1
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Houghton FM, Adams SE, Ríos AS, Masino L, Purkiss AG, Briggs DC, Ledda F, McDonald NQ. Architecture and regulation of a GDNF-GFRα1 synaptic adhesion assembly. Nat Commun 2023; 14:7551. [PMID: 37985758 PMCID: PMC10661694 DOI: 10.1038/s41467-023-43148-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/19/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Glial-cell line derived neurotrophic factor (GDNF) bound to its co-receptor GFRα1 stimulates the RET receptor tyrosine kinase, promoting neuronal survival and neuroprotection. The GDNF-GFRα1 complex also supports synaptic cell adhesion independently of RET. Here, we describe the structure of a decameric GDNF-GFRα1 assembly determined by crystallography and electron microscopy, revealing two GFRα1 pentamers bridged by five GDNF dimers. We reconsitituted the assembly between adhering liposomes and used cryo-electron tomography to visualize how the complex fulfils its membrane adhesion function. The GFRα1:GFRα1 pentameric interface was further validated both in vitro by native PAGE and in cellulo by cell-clustering and dendritic spine assays. Finally, we provide biochemical and cell-based evidence that RET and heparan sulfate cooperate to prevent assembly of the adhesion complex by competing for the adhesion interface. Our results provide a mechanistic framework to understand GDNF-driven cell adhesion, its relationship to trophic signalling, and the central role played by GFRα1.
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Affiliation(s)
- F M Houghton
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - S E Adams
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Vertex Pharmaceuticals, 86-88 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW, UK
| | - A S Ríos
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - L Masino
- Structural Biology Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - A G Purkiss
- Structural Biology Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - D C Briggs
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - F Ledda
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - N Q McDonald
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
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2
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Rzechorzek NJ, Kunzelmann S, Purkiss AG, Silva Dos Santos M, MacRae JI, Taylor IA, Fugger K, West SC. Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1. Nat Commun 2023; 14:6809. [PMID: 37884503 PMCID: PMC10603095 DOI: 10.1038/s41467-023-42544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors are used in the clinic to treat BRCA-deficient breast, ovarian and prostate cancers. As their efficacy is potentiated by loss of the nucleotide salvage factor DNPH1 there is considerable interest in the development of highly specific small molecule DNPH1 inhibitors. Here, we present X-ray crystal structures of dimeric DNPH1 bound to its substrate hydroxymethyl deoxyuridine monophosphate (hmdUMP). Direct interaction with the hydroxymethyl group is important for substrate positioning, while conserved residues surrounding the base facilitate target discrimination. Glycosidic bond cleavage is driven by a conserved catalytic triad and proceeds via a two-step mechanism involving formation and subsequent disruption of a covalent glycosyl-enzyme intermediate. Mutation of a previously uncharacterised yet conserved glutamate traps the intermediate in the active site, demonstrating its role in the hydrolytic step. These observations define the enzyme's catalytic site and mechanism of hydrolysis, and provide important insights for inhibitor discovery.
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Affiliation(s)
- Neil J Rzechorzek
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mariana Silva Dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - James I MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kasper Fugger
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- University College London Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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3
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Adams SE, Purkiss AG, Knowles PP, Nans A, Briggs DC, Borg A, Earl CP, Goodman KM, Nawrotek A, Borg AJ, McIntosh PB, Houghton FM, Kjær S, McDonald NQ. A two-site flexible clamp mechanism for RET-GDNF-GFRα1 assembly reveals both conformational adaptation and strict geometric spacing. Structure 2021; 29:694-708.e7. [PMID: 33484636 PMCID: PMC8266384 DOI: 10.1016/j.str.2020.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/13/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 11/04/2022]
Abstract
RET receptor tyrosine kinase plays vital developmental and neuroprotective roles in metazoans. GDNF family ligands (GFLs) when bound to cognate GFRα co-receptors recognize and activate RET stimulating its cytoplasmic kinase function. The principles for RET ligand-co-receptor recognition are incompletely understood. Here, we report a crystal structure of the cadherin-like module (CLD1-4) from zebrafish RET revealing interdomain flexibility between CLD2 and CLD3. Comparison with a cryo-electron microscopy structure of a ligand-engaged zebrafish RETECD-GDNF-GFRα1a complex indicates conformational changes within a clade-specific CLD3 loop adjacent to the co-receptor. Our observations indicate that RET is a molecular clamp with a flexible calcium-dependent arm that adapts to different GFRα co-receptors, while its rigid arm recognizes a GFL dimer to align both membrane-proximal cysteine-rich domains. We also visualize linear arrays of RETECD-GDNF-GFRα1a suggesting that a conserved contact stabilizes higher-order species. Our study reveals that ligand-co-receptor recognition by RET involves both receptor plasticity and strict spacing of receptor dimers by GFL ligands.
