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Berlin M, Cantley J, Bookbinder M, Bortolon E, Broccatelli F, Cadelina G, Chan EW, Chen H, Chen X, Cheng Y, Cheung TK, Davenport K, DiNicola D, Gordon D, Hamman BD, Harbin A, Haskell R, He M, Hole AJ, Januario T, Kerry PS, Koenig SG, Li L, Merchant M, Pérez-Dorado I, Pizzano J, Quinn C, Rose CM, Rousseau E, Soto L, Staben LR, Sun H, Tian Q, Wang J, Wang W, Ye CS, Ye X, Zhang P, Zhou Y, Yauch R, Dragovich PS. PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. J Med Chem 2024; 67:1262-1313. [PMID: 38180485 DOI: 10.1021/acs.jmedchem.3c01781] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The identification of VHL-binding proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) in SW1573 cell-based experiments is described. These molecules exhibit between 10- and 100-fold degradation selectivity for BRM over the closely related paralog protein BRG1 (SMARCA4). They also selectively impair the proliferation of the H1944 "BRG1-mutant" NSCLC cell line, which lacks functional BRG1 protein and is thus highly dependent on BRM for growth, relative to the wild-type Calu6 line. In vivo experiments performed with a subset of compounds identified PROTACs that potently and selectively degraded BRM in the Calu6 and/or the HCC2302 BRG1 mutant NSCLC xenograft models and also afforded antitumor efficacy in the latter system. Subsequent PK/PD analysis established a need to achieve strong BRM degradation (>95%) in order to trigger meaningful antitumor activity in vivo. Intratumor quantitation of mRNA associated with two genes whose transcription was controlled by BRM (PLAU and KRT80) also supported this conclusion.
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Affiliation(s)
- Michael Berlin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Jennifer Cantley
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mark Bookbinder
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Elizabeth Bortolon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Fabio Broccatelli
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Greg Cadelina
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Emily W Chan
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Huifen Chen
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xin Chen
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Yunxing Cheng
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Tommy K Cheung
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kim Davenport
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Dean DiNicola
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Debbie Gordon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Brian D Hamman
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Alicia Harbin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Roy Haskell
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mingtao He
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Alison J Hole
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Thomas Januario
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Philip S Kerry
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Stefan G Koenig
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Limei Li
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Mark Merchant
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Jennifer Pizzano
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Connor Quinn
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Christopher M Rose
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Emma Rousseau
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leofal Soto
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leanna R Staben
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hongming Sun
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Qingping Tian
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Wang
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Weifeng Wang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Crystal S Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xiaofen Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Penghong Zhang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Yuhui Zhou
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Yauch
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter S Dragovich
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Fedoryshchak RO, Gorelik A, Shen M, Shchepinova MM, Pérez-Dorado I, Tate EW. Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes. Chem Sci 2023; 14:2419-2430. [PMID: 36873846 PMCID: PMC9977449 DOI: 10.1039/d2sc06116c] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in biology. Despite the development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report the design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N-myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions in the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein 1 (FSP1) and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome without the requirement for genetic modification, which may prove broadly applicable to other PTMs.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Andrii Gorelik
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Mengjie Shen
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Maria M Shchepinova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
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3
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Jamshidiha M, Lanyon-Hogg T, Sutherell CL, Craven GB, Tersa M, De Vita E, Brustur D, Pérez-Dorado I, Hassan S, Petracca R, Morgan RM, Sanz-Hernández M, Norman JC, Armstrong A, Mann DJ, Cota E, Tate EW. Identification of the first structurally validated covalent ligands of the small GTPase RAB27A. RSC Med Chem 2022; 13:150-155. [PMID: 35308027 PMCID: PMC8864489 DOI: 10.1039/d1md00225b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Rab27A is a small GTPase, which mediates transport and docking of secretory vesicles at the plasma membrane via protein-protein interactions (PPIs) with effector proteins. Rab27A promotes the growth and invasion of multiple cancer types such as breast, lung and pancreatic, by enhancing secretion of chemokines, metalloproteases and exosomes. The significant role of Rab27A in multiple cancer types and the minor role in adults suggest that Rab27A may be a suitable target to disrupt cancer metastasis. Similar to many GTPases, the flat topology of the Rab27A-effector PPI interface and the high affinity for GTP make it a challenging target for inhibition by small molecules. Reported co-crystal structures show that several effectors of Rab27A interact with the Rab27A SF4 pocket ('WF-binding pocket') via a conserved tryptophan-phenylalanine (WF) dipeptide motif. To obtain structural insight into the ligandability of this pocket, a novel construct was designed fusing Rab27A to part of an effector protein (fRab27A), allowing crystallisation of Rab27A in high throughput. The paradigm of KRas covalent inhibitor development highlights the challenge presented by GTPase proteins as targets. However, taking advantage of two cysteine residues, C123 and C188, that flank the WF pocket and are unique to Rab27A and Rab27B among the >60 Rab family proteins, we used the quantitative Irreversible Tethering (qIT) assay to identify the first covalent ligands for native Rab27A. The binding modes of two hits were elucidated by co-crystallisation with fRab27A, exemplifying a platform for identifying suitable lead fragments for future development of competitive inhibitors of the Rab27A-effector interaction interface, corroborating the use of covalent libraries to tackle challenging targets.
