1
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. Nat Struct Mol Biol 2024:10.1038/s41594-024-01268-9. [PMID: 38600324 DOI: 10.1038/s41594-024-01268-9] [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] [Received: 11/05/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Dedicated assembly factors orchestrate the stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here we report cryo-electron microscopy reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, as well as how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors and reveals conceptual principles underlying human proteasome biogenesis, thus providing an explanation for many previous biochemical and genetic observations.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen A Goodall
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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2
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Velez B, Walsh RM, Rawson S, Razi A, Adams L, Perez EF, Jiao F, Blickling M, Rajakumar T, Fung D, Huang L, Hanna J. Mechanism of autocatalytic activation during proteasome assembly. Nat Struct Mol Biol 2024:10.1038/s41594-024-01262-1. [PMID: 38600323 DOI: 10.1038/s41594-024-01262-1] [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] [Received: 11/14/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024]
Abstract
Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the proteasome, where protein degradation occurs, its six active sites are simultaneously activated via cleavage of N-terminal propeptides. Such activation is autocatalytic and coupled to fusion of two half-CP intermediates, which protects cells by preventing activation until enclosure of the active sites within the CP interior. Here we uncover key mechanistic aspects of autocatalytic activation, which proceeds through alignment of the β5 and β2 catalytic triad residues, respectively, with these triads being misaligned before fusion. This mechanism contrasts with most other zymogens, in which catalytic centers are preformed. Our data also clarify the mechanism by which individual subunits can be added in a precise, temporally ordered manner. This work informs two decades-old mysteries in the proteasome field, with broader implications for protease biology and multisubunit complex assembly.
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Affiliation(s)
- Benjamin Velez
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Aida Razi
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Lea Adams
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Erignacio Fermin Perez
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Fenglong Jiao
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA, USA
| | - Marie Blickling
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Tamayanthi Rajakumar
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Darlene Fung
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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3
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. bioRxiv 2024:2024.01.27.577538. [PMID: 38328185 PMCID: PMC10849659 DOI: 10.1101/2024.01.27.577538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo-EM reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, and how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates, and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. The structural findings reported here explain many previous biochemical and genetic observations. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors, and reveals conceptual principles underlying human proteasome biogenesis.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ellen A. Goodall
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J. Wade Harper
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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4
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Velez B, Razi A, Hubbard RD, Walsh R, Rawson S, Tian G, Finley D, Hanna J. Rational design of proteasome inhibitors based on the structure of the endogenous inhibitor PI31/Fub1. Proc Natl Acad Sci U S A 2023; 120:e2308417120. [PMID: 38091293 PMCID: PMC10743371 DOI: 10.1073/pnas.2308417120] [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: 05/19/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Proteasome inhibitors are widely used anticancer drugs. The three clinically approved agents are modified small peptides that preferentially target one of the proteasome's three active sites (β5) at physiologic concentrations. In addition to these drugs, there is also an endogenous proteasome inhibitor, PI31/Fub1, that enters the proteasome's interior to simultaneously yet specifically inhibit all three active sites. Here, we have used PI31's evolutionarily optimized inhibitory mechanisms to develop a suite of potent and specific β2 inhibitors. The lead compound strongly inhibited growth of multiple myeloma cells as a standalone agent, indicating the compound's cell permeability and establishing β2 as a potential therapeutic target in multiple myeloma. The lead compound also showed strong synergy with the existing β5 inhibitor bortezomib; such combination therapies might help with existing challenges of resistance and severe side effects. These results represent an effective method for rational structure-guided development of proteasome inhibitors.
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Affiliation(s)
- Benjamin Velez
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
| | - Aida Razi
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
| | | | - Richard Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology,Harvard Medical School,Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology,Harvard Medical School,Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
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5
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Zheng W, Rawson S, Shen Z, Tamilselvan E, Smith HE, Halford J, Shen C, Murthy SE, Ulbrich MH, Sotomayor M, Fu TM, Holt JR. TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels. Neuron 2023; 111:3195-3210.e7. [PMID: 37543036 PMCID: PMC10592209 DOI: 10.1016/j.neuron.2023.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 10/17/2022] [Revised: 05/12/2023] [Accepted: 07/08/2023] [Indexed: 08/07/2023]
Abstract
OSCA/TMEM63s form mechanically activated (MA) ion channels in plants and animals, respectively. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. Here, we uncover an unanticipated monomeric configuration of TMEM63 proteins. Structures of TMEM63A and TMEM63B (referred to as TMEM63s) revealed a single highly restricted pore. Functional analyses demonstrated that TMEM63s are bona fide mechanosensitive ion channels, characterized by small conductance and high thresholds. TMEM63s possess evolutionary variations in the intracellular linker IL2, which mediates dimerization in OSCAs. Replacement of OSCA1.2 IL2 with TMEM63A IL2 or mutations to key variable residues resulted in monomeric OSCA1.2 and MA currents with significantly higher thresholds. Structural analyses revealed substantial conformational differences in the mechano-sensing domain IL2 and gating helix TM6 between TMEM63s and OSCA1.2. Our studies reveal that mechanosensitivity in OSCA/TMEM63 channels is affected by oligomerization and suggest gating mechanisms that may be shared by OSCA/TMEM63, TMEM16, and TMC channels.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Harper E Smith
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Halford
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Chen Shen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Swetha E Murthy
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maximilian H Ulbrich
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Internal Medicine IV, University of Freiburg Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.