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Affiliation(s)
- Sarah E Adams
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT London, UK
| | - Phillip P Knowles
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT London, UK
| | - David C Briggs
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Annabel Borg
- Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT London, UK
| | - Christopher P Earl
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Kerry M Goodman
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Agata Nawrotek
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Aaron J Borg
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, NW1 1AT London, UK
| | - Pauline B McIntosh
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francesca M Houghton
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT London, UK
| | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK; Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
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4
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Morris ER, Kunzelmann S, Caswell SJ, Purkiss AG, Kelly G, Taylor IA. Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p- and S p-dNTPαS Diastereomers. Biochemistry 2021; 60:1682-1698. [PMID: 33988981 PMCID: PMC8173608 DOI: 10.1021/acs.biochem.0c00944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in CD4+ myeloid lineage and resting T-cells. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome (AGS) and certain cancers. More recently, SAMHD1 has been linked to anticancer drug resistance and the suppression of the interferon response to cytosolic nucleic acids after DNA damage. Here, we probe dNTP hydrolysis and inhibition of SAMHD1 using the Rp and Sp diastereomers of dNTPαS nucleotides. Our biochemical and enzymological data show that the α-phosphorothioate substitution in Sp-dNTPαS but not Rp-dNTPαS diastereomers prevents Mg2+ ion coordination at both the allosteric and catalytic sites, rendering SAMHD1 unable to form stable, catalytically active homotetramers or hydrolyze substrate dNTPs at the catalytic site. Furthermore, we find that Sp-dNTPαS diastereomers competitively inhibit dNTP hydrolysis, while Rp-dNTPαS nucleotides stabilize tetramerization and are hydrolyzed with similar kinetic parameters to cognate dNTPs. For the first time, we present a cocrystal structure of SAMHD1 with a substrate, Rp-dGTPαS, in which an Fe-Mg-bridging water species is poised for nucleophilic attack on the Pα. We conclude that it is the incompatibility of Mg2+, a hard Lewis acid, and the α-phosphorothioate thiol, a soft Lewis base, that prevents the Sp-dNTPαS nucleotides coordinating in a catalytically productive conformation. On the basis of these data, we present a model for SAMHD1 stereospecific hydrolysis of Rp-dNTPαS nucleotides and for a mode of competitive inhibition by Sp-dNTPαS nucleotides that competes with formation of the enzyme-substrate complex.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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5
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Gori I, George R, Purkiss AG, Strohbuecker S, Randall RA, Ogrodowicz R, Carmignac V, Faivre L, Joshi D, Kjær S, Hill CS. Mutations in SKI in Shprintzen-Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization. eLife 2021; 10:e63545. [PMID: 33416497 PMCID: PMC7834018 DOI: 10.7554/elife.63545] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Shprintzen-Goldberg syndrome (SGS) is a multisystemic connective tissue disorder, with considerable clinical overlap with Marfan and Loeys-Dietz syndromes. These syndromes have commonly been associated with enhanced TGF-β signaling. In SGS patients, heterozygous point mutations have been mapped to the transcriptional co-repressor SKI, which is a negative regulator of TGF-β signaling that is rapidly degraded upon ligand stimulation. The molecular consequences of these mutations, however, are not understood. Here we use a combination of structural biology, genome editing, and biochemistry to show that SGS mutations in SKI abolish its binding to phosphorylated SMAD2 and SMAD3. This results in stabilization of SKI and consequently attenuation of TGF-β responses, both in knockin cells expressing an SGS mutation and in fibroblasts from SGS patients. Thus, we reveal that SGS is associated with an attenuation of TGF-β-induced transcriptional responses, and not enhancement, which has important implications for other Marfan-related syndromes.
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Affiliation(s)
- Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Roger George
- Structural Biology Facility, The Francis Crick InstituteLondonUnited Kingdom
| | - Andrew G Purkiss
- Structural Biology Facility, The Francis Crick InstituteLondonUnited Kingdom
| | - Stephanie Strohbuecker
- Bioinformatics and Biostatistics Facility, The Francis Crick InstituteLondonUnited Kingdom
| | - Rebecca A Randall
- Developmental Signalling Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Roksana Ogrodowicz
- Structural Biology Facility, The Francis Crick InstituteLondonUnited Kingdom
| | | | - Laurence Faivre
- INSERM - Université de Bourgogne UMR1231 GAD, FHU-TRANSLADDijonFrance
| | - Dhira Joshi
- Peptide Chemistry Facility, The Francis Crick InstituteLondonUnited Kingdom
| | - Svend Kjær
- Structural Biology Facility, The Francis Crick InstituteLondonUnited Kingdom
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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6
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Morris ER, Caswell SJ, Kunzelmann S, Arnold LH, Purkiss AG, Kelly G, Taylor IA. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nat Commun 2020; 11:3165. [PMID: 32576829 PMCID: PMC7311409 DOI: 10.1038/s41467-020-16983-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,AstraZeneca, 50F49, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Laurence H Arnold
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Pelago Bioscience, Banvaktsvägen 20, 171 48, Solna, Sweden
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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7
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Dagil R, Ball NJ, Ogrodowicz RW, Hobor F, Purkiss AG, Kelly G, Martin SR, Taylor IA, Ramos A. IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties. Nucleic Acids Res 2019; 47:4334-4348. [PMID: 30864660 PMCID: PMC6486635 DOI: 10.1093/nar/gkz136] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 02/25/2019] [Indexed: 11/27/2022] Open
Abstract
IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinatorial action of multiple RNA-binding domains. Here, we dissect the structure and RNA-binding properties of two key RNA-binding domains of IMP1, KH1 and KH2, and we build a kinetic model for the recognition of RNA targets. Our data and model explain how the two domains are organized as an intermolecular pseudo-dimer and that the important role they play in mRNA target recognition is underpinned by the high RNA-binding affinity and fast kinetics of this KH1KH2-RNA recognition unit. Importantly, the high-affinity RNA-binding by KH1KH2 is achieved by an inter-domain coupling 50-fold stronger than that existing in a second pseudo-dimer in the protein, KH3KH4. The presence of this strong coupling supports a role of RNA re-modelling in IMP1 recognition of known cancer targets.