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Affiliation(s)
- Mostafa Jamshidiha
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Thomas Lanyon-Hogg
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | | | - Gregory B Craven
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Montse Tersa
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Elena De Vita
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Delia Brustur
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | | | - Sarah Hassan
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Rita Petracca
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - Rhodri M Morgan
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | | | - Jim C Norman
- Beatson Institute for Cancer Research, Garscube Estate Glasgow G61 1BD UK
| | - Alan Armstrong
- Department of Chemistry, Imperial College London London W12 0BZ UK
| | - David J Mann
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Ernesto Cota
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London London W12 0BZ UK
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Dian C, Pérez-Dorado I, Rivière F, Asensio T, Legrand P, Ritzefeld M, Shen M, Cota E, Meinnel T, Tate EW, Giglione C. High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Nat Commun 2020; 11:1132. [PMID: 32111831 PMCID: PMC7048800 DOI: 10.1038/s41467-020-14847-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 01/09/2023] Open
Abstract
The promising drug target N-myristoyltransferase (NMT) catalyses an essential protein modification thought to occur exclusively at N-terminal glycines (Gly). Here, we present high-resolution human NMT1 structures co-crystallised with reactive cognate lipid and peptide substrates, revealing high-resolution snapshots of the entire catalytic mechanism from the initial to final reaction states. Structural comparisons, together with biochemical analysis, provide unforeseen details about how NMT1 reaches a catalytically competent conformation in which the reactive groups are brought into close proximity to enable catalysis. We demonstrate that this mechanism further supports efficient and unprecedented myristoylation of an N-terminal lysine side chain, providing evidence that NMT acts both as N-terminal-lysine and glycine myristoyltransferase.
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Affiliation(s)
- Cyril Dian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK
- Evotec Ltd, 114 Innovation Dr, Milton Park, Milton, Abingdon, OX14 4RZ, UK
| | - Frédéric Rivière
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Thomas Asensio
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Pierre Legrand
- Synchrotron SOLEIL, Gif-sur-Yvette, Cedex, 91192, France
| | - Markus Ritzefeld
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Evotec SE, Essener Bogen 7, Hamburg, 22419, Germany
| | - Mengjie Shen
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Oakland Innovation, Mill Rd, Harston, Cambridge, CB22 7GG, UK
| | - Ernesto Cota
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
| | - Edward W Tate
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Rd, London, NW 1AT, UK.
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
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5
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Jamshidiha M, Pérez-Dorado I, Murray JW, Tate EW, Cota E, Read RJ. Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a. Acta Crystallogr D Struct Biol 2019; 75:342-353. [PMID: 30950405 PMCID: PMC6450061 DOI: 10.1107/s2059798318017825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 10/27/2018] [Accepted: 12/17/2018] [Indexed: 01/22/2023] Open
Abstract
Data pathologies caused by effects such as diffraction anisotropy and translational noncrystallographic symmetry (tNCS) can dramatically complicate the solution of the crystal structures of macromolecules. Such problems were encountered in determining the structure of a mutant form of Rab27a, a member of the Rab GTPases. Mutant Rab27a constructs that crystallize in the free form were designed for use in the discovery of drugs to reduce primary tumour invasiveness and metastasis. One construct, hRab27aMut, crystallized within 24 h and diffracted to 2.82 Å resolution, with a unit cell possessing room for a large number of protein copies. Initial efforts to solve the structure using molecular replacement by Phaser were not successful. Analysis of the data set revealed that the crystals suffered from both extreme anisotropy and strong tNCS. As a result, large numbers of reflections had estimated standard deviations that were much larger than their measured intensities and their expected intensities, revealing problems with the use of such data at the time in Phaser. By eliminating extremely weak reflections with the largest combined effects of anisotropy and tNCS, these problems could be avoided, allowing a molecular-replacement solution to be found. The lessons that were learned in solving this structure have guided improvements in the numerical analysis used in Phaser, particularly in identifying diffraction measurements that convey very little information content. The calculation of information content could also be applied as an alternative to ellipsoidal truncation. The post-mortem analysis also revealed an oversight in accounting for measurement errors in the fast rotation function. While the crystal of mutant Rab27a is not amenable to drug screening, the structure can guide new modifications to obtain more suitable crystal forms.
