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Deák G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson J, Tuijtel M, Webb S, Wilson M. Histone divergence in trypanosomes results in unique alterations to nucleosome structure. Nucleic Acids Res 2023; 51:7882-7899. [PMID: 37427792 PMCID: PMC10450195 DOI: 10.1093/nar/gkad577] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023] Open
Abstract
Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.
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Affiliation(s)
- Gauri Deák
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Gorka Sandoval
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Ruofan Chen
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Mark R D Taylor
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hayden Burdett
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - James A Watson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Maarten W Tuijtel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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Hutchinson JP, Rowland P, Taylor MRD, Christodoulou EM, Haslam C, Hobbs CI, Holmes DS, Homes P, Liddle J, Mole DJ, Uings I, Walker AL, Webster SP, Mowat CG, Chung CW. Structural and mechanistic basis of differentiated inhibitors of the acute pancreatitis target kynurenine-3-monooxygenase. Nat Commun 2017; 8:15827. [PMID: 28604669 PMCID: PMC5477544 DOI: 10.1038/ncomms15827] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 01/07/2017] [Accepted: 04/28/2017] [Indexed: 12/31/2022] Open
Abstract
Kynurenine-3-monooxygenase (KMO) is a key FAD-dependent enzyme of tryptophan metabolism. In animal models, KMO inhibition has shown benefit in neurodegenerative diseases such as Huntington's and Alzheimer's. Most recently it has been identified as a target for acute pancreatitis multiple organ dysfunction syndrome (AP-MODS); a devastating inflammatory condition with a mortality rate in excess of 20%. Here we report and dissect the molecular mechanism of action of three classes of KMO inhibitors with differentiated binding modes and kinetics. Two novel inhibitor classes trap the catalytic flavin in a previously unobserved tilting conformation. This correlates with picomolar affinities, increased residence times and an absence of the peroxide production seen with previous substrate site inhibitors. These structural and mechanistic insights culminated in GSK065(C1) and GSK366(C2), molecules suitable for preclinical evaluation. Moreover, revising the repertoire of flavin dynamics in this enzyme class offers exciting new opportunities for inhibitor design. Kynurenine-3-monooxygenase (KMO) is an emerging clinical target for treatment of neurodegenerative diseases and acute pancreatitis. Here, the authors report potent inhibitors that bind KMO in an unexpected conformation, offering structural and mechanistic insights for future drug discovery ventures.
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Affiliation(s)
| | - Paul Rowland
- Platform Technologies and Science, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Mark R D Taylor
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | | | - Carl Haslam
- Platform Technologies and Science, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Clare I Hobbs
- Platform Technologies and Science, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Duncan S Holmes
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, UK
| | - Paul Homes
- Platform Technologies and Science, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - John Liddle
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, UK
| | - Damian J Mole
- Medical Research Council Centre for Inflammation Research, Edinburgh EH16 4TJ, UK.,Clinical Surgery, University of Edinburgh, Edinburgh EH16 4SA, UK
| | - Iain Uings
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, UK
| | - Ann L Walker
- Discovery Partnerships with Academia, GlaxoSmithKline, Stevenage, UK
| | - Scott P Webster
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Christopher G Mowat
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Chun-Wa Chung
- Platform Technologies and Science, GlaxoSmithKline, Stevenage SG1 2NY, UK
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