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Affiliation(s)
- Robert Dagil
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6XA, UK
| | - Neil J Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Roksana W Ogrodowicz
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fruzsina Hobor
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6XA, UK
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6XA, UK
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8
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Chao WCH, Wade BO, Bouchoux C, Jones AW, Purkiss AG, Federico S, O’Reilly N, Snijders AP, Uhlmann F, Singleton MR. Structural Basis of Eco1-Mediated Cohesin Acetylation. Sci Rep 2017; 7:44313. [PMID: 28290497 PMCID: PMC5349539 DOI: 10.1038/srep44313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
Sister-chromatid cohesion is established by Eco1-mediated acetylation on two conserved tandem lysines in the cohesin Smc3 subunit. However, the molecular basis of Eco1 substrate recognition and acetylation in cohesion is not fully understood. Here, we discover and rationalize the substrate specificity of Eco1 using mass spectrometry coupled with in-vitro acetylation assays and crystallography. Our structures of the X. laevis Eco2 (xEco2) bound to its primary and secondary Smc3 substrates demonstrate the plasticity of the substrate-binding site, which confers substrate specificity by concerted conformational changes of the central β hairpin and the C-terminal extension.
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Affiliation(s)
- William C. H. Chao
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin O. Wade
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew W. Jones
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew G. Purkiss
- Structural Biology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefania Federico
- Peptide Chemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicola O’Reilly
- Peptide Chemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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9
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Chao WCH, Murayama Y, Muñoz S, Jones AW, Wade BO, Purkiss AG, Hu XW, Borg A, Snijders AP, Uhlmann F, Singleton MR. Structure of the cohesin loader Scc2. Nat Commun 2017; 8:13952. [PMID: 28059076 PMCID: PMC5227109 DOI: 10.1038/ncomms13952] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
The functions of cohesin are central to genome integrity, chromosome organization and transcription regulation through its prevention of premature sister-chromatid separation and the formation of DNA loops. The loading of cohesin onto chromatin depends on the Scc2-Scc4 complex; however, little is known about how it stimulates the cohesion-loading activity. Here we determine the large 'hook' structure of Scc2 responsible for catalysing cohesin loading. We identify key Scc2 surfaces that are crucial for cohesin loading in vivo. With the aid of previously determined structures and homology modelling, we derive a pseudo-atomic structure of the full-length Scc2-Scc4 complex. Finally, using recombinantly purified Scc2-Scc4 and cohesin, we performed crosslinking mass spectrometry and interaction assays that suggest Scc2-Scc4 uses its modular structure to make multiple contacts with cohesin.
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Affiliation(s)
- William C. H. Chao
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yasuto Murayama
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew W. Jones
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin O. Wade
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew G. Purkiss
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Xiao-Wen Hu
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aaron Borg
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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10
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Newton R, Bowler KA, Burns EM, Chapman PJ, Fairweather EE, Fritzl SJR, Goldberg KM, Hamilton NM, Holt SV, Hopkins GV, Jones SD, Jordan AM, Lyons AJ, Nikki March H, McDonald NQ, Maguire LA, Mould DP, Purkiss AG, Small HF, Stowell AIJ, Thomson GJ, Waddell ID, Waszkowycz B, Watson AJ, Ogilvie DJ. The discovery of 2-substituted phenol quinazolines as potent RET kinase inhibitors with improved KDR selectivity. Eur J Med Chem 2016; 112:20-32. [PMID: 26874741 PMCID: PMC4896931 DOI: 10.1016/j.ejmech.2016.01.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 12/11/2022]
Abstract
Deregulation of the receptor tyrosine kinase RET has been implicated in medullary thyroid cancer, a small percentage of lung adenocarcinomas, endocrine-resistant breast cancer and pancreatic cancer. There are several clinically approved multi-kinase inhibitors that target RET as a secondary pharmacology but additional activities, most notably inhibition of KDR, lead to dose-limiting toxicities. There is, therefore, a clinical need for more specific RET kinase inhibitors. Herein we report our efforts towards identifying a potent and selective RET inhibitor using vandetanib 1 as the starting point for structure-based drug design. Phenolic anilinoquinazolines exemplified by 6 showed improved affinities towards RET but, unsurprisingly, suffered from high metabolic clearance. Efforts to mitigate the metabolic liability of the phenol led to the discovery that a flanking substituent not only improved the hepatocyte stability, but could also impart a significant gain in selectivity. This culminated in the identification of 36; a potent RET inhibitor with much improved selectivity against KDR.
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Affiliation(s)
- Rebecca Newton
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK.
| | - Katherine A Bowler
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Emily M Burns
- Structural Biology Laboratory, Cancer Research UK London Research Institute, London, WC2A 3LY, England, UK
| | - Philip J Chapman
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Emma E Fairweather
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Samantha J R Fritzl
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Kristin M Goldberg
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Niall M Hamilton
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Sarah V Holt
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Gemma V Hopkins
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Stuart D Jones
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Allan M Jordan
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Amanda J Lyons
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - H Nikki March
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Neil Q McDonald
- Structural Biology Laboratory, Cancer Research UK London Research Institute, London, WC2A 3LY, England, UK; Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, England, UK
| | - Laura A Maguire
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Daniel P Mould
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Andrew G Purkiss
- Structural Biology Laboratory, Cancer Research UK London Research Institute, London, WC2A 3LY, England, UK
| | - Helen F Small
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Alexandra I J Stowell
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Graeme J Thomson
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Ian D Waddell
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Bohdan Waszkowycz
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Amanda J Watson
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
| | - Donald J Ogilvie
- Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK
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11
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Ivanova ME, Fletcher GC, O’Reilly N, Purkiss AG, Thompson BJ, McDonald NQ. Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove. Acta Crystallogr D Biol Crystallogr 2015; 71:555-64. [PMID: 25760605 PMCID: PMC4356366 DOI: 10.1107/s139900471402776x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 12/21/2022]
Abstract
Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein-protein interaction.