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Affiliation(s)
- Mostafa Jamshidiha
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London W12 0BZ, England
| | - Inmaculada Pérez-Dorado
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England
| | - James W. Murray
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England
| | - Edward W. Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London W12 0BZ, England
| | - Ernesto Cota
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England
| | - Randy J. Read
- Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
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6
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Mousnier A, Bell AS, Swieboda DP, Morales-Sanfrutos J, Pérez-Dorado I, Brannigan JA, Newman J, Ritzefeld M, Hutton JA, Guedán A, Asfor AS, Robinson SW, Hopkins-Navratilova I, Wilkinson AJ, Johnston SL, Leatherbarrow RJ, Tuthill TJ, Solari R, Tate EW. Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nat Chem 2018; 10:599-606. [PMID: 29760414 PMCID: PMC6015761 DOI: 10.1038/s41557-018-0039-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [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: 08/14/2017] [Accepted: 03/01/2018] [Indexed: 12/18/2022]
Abstract
Rhinoviruses (RVs) are the pathogens most often responsible for the common cold, and are a frequent cause of exacerbations in asthma, chronic obstructive pulmonary disease and cystic fibrosis. Here we report the discovery of IMP-1088, a picomolar dual inhibitor of the human N-myristoyltransferases NMT1 and NMT2, and use it to demonstrate that pharmacological inhibition of host-cell N-myristoylation rapidly and completely prevents rhinoviral replication without inducing cytotoxicity. The identification of cooperative binding between weak-binding fragments led to rapid inhibitor optimization through fragment reconstruction, structure-guided fragment linking and conformational control over linker geometry. We show that inhibition of the co-translational myristoylation of a specific virus-encoded protein (VP0) by IMP-1088 potently blocks a key step in viral capsid assembly, to deliver a low nanomolar antiviral activity against multiple RV strains, poliovirus and foot and-mouth disease virus, and protection of cells against virus-induced killing, highlighting the potential of host myristoylation as a drug target in picornaviral infections.
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Affiliation(s)
- Aurélie Mousnier
- National Heart & Lung Institute, Imperial College London, London, UK
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Andrew S Bell
- Department of Chemistry, Imperial College London, London, UK
| | - Dawid P Swieboda
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Inmaculada Pérez-Dorado
- Department of Chemistry, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - James A Brannigan
- Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | | | | | - Jennie A Hutton
- Department of Chemistry, Imperial College London, London, UK
| | - Anabel Guedán
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | | | - Iva Hopkins-Navratilova
- Kinetic Discovery Limited, Dundee, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | | | - Robin J Leatherbarrow
- Department of Chemistry, Imperial College London, London, UK
- Liverpool John Moores University, Liverpool, UK
| | | | - Roberto Solari
- National Heart & Lung Institute, Imperial College London, London, UK.
| | - Edward W Tate
- Department of Chemistry, Imperial College London, London, UK.
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7
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Rasheed M, Garnett J, Pérez-Dorado I, Muhl D, Filloux A, Matthews S. Crystal structure of the CupB6 adhesive tip from the chaperone-usher family of pili from Pseudomonas aeruginosa. Biochim Biophys Acta 2016; 1864:1500-5. [PMID: 27481165 PMCID: PMC5022761 DOI: 10.1016/j.bbapap.2016.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/14/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterial pathogen that can cause chronic infection of the lungs of cystic fibrosis patients. Chaperone-usher systems in P. aeruginosa are known to translocate and assemble adhesive pili on the bacterial surface and contribute to biofilm formation within the host. Here, we report the crystal structure of the tip adhesion subunit CupB6 from the cupB1–6 gene cluster. The tip domain is connected to the pilus via the N-terminal donor strand from the main pilus subunit CupB1. Although the CupB6 adhesion domain bears structural features similar to other CU adhesins it displays an unusual polyproline helix adjacent to a prominent surface pocket, which are likely the site for receptor recognition. Crystal structure of the tip adhesion subunit CupB6 from the cupB1-6 gene cluster of Pseudomonas aeruginosa CupB6 possesses an atypical adhesion domain connected to a canonical chaperone-usher pilus subunit CupB6 caps the pilus shaft via donor strand complementation with the N-terminus of CupB1 CupB6 possesses unusual polyproline helices adjacent to a prominent surface pocket
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Affiliation(s)
- Masooma Rasheed
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James Garnett
- Queen Mary University of London, Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | | | - Daniela Muhl
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alain Filloux
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
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8
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Miliara X, Garnett JA, Tatsuta T, Abid Ali F, Baldie H, Pérez-Dorado I, Simpson P, Yague E, Langer T, Matthews S. Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes. EMBO Rep 2015; 16:824-35. [PMID: 26071602 PMCID: PMC4515122 DOI: 10.15252/embr.201540229] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/20/2015] [Indexed: 11/09/2022] Open
Abstract
The composition of the mitochondrial membrane is important for its architecture and proper function. Mitochondria depend on a tightly regulated supply of phospholipid via intra-mitochondrial synthesis and by direct import from the endoplasmic reticulum. The Ups1/PRELI-like family together with its mitochondrial chaperones (TRIAP1/Mdm35) represent a unique heterodimeric lipid transfer system that is evolutionary conserved from yeast to man. Work presented here provides new atomic resolution insight into the function of a human member of this system. Crystal structures of free TRIAP1 and the TRIAP1-SLMO1 complex reveal how the PRELI domain is chaperoned during import into the intermembrane mitochondrial space. The structural resemblance of PRELI-like domain of SLMO1 with that of mammalian phoshatidylinositol transfer proteins (PITPs) suggest that they share similar lipid transfer mechanisms, in which access to a buried phospholipid-binding cavity is regulated by conformationally adaptable loops.
