = 160, 29% (78/266) for immunoblot positive (+ve), and 31% (82/266) for IFAT > or = 160 and/or immunoblot +ve; 94% (59/63) of animals with IFAT > or = 160 were immunoblot +ve. The association between seropositivity (IFAT > or = 160 and/or immunoblot +ve) and history of abortion was highly significant (P < 0.001); the seroprevalence was 86% (18/21) in aborting cows, compared with 30% (50/164) in non-aborting animals. The abortion rate for seropositive cows was 26% (18/68) compared with 3% (3/117) for seronegative animals. IFAT titres of infected cows were higher within 2 months of calving than at other times (P < 0.001). The association between seropositivity in dams and daughters was highly significant (P = 0.009). CONCLUSIONS The abortions were associated with N caninum infection and there was evidence of reactivation of latent infection close to calving and congenital transmission of infection. Immunodominant antigens identified by immunoblots may prove useful for improved diagnostic tests.
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Affiliation(s)
- R A Atkinson
- Molecular Parasitology Unit, University of Technology, Sydney, New South Wales
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47
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Atkinson RA, Joseph C, Kelly G, Muskett FW, Frenkiel TA, Pastor A. Assignment of the 1H, 13C and 15N resonances of the C-terminal EF-hands of alpha-actinin in a 14 kDa complex with Z-repeat 7 of titin. J Biomol NMR 2000; 16:277-278. [PMID: 10805138 DOI: 10.1023/a:1008358431571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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48
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Abstract
Spectral density mapping provides direct access to protein dynamics with no assumptions as to the nature of the molecule or its dynamic behaviour. Reduced spectral density mapping characterises a protein's motions at a lower experimental burden, assuming that the spectral density function J(ω) is flat around ωH. This introduces little error for 15N relaxation data but is less valid for 13C studies, perturbing J(ωC) considerably to an extent that depends on the nature of the molecule's motions. We propose the fitting of spectral density at high frequencies to a single Lorentzian and show that the true values of the spectral density lie between those determined by the two approximations.
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Affiliation(s)
- R A Atkinson
- UPR 9003 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Bld. Sébastien Brant, F-67400, Illkirch, France
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49
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Improta S, Krueger JK, Gautel M, Atkinson RA, Lefèvre JF, Moulton S, Trewhella J, Pastore A. The assembly of immunoglobulin-like modules in titin: implications for muscle elasticity. J Mol Biol 1998; 284:761-77. [PMID: 9826514 DOI: 10.1006/jmbi.1998.2028] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [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] [Indexed: 11/22/2022]
Abstract
Titin, a giant muscle protein, forms filaments that span half of the sarcomere and cover, along their length, quite diversified functions. The region of titin located in the sarcomere I-band is believed to play a major rôle in extensibility and passive elasticity of muscle. In the I-band, the titin sequence contains tandem immunoglobulin-like (Ig) modules intercalated by a potentially non-globular region. By a combined approach making use of small angle X-ray scattering and nuclear magnetic resonance techniques, we have addressed the questions of what are the average mutual orientation of poly-Igs and the degree of flexibility around the domain interfaces. Various recombinant fragments containing one, two and four titin I-band tandem domains were analysed. The small-angle scattering data provide a picture of the domains in a mostly extended configuration with their long axes aligned head-to-tail. There is a small degree of bending and twisting of the modules with respect to each other that results in an overall shortening in their maximum linear dimension compared with that expected for the fully extended, linear configurations. This shortening is greatest for the four module construct ( approximately 15%). 15N NMR relaxation studies of one and two-domain constructs show that the motions around the interdomain connecting regions are restricted, suggesting that titin behaves as a row of beads connected by rigid hinges. The length of the residues in the interface seems to be the major determinant of the degree of flexibility. Possible implications of our results for the structure and function of titin in muscles are discussed.
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Affiliation(s)
- S Improta
- EMBL, Meyerhofstrasse 1, Heidelberg, 69117, Germany
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50
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Atkinson RA, Salah El Din AL, Kieffer B, Lefèvre JF, Abdallah MA. Bacterial iron transport: 1H NMR determination of the three-dimensional structure of the gallium complex of pyoverdin G4R, the peptidic siderophore of Pseudomonas putida G4R. Biochemistry 1998; 37:15965-73. [PMID: 9843403 DOI: 10.1021/bi981194m] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [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: 11/28/2022]
Abstract
Among the fluorescent Pseudomonas species, Pseudomonas putida is a rare case of a nitrogen-fixing bacterium that transforms nitrogen into ammonia. When grown under iron-deficient conditions, it produces two major pyoverdins: pyoverdin G4R and pyoverdin G4RA. Their primary structures have been established using FAB-MS and one- and two-dimensional 15N, 13C, and 1H NMR on both the unlabeled and 15N-labeled compounds [Salah El Din, A. L. M., et al. (1997) Tetrahedron 53, 12539-12552]. The two pyoverdins have a common chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline. The chromophore is bound to the linear heptapeptide L-Asp-L-Orn-D-beta-threo-OHAsp-L-Dab-Gly-L-Ser-L-cyclo-OHOrn . Circular dichroism spectra suggest that the absolute configuration of the metal complex is Delta. The three-dimensional structure in solution of pyoverdin G4R-Ga(III) was determined after interpretation of two-dimensional 1H NMR spectra recorded at 283 and 303 K. The complex is tightly defined with a compact structure with a Delta absolute configuration. The site of complexation of the metal ion is found to be located on the surface of the molecule, showing that the ion can be released without large conformational changes, while the polar groups of the peptide chain, which may be responsible for the recognition of the receptor, are placed on the opposite side of the overall shape. The three-dimensional structure of pyoverdin G4R-Ga(III) is compared with those of other pyoverdins, and the role of the structure in iron uptake is discussed.
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Affiliation(s)
- R A Atkinson
- Laboratoire de Chimie Microbienne, Associé au CNRS, UPR 9003 du CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
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