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Affiliation(s)
- Marina E. Ivanova
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Georgina C. Fletcher
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Nicola O’Reilly
- Peptide Chemistry Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Andrew G. Purkiss
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Barry J. Thompson
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Neil Q. McDonald
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England
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12
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Goodman KM, Kjær S, Beuron F, Knowles PP, Nawrotek A, Burns EM, Purkiss AG, George R, Santoro M, Morris EP, McDonald NQ. RET recognition of GDNF-GFRα1 ligand by a composite binding site promotes membrane-proximal self-association. Cell Rep 2014; 8:1894-1904. [PMID: 25242331 DOI: 10.1016/j.celrep.2014.08.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 06/13/2014] [Revised: 08/04/2014] [Accepted: 08/17/2014] [Indexed: 11/20/2022] Open
Abstract
The RET receptor tyrosine kinase is essential to vertebrate development and implicated in multiple human diseases. RET binds a cell surface bipartite ligand comprising a GDNF family ligand and a GFRα coreceptor, resulting in RET transmembrane signaling. We present a hybrid structural model, derived from electron microscopy (EM) and low-angle X-ray scattering (SAXS) data, of the RET extracellular domain (RET(ECD)), GDNF, and GFRα1 ternary complex, defining the basis for ligand recognition. RET(ECD) envelopes the dimeric ligand complex through a composite binding site comprising four discrete contact sites. The GFRα1-mediated contacts are crucial, particularly close to the invariant RET calcium-binding site, whereas few direct contacts are made by GDNF, explaining how distinct ligand/coreceptor pairs are accommodated. The RET(ECD) cysteine-rich domain (CRD) contacts both ligand components and makes homotypic membrane-proximal interactions occluding three different antibody epitopes. Coupling of these CRD-mediated interactions suggests models for ligand-induced RET activation and ligand-independent oncogenic deregulation.
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Affiliation(s)
- Kerry M Goodman
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Svend Kjær
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; Protein Purification Facility, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Phillip P Knowles
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Agata Nawrotek
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Emily M Burns
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Andrew G Purkiss
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Roger George
- Protein Purification Facility, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Massimo Santoro
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università di Napoli Federico II, via S. Pansini 5, 80131 Naples, Italy
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Neil Q McDonald
- Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
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13
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Kappé G, Purkiss AG, van Genesen ST, Slingsby C, Lubsen NH. Erratum to: Explosive Expansion of βγ-Crystallin Genes in the Ancestral Vertebrate. J Mol Evol 2010. [PMCID: PMC3462978 DOI: 10.1007/s00239-010-9387-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Guido Kappé
- Biomolecular Chemistry 271, NCMLS, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Andrew G. Purkiss
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London, WC1E 7HX UK
| | - Siebe T. van Genesen
- Biomolecular Chemistry 271, NCMLS, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Christine Slingsby
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London, WC1E 7HX UK
| | - Nicolette H. Lubsen
- Biomolecular Chemistry 271, NCMLS, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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14
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Purkiss AG, Bateman OA, Wyatt K, Wilmarth PA, David LL, Wistow GJ, Slingsby C. Biophysical properties of gammaC-crystallin in human and mouse eye lens: the role of molecular dipoles. J Mol Biol 2007; 372:205-22. [PMID: 17659303 PMCID: PMC2034304 DOI: 10.1016/j.jmb.2007.06.049] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/18/2007] [Accepted: 06/20/2007] [Indexed: 11/22/2022]
Abstract
The eye lens is packed with soluble crystallin proteins, providing a lifetime of transparency and light refraction. gamma-Crystallins are major components of the dense, high refractive index central regions of the lens and generally have high solubility, high stability and high levels of cysteine residues. Human gammaC belongs to a group of gamma-crystallins with a pair of cysteine residues at positions 78 and 79. Unlike other gamma-crystallins it has relatively low solubility, whereas mouse gammaC, which has the exposed C79 replaced with arginine, and a novel mouse splice variant, gammaCins, are both highly soluble. Furthermore, human gammaC is extremely stable, while the mouse orthologs are less stable. Evolutionary pressure may have favoured stability over solubility for human gammaC and the reverse for the orthologs in the mouse. Mutation of C79 to R79, in human gammaC, greatly increased solubility, however, neither form produced crystals. Remarkably, when the human gammaD R36S crystallization cataract mutation was mimicked in human gammaC-crystallin, the solubility of gammaC was dramatically increased, although it still did not crystallize. The highly soluble mouse gammaC-crystallin did crystallize. Its X-ray structure was solved and used in homology modelling of human gammaC, and its mutants C79R and R36S. The human gammaD R36S mutant was also modelled from human gammaD coordinates. Molecular dynamics simulation of the six molecules in the solution state showed that the human gammaCs differed from gammaDs in domain pairing, behaviour that correlates with interface sequence changes. When the fluctuations of the calculated molecular dipoles, for the six structures, over time were analysed, characteristic patterns for soluble gammaC and gammaD proteins were observed. Individual sequence changes that increase or decrease solubility correlated well with changes in the magnitude and direction of these dipoles. It is suggested that changes in surface residues have allowed adaptation for the differing needs of human and mouse lenses.
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Affiliation(s)
- Andrew G Purkiss
- Birkbeck College, Department of Crystallography, Institute of Structural Molecular Biology, University of London, Malet Street, London, UK
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15
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Shimeld SM, Purkiss AG, Dirks RPH, Bateman OA, Slingsby C, Lubsen NH. Urochordate betagamma-crystallin and the evolutionary origin of the vertebrate eye lens. Curr Biol 2006; 15:1684-9. [PMID: 16169492 DOI: 10.1016/j.cub.2005.08.046] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [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: 05/25/2005] [Revised: 08/05/2005] [Accepted: 08/09/2005] [Indexed: 11/22/2022]
Abstract
A refracting lens is a key component of our image-forming camera eye; however, its evolutionary origin is unknown because precursor structures appear absent in nonvertebrates. The vertebrate betagamma-crystallin genes encode abundant structural proteins critical for the function of the lens. We show that the urochordate Ciona intestinalis, which split from the vertebrate lineage before the evolution of the lens, has a single gene coding for a single domain monomeric betagamma-crystallin. The crystal structure of Ciona betagamma-crystallin is very similar to that of a vertebrate betagamma-crystallin domain, except for paired, occupied calcium binding sites. The Ciona betagamma-crystallin is only expressed in the palps and in the otolith, the pigmented sister cell of the light-sensing ocellus. The Ciona betagamma-crystallin promoter region targeted expression to the visual system, including lens, in transgenic Xenopus tadpoles. We conclude that the vertebrate betagamma-crystallins evolved from a single domain protein already expressed in the neuroectoderm of the prevertebrate ancestor. The conservation of the regulatory hierarchy controlling betagamma-crystallin expression between organisms with and without a lens shows that the evolutionary origin of the lens was based on co-option of pre-existing regulatory circuits controlling the expression of a key structural gene in a primitive light-sensing system.