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Affiliation(s)
- Xeni Miliara
- Department of Life Sciences, Imperial College London, London, UK
| | - James A Garnett
- Department of Life Sciences, Imperial College London, London, UK School of Biological and Chemical Sciences, Joseph Priestley Building Queen Mary University of London, London, UK
| | - Takashi Tatsuta
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Ferdos Abid Ali
- Department of Life Sciences, Imperial College London, London, UK
| | - Heather Baldie
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Peter Simpson
- Department of Life Sciences, Imperial College London, London, UK
| | - Ernesto Yague
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Thomas Langer
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, London, UK
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9
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Hesketh GG, Pérez-Dorado I, Jackson LP, Wartosch L, Schäfer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ. VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface. Dev Cell 2014; 29:591-606. [PMID: 24856514 PMCID: PMC4059916 DOI: 10.1016/j.devcel.2014.04.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [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: 08/02/2013] [Revised: 02/03/2014] [Accepted: 04/09/2014] [Indexed: 11/18/2022]
Abstract
VARP is a Rab32/38 effector that also binds to the endosomal/lysosomal R-SNARE VAMP7. VARP binding regulates VAMP7 participation in SNARE complex formation and can therefore influence VAMP7-mediated membrane fusion events. Mutant versions of VARP that cannot bind Rab32:GTP, designed on the basis of the VARP ankyrin repeat/Rab32:GTP complex structure described here, unexpectedly retain endosomal localization, showing that VARP recruitment is not dependent on Rab32 binding. We show that recruitment of VARP to the endosomal membrane is mediated by its direct interaction with VPS29, a subunit of the retromer complex, which is involved in trafficking from endosomes to the TGN and the cell surface. Transport of GLUT1 from endosomes to the cell surface requires VARP, VPS29, and VAMP7 and depends on the direct interaction between VPS29 and VARP. Finally, we propose that endocytic cycling of VAMP7 depends on its interaction with VARP and, consequently, also on retromer.
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Affiliation(s)
- Geoffrey G Hesketh
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Inmaculada Pérez-Dorado
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Lauren P Jackson
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Lena Wartosch
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ingmar B Schäfer
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Sally R Gray
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Airlie J McCoy
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Oliver B Zeldin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Michael E Harbour
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Philip R Evans
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Matthew N J Seaman
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - J Paul Luzio
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - David J Owen
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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10
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Abstract
Surface-exposed proteins of pathogenic bacteria are considered as potential virulence factors through their direct contribution to host-pathogen interactions. Four families of surface proteins decorate the cell surface of the human pathogen Streptococcus pneumoniae. Besides lipoproteins and LPXTG proteins, also present in other gram-positive bacteria, the pneumococcus presents the choline-binding protein (CBP) family and the non-classical surface proteins (NCSPs). The CBPs present specific structural features that allow their anchorage to the cell envelope through non-covalent interaction with choline residues of lipoteichoic acid and teichoic acid. NCSP is an umbrella term for less characterized proteins displaying moonlighting functions on the pneumococcal surface that lack a leader peptide and membrane-anchor motif. Considering the unceasing evolution of microbial species under the selective pressure of antibiotic use, detailed understanding of the interaction between pathogen and the host cells is required for the development of novel therapeutic strategies to combat pneumococcal infections. This article reviews recent progress in the investigation of the three-dimensional structures of surface-exposed pneumococcal proteins. The modular nature of some of them produces a great versatility and sophistication of the virulence functions that, in most cases, cannot be deduced by the structural analysis of the isolated modules.
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Affiliation(s)
- I Pérez-Dorado
- Department of Crystallography and Structural Biology, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
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11
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Hermoso JA, Pérez-Dorado I, Martínez-Ripoll M. Structure and role in pathogenesis of pneumococcal cell-wall associated proteins. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310099290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Pérez-Dorado I, González A, Morales M, Sanles R, Striker W, Vollmer W, Mobashery S, García JL, Martínez-Ripoll M, García P, Hermoso JA. Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC. Nat Struct Mol Biol 2010; 17:576-81. [PMID: 20400948 DOI: 10.1038/nsmb.1817] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 02/23/2010] [Indexed: 11/09/2022]
Abstract
The first structure of a pneumococcal autolysin, that of the LytC lysozyme, has been solved in ternary complex with choline and a pneumococcal peptidoglycan (PG) fragment. The active site of the hydrolase module is not fully exposed but is oriented toward the choline-binding module, which accounts for its unique in vivo features in PG hydrolysis, its activation and its regulatory mechanisms. Because of the unusual hook-shaped conformation of the multimodular protein, it is only able to hydrolyze non-cross-linked PG chains, an assertion validated by additional experiments. These results explain the activation of LytC by choline-binding protein D (CbpD) in fratricide, a competence-programmed mechanism of predation of noncompetent sister cells. The results provide the first structural insights to our knowledge into the critical and central function that LytC plays in pneumococcal virulence and explain a long-standing puzzle of how murein hydrolases can be controlled to avoid self-lysis during bacterial growth and division.