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Affiliation(s)
- Sebastian M Shimeld
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, United Kingdom.
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16
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MacDonald JT, Purkiss AG, Smith MA, Evans P, Goodfellow JM, Slingsby C. Unfolding crystallins: the destabilizing role of a beta-hairpin cysteine in betaB2-crystallin by simulation and experiment. Protein Sci 2005; 14:1282-92. [PMID: 15840832 PMCID: PMC2253261 DOI: 10.1110/ps.041227805] [Citation(s) in RCA: 24] [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: 10/25/2022]
Abstract
The thermodynamic and kinetic stabilities of the eye lens family of betagamma-crystallins are important factors in the etiology of senile cataract. They control the chance of proteins unfolding, which can lead to aggregation and loss of transparency. betaB2-Crystallin orthologs are of low stability and comprise two typical betagamma-crystallin domains, although, uniquely, the N-terminal domain has a cysteine in one of the conserved folded beta-hairpins. Using high-temperature (500 K) molecular dynamics simulations with explicit solvent on the N-terminal domain of rodent betaB2-crystallin, we have identified in silico local flexibility in this folded beta-hairpin. We have shown in vitro using two-domain human betaB2-crystallin that replacement of this cysteine with a more usual aromatic residue (phenylalanine) results in a gain in conformational stability and a reduction in the rate of unfolding. We have used principal components analysis to visualize and cluster the coordinates from eight separate simulated unfolding trajectories of both the wild-type and the C50F mutant N-terminal domains. These data, representing fluctuations around the native well, show that although the mutant and wild-type appear to behave similarly over the early time period, the wild type appears to explore a different region of conformational space. It is proposed that the advantage of having this low-stability cysteine may be correlated with a subunit-exchange mechanism that allows betaB2-crystallin to interact with a range of other beta-crystallin subunits.
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Affiliation(s)
- James T MacDonald
- School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK
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17
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Fan J, Fariss RN, Purkiss AG, Slingsby C, Sandilands A, Quinlan R, Wistow G, Chepelinsky AB. Specific interaction between lens MIP/Aquaporin-0 and two members of the gamma-crystallin family. Mol Vis 2005; 11:76-87. [PMID: 15692460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
PURPOSE Major Intrinsic Protein (MIP)/Aquaporin 0 is required for lens transparency and is specifically expressed in lens fiber cell membranes. We have demonstrated previously that in the rat lens MIP interacts specifically with gammaE-crystallin, resulting in its recruitment to the plasma membrane. Our goal was to examine the interaction or lack of interaction between MIP and all members of the gamma-crystallin family and to provide evidence for a physiological role these interactions may play in gamma-crystallin or MIP function. METHODS Full length MIP was expressed as untagged, enhanced green fluorescent protein (EGFP) tagged, or myc tagged proteins. Members of the gamma-crystallin family were expressed as red fluorescent protein (HcRed) tagged proteins in the rabbit kidney epithelial cell line RK13. Co-localization of tagged proteins was analyzed by confocal fluorescence microscopy. RESULTS Confocal fluorescence microscopy demonstrated that gammaE- and gammaF-crystallin co-localize specifically with full length MIP in mammalian cells while other gamma-crystallins, including gammaA-, gammaB-, gammaC-, gammaD-, and gammaS-crystallin do not. As a result of this interaction, either gammaE- or gammaF-crystallin was recruited to the plasma membrane from the cytoplasm. MIP does not interact with the Elo mutant of gammaE-crystallin, which has been linked to a dominant cataract phenotype in mice. CONCLUSIONS These experiments demonstrate that MIP interacts selectively with gammaE- and gammaF-crystallin, and not with other gamma-crystallins. This raises the possibility of MIP playing a structural role in the organization of gamma-crystallins in rodent lens fibers and/or that gammaE- and gammaF-crystallin may have a specific role in MIP function in the rodent lens.
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Affiliation(s)
- Jianguo Fan
- Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-0704, USA.
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18
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Abstract
Molecular models of human gamma-crystallins and the 'alpha-crystallin domain' of human alphaA-crystallin have been built based on available related X-ray crystal structures. The accessibilities of the component cysteine, methionine and tryptophan side chains in the crystallin models have been calculated. The reactivities of these cysteines, which are oxidised in cataract, are assessed based on their known modifications and within the context of their location within the 3D models.
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Affiliation(s)
- Durga Srikanthan
- Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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19
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Bateman OA, Purkiss AG, van Montfort R, Slingsby C, Graham C, Wistow G. Crystal structure of eta-crystallin: adaptation of a class 1 aldehyde dehydrogenase for a new role in the eye lens. Biochemistry 2003; 42:4349-56. [PMID: 12693930 DOI: 10.1021/bi027367w] [Citation(s) in RCA: 23] [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: 11/29/2022]
Abstract
Eta-crystallin is a retinal dehydrogenase that has acquired a role as a structural protein in the eye lens of elephant shrews, members of an ancient order of mammals. While it retains some activity toward retinal, which is oxidized to retinoic acid, the protein has acquired a number of specific sequence changes that have presumably been selected to enhance the lens role. The crystal structure of eta-crystallin, in common with class 1 and 2 ALDHs, is a dimer of dimers. It has a better-defined NAD binding site than those of related mammalian ALDH1 enzymes with the cofactor bound in the "hydride transfer" position in all four monomers with small differences about the dimer dyads. Although the active site is well conserved, the substrate-binding site is larger in eta-crystallin, and there are some mutations to the substrate access tunnel that might affect binding or release of substrate and product. It is possible that eta-crystallin has lost flexibility to improve its role in the lens. Enhanced binding of cofactor could enable it to act as a UV/blue light filter in the lens, improving visual acuity. The structure not only gives a view of a "natural mutant" of ALDH1 illustrating the adaptive conflict that can arise in multifunctional proteins, but also provides a well-ordered NAD binding site structure for this class of enzymes with important roles in development and health.
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Affiliation(s)
- O A Bateman
- Birkbeck College, School of Crystallography, Malet Street, London WC1E 7HX, UK
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Abstract
A major component of human nuclear cataracts is water-insoluble, high molecular weight protein. A significant component of this protein is disulfide bonded gamma S-crystallin that can be reduced to monomers by dithiothreitol. Analysis of this reduced gamma S-crystallin showed that deamidation of glutamine and asparagine residues is a principal modification. Deamidation is one of the modifications of lens crystallins associated with aging and cataractogenesis. One proposed hypothesis of cataractogenesis is that it develops in response to altered surface charges that cause conformational changes, which, in turn, permit formation of disulfide bonds and crystallin insolubility. This report, showing deamidation among the disulfide bonded gamma S-crystallins from cataractous lenses, supports this hypothesis.
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Affiliation(s)
- Veniamin N Lapko
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, USA
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21
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Abstract
gammaS-crystallin is a major human lens protein found in the outer region of the eye lens, where the refractive index is low. Because crystallins are not renewed they acquire post-translational modifications that may perturb stability and solubility. In common with other members of the betagamma-crystallin superfamily, gammaS-crystallin comprises two similar beta-sheet domains. The crystal structure of the C-terminal domain of human gammaS-crystallin has been solved at 2.4 A resolution. The structure shows that in the in vitro expressed protein, the buried cysteines remain reduced. The backbone conformation of the "tyrosine corner" differs from that of other betagamma-crystallins because of deviation from the consensus sequence. The two C-terminal domains in the asymmetric unit are organized about a slightly distorted 2-fold axis to form a dimer with similar geometry to full-length two-domain family members. Two glutamines found in lattice contacts may be important for short range interactions in the lens. An asparagine known to be deamidated in human cataract is located in a highly ordered structural region.
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Affiliation(s)
- Andrew G Purkiss
- School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom .
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22
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Goodfellow JM, Purkiss AG, Slingsby C. Simulation of the highly stable protein: bovine γb-crystallin at room and high temperature. Protein Pept Lett 2000. [DOI: 10.2174/092986650704221206152154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract:
The behavior of the eye-lens protein bovine γB-crystallin is investigated at both room temperature and at an elevated temperature (at which unfolding would be expected to occur) using molecular dynamics. Even in the high temperature simulation, there is little loss ·of secondary structure. Although only small changes in the tertiary contacts occur, even at high temperature, fluctuations in conformation are much more pronounced at 500K than 300K. These results agree with the experimental observations on the remarkable stability of the eye lens proteins and also indicate where the initial events in unfolding are occurring.
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Affiliation(s)
- Julia M. Goodfellow
- Department of Crystallography, Birkbeck College, University of London, Malet Street, London,
WCIE 7HX, UK
| | - Andrew G. Purkiss
- Department of Crystallography, Birkbeck College, University of London, Malet Street, London,
WCIE 7HX, UK
| | - Christine Slingsby
- Department of Crystallography, Birkbeck College, University of London, Malet Street, London,
WCIE 7HX, UK
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Abstract
INTRODUCTION We propose that the increase in TNF-alpha and IL-6 in the brain in idiopathic parkinsonism is in response to a peripheral immune/ inflammatory process, so ubiquitous as to be responsible for the resemblance between ageing and parkinsonism. METHODS Circulating cytokine was measured in 78 subjects with idiopathic parkinsonism and 140 without, aged 30 to 90 years, all obeying inclusion/exclusion criteria. RESULTS Serum TNF-alpha increased (P<0.0001) by 1.37 (95% CI 0.75, 2.00)% x y(-1), IL-6 by 2.63 (1.75, 3.52) (P<0.0005). TNF-alpha appeared elevated in parkinsonians whose postural and psychomotor responses were abnormal, being suppressed where they were normal: trends which contrasted with those in controls (P = 0.015 and 0.05, respectively). Parkinsonism appeared (P = 0.08) to have an effect on IL-6, equivalent to that of >10 years of ageing (28(-3, 69)%), but was not immediately related to between-subject differences in performance. CONCLUSION Ageing and pathogenetic insult may be confounded, age being a progression, not a risk, factor.