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Affiliation(s)
- Inmaculada Pérez-Dorado
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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13
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Pérez-Dorado I, Sanles R, González A, García P, García JL, Martínez-Ripoll M, Hermoso JA. Crystallization of the pneumococcal autolysin LytC: in-house phasing using novel lanthanide complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:448-51. [PMID: 20383019 PMCID: PMC2852341 DOI: 10.1107/s1744309110006081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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] [Received: 11/13/2009] [Accepted: 02/15/2010] [Indexed: 11/10/2022]
Abstract
LytC, one of the major autolysins from the human pathogen Streptococcus pneumoniae, has been crystallized as needles by the hanging-drop technique using 10%(w/v) PEG 3350 as precipitant and 10 mM HEPES pH 7.5. LytC crystals were quickly soaked in mother liquor containing 2 mM of the complex Gd-HPDO3A to produce derivatized crystals (LytC(Gd-HPDO3A)). Both native LytC and isomorphous LytC(Gd-HPDO3A) crystals were flash-cooled in a nitrogen flow at 120 K prior to X-ray data collection using an in-house Enraf-Nonius rotating-anode generator (lambda = 1.5418 A) and a MAR345 imaging-plate detector. In both cases, good-quality diffraction patterns were obtained at high resolution. LytC(Gd-HPDO3A) crystals allowed the collection of a SAD X-ray data set to 2.6 A resolution indexed in terms of a P2(1) monoclinic unit cell with parameters a = 59.37, b = 67.16, c = 78.85 A, beta = 105.69 degrees . The anomalous Patterson map allowed the identification of one heavy-atom binding site, which was sufficient for the calculation of an interpretable anomalous map at 2.6 A resolution.
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Affiliation(s)
- Inmaculada Pérez-Dorado
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Reyes Sanles
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Ana González
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pedro García
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Spain
| | - José L. García
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Martín Martínez-Ripoll
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A. Hermoso
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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14
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Cremades N, Velázquez-Campoy A, Martínez-Júlvez M, Neira JL, Pérez-Dorado I, Hermoso J, Jiménez P, Lanas A, Hoffman PS, Sancho J. Discovery of specific flavodoxin inhibitors as potential therapeutic agents against Helicobacter pylori infection. ACS Chem Biol 2009; 4:928-38. [PMID: 19725577 DOI: 10.1021/cb900166q] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Helicobacter pylori establishes life-long infections in the gastric mucosa of over 1 billion people worldwide. In many cases, without specific antimicrobial intervention, H. pylori infected individuals will develop type B gastritis, chronic peptic ulcers and, more rarely, gastric neoplasias. Conventional antimicrobial therapy has been complicated by dramatic increases in resistance to macrolides, metronidazole and fluoroquinolones. Here, we report the development of novel therapeutics that specifically target the unique flavodoxin component of an essential metabolic pathway of H. pylori. With the use of high-throughput screening methodology, we have tested 10,000 chemicals and have identified 29 compounds that bind flavodoxin, four of which interrupted in vitro electron transfer to flavodoxin physiological partners. Three of these compounds are bactericidal and promisingly selective for H. pylori. The minimal inhibitory concentrations of two of them are 10 times lower than their minimal cytotoxic concentrations for HeLa cells. Importantly, neither of the four inhibitors is toxic for mice after administration of 1-10 mg kg(-1) doses twice a day for 5 days. Enzymatic, thermodynamic and structural characterization of the inhibitor-flavodoxin complexes suggests these compounds could act by modifying the redox potentials of flavodoxin. These newly discovered inhibitors represent promising selective leads against the different diseases associated to H. pylori infection.