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Affiliation(s)
- R J Dobbs
- Therapeutics in the Elderly, Research Group, The Hillingdon Hospital Postgraduate and Research Centre, Uxbridge, Hatfield, Hertfordshire, UK
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Abstract
INTRODUCTION We propose an active pathogenic mechanism, involving circulating cortisol, in parkinsonism. MATERIALS AND METHODS Serum cortisol was measured in 96 subjects with idiopathic parkinsonism, 170 without, and in 17 spouses and 36 siblings of elderly sufferers with double the number of controls, all obeying inclusion/exclusion criteria. RESULTS Cortisol, adjusted for sampling time, was greater (17%, on average, P<0.001) in parkinsonians, but not in relatives. The central cortisol lowering effect of anti-muscarinics was seen (P=0.025). Selegiline may attenuate the disease, and parkinsonism is less frequent in tobacco smokers. Selegiline was associated with a lower cortisol (P=0.03): chronic smoking appeared (P=0.08) to be, irrespective of parkinsonism. Bowel stasis has been implicated in the pathogenesis: cortisol was higher in parkinsonians requiring laxatives (P=0.05). In controls, cortisol was lower, the longer the stride (P=0.02): in parkinsonians, this relationship was numerically reversed. A similar (P=0.01) group performance interaction was seen for deterioration, over 4 years, in gait. CONCLUSION Cortisol is doing harm or mirroring something which is. A common pathway for neuronal protection/rescue emerges.
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Affiliation(s)
- A Charlett
- Statistics Unit, Public Health Laboratories Service, London, UK
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Abstract
BACKGROUND The effect of healthy ageing and of parkinsonism on breadth of base whilst walking had not been adequately documented. DESIGN Height-specific reference ranges for mean foot separation at mid-swing were derived for males and females, age not proving to be a significant influence. METHOD Normative data were obtained from 164 healthy volunteers, and foot separation in idiopathic parkinsonism (99 patients) was characterized by comparison. RESULTS Parkinsonism was associated with significantly greater within- and between-subject variability in foot separation. There was a linear trend from increased separation in those with bilateral signs but little functional impairment, to decreased separation in the severely impaired but not yet chair or bed bound. Foot separation was best explained by two clinical signs, rigidity and anatomical postural abnormality. A flexed posture was associated with increased separation, rigidity with decreased, the separation manifested being determined by the net effect. CONCLUSION In early idiopathic parkinsonism, falling may depend on abnormal posture, and increased breadth of base be compensatory. Later, the decrement in foot separation may become a primary determinant of falls.
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Affiliation(s)
- A Charlett
- Medical Statistics Unit, Public Health Laboratories Service, London, UK
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26
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Kirollos C, Charlett A, O'Neill CJ, Kosik R, Mozol K, Purkiss AG, Bowes SG, Nicholson PW, Hunt WB, Weller C, Dobbs SM, Dobbs RJ. Objective measurement of activation of rigidity: diagnostic, pathogenetic and therapeutic implications in parkinsonism. Br J Clin Pharmacol 1996; 41:557-64. [PMID: 8799522 PMCID: PMC2042619 DOI: 10.1046/j.1365-2125.1996.38313.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
1. Quantification of the effect on rigidity of its 'activation', by isometric grip, of standardized pressure, of the contralateral hand, was explored. Torque required to move the forearm through a fixed angle of 40 degrees, at a controlled rate of 0.5 Hz, in a horizontal plane about a pivotal axis aligned to the elbow joint, was recorded before (12 'baseline' recordings), during (10), and after (> or = 8) activation. Work required per unit displacement was calculated. 2. Specificity: Pilot serial daytime measurements gave an overall mean ratio, work required on activation over baseline, of 2.94 (95% CI 2.53, 3.42) in two elderly untreated parkinsonians, and 3.19 (2.75, 3.71) in two elderly subjects with isolated, clinically activation phenomenon, compared with 1.90 (1.64, 2.21) in two elderly without (P < 0.001), whilst two young adults did not activate, 0.98 (0.85, 1.14). In elderly subjects, work required under activation decreased during the day in health (-10 (-5, -14)% h-1, P = 0.0002), showed no significant change in those with clinical activation (4 (-1, 9)% h-1), and increased in parkinsonians (6 (0, 12)% h-1, P = 0.05): there appeared to be a transitionary state. 3. Validation of methodology: Quantifying the same work ratio on a single occasion in 20 aged parkinsonians (P), their spouses (Ps), 20 index controls (C) without parkinsonism, matched to (P), and their spouses (Cs) gave corroborative evidence of a pre-clinical state, defined by other measurements, in the spouses of sufferers. Values for C, Cs and Ps, 1.89 (1.42, 2.52), 2.38 (1.79, 3.17) and 2.93 (2.20, 3.90) respectively, were in consecutive positions, from health to (P, 2.96 (2.22, 3.95)) disease (P = 0.001 for Ps c.f. C; P = 0.1 for Ps c.f. Cs). Data on change over the day may enhance discrimination. 4. Sensitivity to medicines was illustrated, in two parkinsonians, by randomised, placebo balanced and controlled challenges: 1 and 2 tablets, Sinemet CR (Du Pont Pharmaceuticals, each levodopa 200 mg/carbidopa 50 mg) and 1 tablet, Sinemet-Plus (levodopa 100 mg/carbidopa 25 mg), then two 2 mg tablets, benzhexol. The dopaminergic effect (P < 0.001) was selective for activation (treatment.test-condition interaction, P = 0.004), and showed the expected time profiles. The effect of benzhexol (P = 0.008) lacked such selectivity. Its onset (> 4, < or = 6 h) was delayed, compatible with a gastrointestinal anti-muscarinic action and the subjects' ages. 5. Reliability (Fleiss's criterion) was shown to be good in 30 untreated parkinsonians.