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Affiliation(s)
- Nunilo Cremades
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
- Fundación Aragón I+D (ARAID-BIFI), Diputación General de Aragón, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
| | - José L. Neira
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Inmaculada Pérez-Dorado
- Grupo de Crystalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan Hermoso
- Grupo de Crystalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | | | - Angel Lanas
- IACS, CIBERehd, University of Zaragoza, Spain
| | - Paul S. Hoffman
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia 22908
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
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15
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Bortolotti A, Pérez-Dorado I, Goñi G, Medina M, Hermoso JA, Carrillo N, Cortez N. Coenzyme binding and hydride transfer in Rhodobacter capsulatus ferredoxin/flavodoxin NADP(H) oxidoreductase. Biochim Biophys Acta 2008; 1794:199-210. [PMID: 18973834 DOI: 10.1016/j.bbapap.2008.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
Abstract
Ferredoxin-NADP(H) reductases catalyse the reversible hydride/electron exchange between NADP(H) and ferredoxin/flavodoxin, comprising a structurally defined family of flavoenzymes with two distinct subclasses. Those present in Gram-negative bacteria (FPRs) display turnover numbers of 1-5 s(-1) while the homologues of cyanobacteria and plants (FNRs) developed a 100-fold activity increase. We investigated nucleotide interactions and hydride transfer in Rhodobacter capsulatus FPR comparing them to those reported for FNRs. NADP(H) binding proceeds as in FNRs with stacking of the nicotinamide on the flavin, which resulted in formation of charge-transfer complexes prior to hydride exchange. The affinity of FPR for both NADP(H) and 2'-P-AMP was 100-fold lower than that of FNRs. The crystal structure of FPR in complex with 2'-P-AMP and NADP(+) allowed modelling of the adenosine ring system bound to the protein, whereas the nicotinamide portion was either not visible or protruding toward solvent in different obtained crystals. Stabilising contacts with the active site residues are different in the two reductase classes. We conclude that evolution to higher activities in FNRs was partially favoured by modification of NADP(H) binding in the initial complexes through changes in the active site residues involved in stabilisation of the adenosine portion of the nucleotide and in the mobile C-terminus of FPR.
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Affiliation(s)
- Ana Bortolotti
- Instituto de Biología Molecular y Celular de Rosario, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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16
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Pérez-Dorado I, Bortolotti A, Cortez N, Hermoso JA. Crystallization of a flavodoxin involved in nitrogen fixation in Rhodobacter capsulatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:375-7. [PMID: 18453705 PMCID: PMC2376390 DOI: 10.1107/s1744309108008038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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] [Received: 02/06/2008] [Accepted: 03/25/2008] [Indexed: 05/26/2023]
Abstract
Flavodoxins are small electron-transfer proteins that contain one molecule of noncovalently bound flavin mononucleotide (FMN). The flavodoxin NifF from the photosynthetic bacterium Rhodobacter capsulatus is reduced by one electron from ferredoxin/flavodoxin:NADP(H) reductase and was postulated to be an electron donor to nitrogenase in vivo. NifF was cloned and overexpressed in Escherichia coli, purified and concentrated for crystallization using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture of PEG 3350 and PEG 400 at pH 5.5 and belong to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 66.49, c = 121.32 A. X-ray data sets have been collected to 2.17 A resolution.
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Affiliation(s)
- Inmaculada Pérez-Dorado
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Ana Bortolotti
- Instituto de Biología Molecular y Celular de Rosario (Universidad Nacional de Rosario y CONICET), Suipacha 531, S2002LRK Rosario, Argentina
| | - Néstor Cortez
- Instituto de Biología Molecular y Celular de Rosario (Universidad Nacional de Rosario y CONICET), Suipacha 531, S2002LRK Rosario, Argentina
| | - Juan A. Hermoso
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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17
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Martínez-Júlvez M, Cremades N, Bueno M, Pérez-Dorado I, Maya C, Cuesta-López S, Prada D, Falo F, Hermoso JA, Sancho J. Common conformational changes in flavodoxins induced by FMN and anion binding: the structure of Helicobacter pylori apoflavodoxin. Proteins 2007; 69:581-94. [PMID: 17623845 DOI: 10.1002/prot.21410] [Citation(s) in RCA: 22] [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: 11/07/2022]
Abstract
Flavodoxins, noncovalent complexes between apoflavodoxins and flavin mononucleotide (FMN), are useful models to investigate the mechanism of protein/flavin recognition. In this respect, the only available crystal structure of an apoflavodoxin (that from Anabaena) showed a closed isoalloxazine pocket and the presence of a bound phosphate ion, which posed many questions on the recognition mechanism and on the potential physiological role exerted by phosphate ions. To address these issues we report here the X-ray structure of the apoflavodoxin from the pathogen Helicobacter pylori. The protein naturally lacks one of the conserved aromatic residues that close the isoalloxazine pocket in Anabaena, and the structure has been determined in a medium lacking phosphate. In spite of these significant differences, the isoallozaxine pocket in H. pylori apoflavodoxin appears also closed and a chloride ion is bound at a native-like FMN phosphate site. It seems thus that it is a general characteristic of apoflavodoxins to display closed, non-native, isoalloxazine binding sites together with native-like, rather promiscuous, phosphate binding sites that can bear other available small anions present in solution. In this respect, both binding energy hot spots of the apoflavodoxin/FMN complex are initially unavailable to FMN binding and the specific spot for FMN recognition may depend on the dynamics of the two candidate regions. Molecular dynamics simulations show that the isoalloxazine binding loops are intrinsically flexible at physiological temperatures, thus facilitating the intercalation of the cofactor, and that their mobility is modulated by the anion bound at the phosphate site.
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Affiliation(s)
- Marta Martínez-Júlvez
- Biocomputation and Complex Systems Physics Institute (BiFi), Universidad de Zaragoza, Unidad Asociada al IQFR-CSIC, Zaragoza, Spain
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18
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Pérez-Dorado I, Campillo NE, Monterroso B, Hesek D, Lee M, Páez JA, García P, Martínez-Ripoll M, García JL, Mobashery S, Menéndez M, Hermoso JA. Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1. J Biol Chem 2007; 282:24990-9. [PMID: 17581815 DOI: 10.1074/jbc.m704317200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pneumococcal bacteriophage-encoded lysins are modular proteins that have been shown to act as enzymatic antimicrobial agents (enzybiotics) in treatment of streptococcal infections. The first x-ray crystal structures of the Cpl-1 lysin, encoded by the pneumococcal phage Cp-1, in complex with three bacterial cell wall peptidoglycan (PG) analogues are reported herein. The Cpl-1 structure is folded in two well defined modules, one responsible for anchoring to the pneumococcal cell wall and the other, a catalytic module, that hydrolyzes the PG. Conformational rearrangement of Tyr-127 is a critical event in molecular recognition of a stretch of five saccharide rings of the polymeric peptidoglycan (cell wall). The PG is bound at a stretch of the surface that is defined as the peptidoglycan-binding sites 1 and 2, the juncture of which catalysis takes place. The peptidoglycan-binding site 1 binds to a stretch of three saccharides of the peptidoglycan in a conformation essentially identical to that of the peptidoglycan in solution. In contrast, binding of two peptidoglycan saccharides at the peptidoglycan-binding site 2 introduces a kink into the solution structure of the peptidoglycan, en route to catalytic turnover. These findings provide the first structural evidence on recognition of the peptidoglycan and shed light on the discrete events of cell wall degradation by Cpl-1.
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Affiliation(s)
- Inmaculada Pérez-Dorado
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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19
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Mayoral T, Martínez-Júlvez M, Pérez-Dorado I, Sanz-Aparicio J, Gómez-Moreno C, Medina M, Hermoso JA. Structural analysis of interactions for complex formation between Ferredoxin-NADP+ reductase and its protein partners. Proteins 2006; 59:592-602. [PMID: 15789405 DOI: 10.1002/prot.20450] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The three-dimensional structures of K72E, K75R, K75S, K75Q, and K75E Anabaena Ferredoxin-NADP+ reductase (FNR) mutants have been solved, and particular structural details of these mutants have been used to assess the role played by residues 72 and 75 in optimal complex formation and electron transfer (ET) between FNR and its protein redox partners Ferredoxin (Fd) and Flavodoxin (Fld). Additionally, because there is no structural information available on the interaction between FNR and Fld, a model for the FNR:Fld complex has also been produced based on the previously reported crystal structures and on that of the rat Cytochrome P450 reductase (CPR), onto which FNR and Fld have been structurally aligned, and those reported for the Anabaena and maize FNR:Fd complexes. The model suggests putative electrostatic and hydrophobic interactions between residues on the FNR and Fld surfaces at the complex interface and provides an adequate orientation and distance between the FAD and FMN redox centers for efficient ET without the presence of any other molecule as electron carrier. Thus, the models now available for the FNR:Fd and FNR:Fld interactions and the structures presented here for the mutants at K72 and K75 in Anabaena FNR have been evaluated in light of previous biochemical data. These structures confirm the key participation of residue K75 and K72 in complex formation with both Fd and Fld. The drastic effect in FNR activity produced by replacement of K75 by Glu in the K75E FNR variant is explained not only by the observed changes in the charge distribution on the surface of the K75E FNR mutant, but also by the formation of a salt bridge interaction between E75 and K72 that simultaneously "neutralizes" two essential positive charged side chains for Fld/Fd recognition.