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Affiliation(s)
- C Kirollos
- Therapeutics in the Elderly, Hillingdon Hospital, Uxbridge, UK
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27
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Kirollos C, Charlett A, Bowes SG, Purkiss AG, O'Neill CJ, Weller C, Dickins J, Faulkner G, Nicholson PW, Hunt WB, Dobbs RJ, Dobbs SM. Time course of physical and psychological responses to selegiline monotherapy in newly diagnosed, idiopathic parkinsonism. Eur J Clin Pharmacol 1996; 50:7-18. [PMID: 8739805 DOI: 10.1007/s002280050062] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RATIONALE Poor specificity of face-value endpoints and the poor sensitivity of gross clinical examination may have militated against demonstrating prophylaxis by selegiline. METHODS Objective measures of the four cardinal signs were used as primary outcome criteria in a randomised, double-blind, placebo-controlled, parallel group study of selegiline monotherapy in 25 newly diagnosed elderly sufferers from idiopathic parkinsonism, stratified for sex and Hoehn and Yahr functional staging. RESULTS There was a significant interaction between time and nature of treatment with respect to rigidity. The effect of time during active treatment was highly significant: rigidity decreased by 1.3% per week. The worsening of rigidity on placebo was not statistically significant. Neuronal rescue is a possible explanation for the long term, progressive improvement produced by selegiline. No significant treatment effect was seen on the other cardinal signs. However, there was a significant quadratic time trend for arousal on active treatment suggesting tolerance to this effect. CONCLUSION The difference in time course between the psychostimulant and physical effects suggests more than one mode of action.
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Affiliation(s)
- C Kirollos
- Hillingdon Hospital, Uxbridge, Middlesex, UK
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28
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O'Neill CJ, Richardson MD, Charlett A, McHugh L, Bowes SG, Purkiss AG, Weller C, Dobbs SM, Dobbs RJ. Could seborrhoeic dermatitis be implicated in the pathogenesis of parkinsonism? Acta Neurol Scand 1994; 89:252-7. [PMID: 8042441 DOI: 10.1111/j.1600-0404.1994.tb01675.x] [Citation(s) in RCA: 17] [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: 01/28/2023]
Abstract
The spouses of a group of aged sufferers have been demonstrated to have multifarious differences relevant to parkinsonism from matched controls, which were difficult to explain by selective mating, learned or reactive behaviour. Could parkinsonism be transmissible? The frequency of inflammation and scaling on head or neck was greater (P = 0.05) in these spouses (19 available) than in controls (36), the best discriminating site of inflammation being scalp (P = 0.02). Both seborrhoeic dermatitis and overt, or pre-clinical, parkinsonism occurred in sufferers and spouses: to presume they are not causally related is to accept multiple entities. In favour of seborrhoeic dermatitis being causal for parkinsonism, rather than vice versa, is the involvement of a known organism, Pityrosporum ovale, in the dermatitis, and that the evidence of parkinsonism in the spouses indicated that they were only part way down the path towards the clinical condition.
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Affiliation(s)
- C J O'Neill
- Hillingdon Hospital, Uxbridge, Middlesex, England
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Kirollos C, O'Neill CJ, Dobbs RJ, Charlett A, Bowes SG, Weller C, Purkiss AG, Hunt WB, Dobbs SM. Quantification of the cardinal signs of parkinsonism and of associated disability in spouses of sufferers. Age Ageing 1993; 22:20-6. [PMID: 8438661 DOI: 10.1093/ageing/22.1.20] [Citation(s) in RCA: 21] [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] [Indexed: 01/30/2023] Open
Abstract
Work on the causation of idiopathic parkinsonism is limited by relying on gross clinical definition and lack of studies in the old. A prognostic index for parkinsonism, based on hypo/bradykinesia of gait, had considerably higher values in spouses of 20 aged suffers, who had been cohabiting for about half a century, than in 40 controls. Postural abnormality, measured by standing sway and foot separation during walking, was also greater in these spouses. Marked differences remained after correction for relevant covariates. A blinded rigidity rating was greater in the spouses of sufferers, tremor rating was not. The differences found are difficult to explain by selective mating, learned or reactive behaviour. This suggests that environmental causative influences operate in adult life.
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Affiliation(s)
- C Kirollos
- Research Group, Northwick Park Hospital, Harrow, Middlesex
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30
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Bowes SG, Dobbs RJ, Henley M, Charlett A, O'Neill CJ, Nicholson PW, Purkiss AG, Weller C, Dobbs SM. Objective evidence for tolerance, against a background of improvement, during maintenance therapy with controlled release levodopa/carbidopa. Eur J Clin Pharmacol 1992; 43:483-9. [PMID: 1483485 DOI: 10.1007/bf02285089] [Citation(s) in RCA: 11] [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: 12/27/2022]
Abstract
We have investigated whether the potential benefits of a controlled release formulation of levodopa (200 mg)/carbidopa (50 mg), Sinemet CR, are realised during maintenance therapy. Eight sufferers from idiopathic Parkinsonism, mean age 69.9 y, were studied: all exhibited "end of dose" effect within 4 h of a dose of their maintenance therapy with levodopa (100 mg)/carbidopa (25 mg) in a conventional release formulation, Sinemet Plus. They received, in random order, initial single dose challenges with one tablet of Sinemet Plus, one and two tablets of Sinemet CR and placebo alone, each on a separate day. After a mean of 21 weeks on maintenance therapy with Sinemet CR, subsequent single dose challenges with Sinemet CR and placebo were made. Objective measures of performance and blood sampling for assay of plasma concentrations of levodopa and the major peripheral metabolite, 3-0-methyldopa (30MD) were carried out immediately before (10.00 h) and serially until 6 h after each challenge. The overall mean stride length was significantly greater in relation to the subsequent (679 mm) than the initial (517 mm) placebo challenge. Moreover, stride length immediately before the challenges was significantly greater on the subsequent occasions. Improved performance, also seen for free walking speed, was not explained by plasma levodopa or 30MD concentrations. In the initial challenges, the mean increment in stride length achieved by active treatment, as compared with placebo, did not differ significantly between the one (210 mm) and two (235 mm) tablet doses of Sinemet CR: a maximal response had been obtained.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S G Bowes
- Division of Medical Statistics, Clinical Research Centre, Harrow, UK
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