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Affiliation(s)
- Tomás Mayoral
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química-Física Rocasolano, C.S.I.C. Serrano 119, 28006-Madrid, Spain
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20
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Nogués I, Pérez-Dorado I, Frago S, Bittel C, Mayhew SG, Gómez-Moreno C, Hermoso JA, Medina M, Cortez N, Carrillo N. The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism. Biochemistry 2005; 44:11730-40. [PMID: 16128574 DOI: 10.1021/bi0508183] [Citation(s) in RCA: 34] [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: 11/28/2022]
Abstract
The photosynthetic bacterium Rhodobacter capsulatus contains a ferredoxin (flavodoxin)-NADP(H) oxidoreductase (FPR) that catalyzes electron transfer between NADP(H) and ferredoxin or flavodoxin. The structure of the enzyme, determined by X-ray crystallography, contains two domains harboring the FAD and NADP(H) binding sites, as is typical of the FPR structural family. The FAD molecule is in a hairpin conformation in which stacking interactions can be established between the dimethylisoalloxazine and adenine moieties. The midpoint redox potentials of the various transitions undergone by R. capsulatus FPR were similar to those reported for their counterparts involved in oxygenic photosynthesis, but its catalytic activity is orders of magnitude lower (1-2 s(-)(1) versus 200-500 s(-)(1)) as is true for most of its prokaryotic homologues. To identify the mechanistic basis for the slow turnover in the bacterial enzymes, we dissected the R. capsulatus FPR reaction into hydride transfer and electron transfer steps, and determined their rates using stopped-flow methods. Hydride exchange between the enzyme and NADP(H) occurred at 30-150 s(-)(1), indicating that this half-reaction does not limit FPR activity. In contrast, electron transfer to flavodoxin proceeds at 2.7 s(-)(1), in the range of steady-state catalysis. Flavodoxin semiquinone was a better electron acceptor for FPR than oxidized flavodoxin under both single turnover and steady-state conditions. The results indicate that one-electron reduction of oxidized flavodoxin limits the enzyme activity in vitro, and support the notion that flavodoxin oscillates between the semiquinone and fully reduced states when FPR operates in vivo.
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Affiliation(s)
- Isabel Nogués
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
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Tejero J, Pérez-Dorado I, Maya C, Martínez-Júlvez M, Sanz-Aparicio J, Gómez-Moreno C, Hermoso JA, Medina M. C-terminal tyrosine of ferredoxin-NADP+ reductase in hydride transfer processes with NAD(P)+/H. Biochemistry 2005; 44:13477-90. [PMID: 16216071 DOI: 10.1021/bi051278c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [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: 11/30/2022]
Abstract
Ferredoxin-NADP+ reductase (FNR) catalyzes the reduction of NADP+ to NADPH in an overall reversible reaction, showing some differences in the mechanisms between cyanobacterial and higher plant FNRs. During hydride transfer it is proposed that the FNR C-terminal Tyr is displaced by the nicotinamide. Thus, this C-terminal Tyr might be involved not only in modulating the flavin redox properties, as already shown, but also in nicotinamide binding and hydride transfer. FNR variants from the cyanobacterium Anabaena in which the C-terminal Tyr has been replaced by Trp, Phe, or Ser have been produced. All FNR variants show enhanced NADP+ and NAD+ binding, especially Tyr303Ser, which correlates with a noticeable improvement of NADH-dependent reactions. Nevertheless, the Tyr303Ser variant shows a decrease in the steady-state kcat value with NADPH. Fast kinetic analysis of the hydride transfer shows that the low efficiency observed for this mutant FNR under steady-state conditions is not due to a lack of catalytic ability but rather to the strong enzyme-coenzyme interaction. Three-dimensional structures for Tyr303Ser and Tyr303Trp variants and its complexes with NADP+ show significant differences between plant and cyanobacterial FNRs. Our results suggest that modulation of coenzyme affinity is highly influenced by the strength of the C-terminus-FAD interaction and that subtle changes between plant and cyanobacterial structures are able to modify the energy of that interaction. Additionally, it is shown that the C-terminal Tyr of FNR lowers the affinity for NADP+/H to levels compatible with steady-state turnover during the catalytic cycle, but it is not involved in the hydride transfer itself.
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Affiliation(s)
- Jesús Tejero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, E-50009 Zaragoza, Spain
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Pérez-Dorado I, Bittel C, Cortez N, Hermoso JA. Crystallization and preliminary X-ray diffraction analysis of ferredoxin-NADP(H) reductase fromRhodobacter capsulatus. Acta Crystallogr D Biol Crystallogr 2004; 60:2332-5. [PMID: 15583382 DOI: 10.1107/s090744490402640x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Accepted: 10/18/2004] [Indexed: 11/10/2022]
Abstract
Ferredoxin-NADP(H) reductase (272 amino acids) from Rhodobacter capsulatus (FPR) has recently been postulated to be involved in the antioxidant response and to facilitate the provision of reduced flavodoxin for the reduction of nitrogenase. Crystallization trials of recombinant FPR were carried out at 291 K by the hanging-drop vapour-diffusion method. Orthorhombic crystals (unit-cell parameters a = 69.3, b = 93.6, c = 103.5 A) were obtained. However, their diffraction pattern was not satisfactory and an extensive detergent screening was carried out over the initial crystallization conditions. The introduction of n-heptyl-beta-D-thioglucoside produced new trigonal crystals (space group P3(1)21; unit-cell parameters a = b = 120.5, c = 51.1 A) that diffracted to 1.8 A resolution at beamline BM16 at the ESRF. Preliminary structural analysis indicated that detergent molecules could increase the quality of diffraction of FPR crystals by stabilizing the disordered regions of the protein and by increasing the number of contacts in the crystal packing.
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Affiliation(s)
- Inmaculada Pérez-Dorado
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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