| | - Jeffrey R Holt
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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6
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Walsh RM, Rawson S, Schnell HM, Velez B, Rajakumar T, Hanna J. Structure of the preholoproteasome reveals late steps in proteasome core particle biogenesis. Nat Struct Mol Biol 2023; 30:1516-1524. [PMID: 37653242 PMCID: PMC10879985 DOI: 10.1038/s41594-023-01081-w] [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: 09/12/2022] [Accepted: 07/26/2023] [Indexed: 09/02/2023]
Abstract
Assembly of the proteasome's core particle (CP), a barrel-shaped chamber of four stacked rings, requires five chaperones and five subunit propeptides. Fusion of two half-CP precursors yields a complete structure but remains immature until active site maturation. Here, using Saccharomyces cerevisiae, we report a high-resolution cryogenic electron microscopy structure of preholoproteasome, a post-fusion assembly intermediate. Our data reveal how CP midline-spanning interactions induce local changes in structure, facilitating maturation. Unexpectedly, we find that cleavage may not be sufficient for propeptide release, as residual interactions with chaperones such as Ump1 hold them in place. We evaluated previous models proposing that dynamic conformational changes in chaperones drive CP fusion and autocatalytic activation by comparing preholoproteasome to pre-fusion intermediates. Instead, the data suggest a scaffolding role for the chaperones Ump1 and Pba1/Pba2. Our data clarify key aspects of CP assembly, suggest that undiscovered mechanisms exist to explain CP fusion/activation, and have relevance for diseases of defective CP biogenesis.
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Affiliation(s)
- Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Helena M Schnell
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin Velez
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Tamayanthi Rajakumar
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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7
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Park E, Rawson S, Schmoker A, Kim BW, Oh S, Song K, Jeon H, Eck MJ. Publisher Correction: Cryo-EM structure of a RAS/RAF recruitment complex. Nat Commun 2023; 14:5517. [PMID: 37679375 PMCID: PMC10485013 DOI: 10.1038/s41467-023-41365-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Pfizer R&D Center, 3200 Walnut St, Boulder, CO, 80301, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anna Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Sehee Oh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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8
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Cao R, Jones DTD, Pan L, Wang S, Rawson S, Aster JC, Blacklow SC. Molecular Mechanism of PP2A/B55α Inhibition by IER5. bioRxiv 2023:2023.08.29.555174. [PMID: 37693604 PMCID: PMC10491241 DOI: 10.1101/2023.08.29.555174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
PP2A serine/threonine protein phosphatases are heterotrimeric complexes that have a wide range of essential physiologic functions. The B55α form of PP2A has critical roles in cell cycle regulation, mitotic exit, and the DNA damage response1-6. Its activity is modulated by additional regulatory proteins, such as ARPP197, FAM122A8, and IER59. However, the precise mechanisms underlying the modulation of PP2A activity by these proteins remain elusive. Here, we show that IER5 inhibits pTau dephosphorylation by PP2A/B55α in biochemical assays and report a cryoelectron microscopy structure of the PP2A/B55α-IER5 complex, which reveals that IER5 occludes a surface on B55α used for substrate recruitment10-12. Mutation of interface residues on IER5 interferes with recovery of B55α in co-immunoprecipitation assays and suppresses events in squamous carcinoma cells, such as KRT1 expression, that depend on inhibition of PP2A/B55α by IER59. These studies define the molecular basis for PP2A inhibition by IER5 and suggest a roadmap for selective pharmacologic modulation of PP2A/B55α complexes.
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Affiliation(s)
- Ruili Cao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Daniel TD Jones
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Li Pan
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Shumei Wang
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA USA
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9
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Skiba MA, Sterling SM, Rawson S, Gilman MS, Xu H, Nemeth GR, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Wingler LM, Kruse AC. Antibodies Expand the Scope of Angiotensin Receptor Pharmacology. bioRxiv 2023:2023.08.23.554128. [PMID: 37662341 PMCID: PMC10473732 DOI: 10.1101/2023.08.23.554128] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
G protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often limited at the receptor, tissue, and cellular level. Antibodies have the potential to address these limitations but their properties as GPCR ligands remain poorly characterized. Here, using protein engineering, pharmacological assays, and structural studies, we develop maternally selective heavy chain-only antibody ("nanobody") antagonists against the angiotensin II type I receptor (AT1R) and uncover the unusual molecular basis of their receptor antagonism. We further show that our nanobodies can simultaneously bind to AT1R with specific small-molecule antagonists and demonstrate that ligand selectivity can be readily tuned. Our work illustrates that antibody fragments can exhibit rich and evolvable pharmacology, attesting to their potential as next-generation GPCR modulators.
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Affiliation(s)
- Meredith A. Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah M. Sterling
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Morgan S.A. Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Huixin Xu
- Department of Pathology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Genevieve R. Nemeth
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph D. Hurley
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pengxiang Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Dean P. Staus
- Department of Medicine and Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Jihee Kim
- Department of Medicine and Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Maria K. Lehtinen
- Department of Pathology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Laura M. Wingler
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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10
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Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC. The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. Nat Chem Biol 2023; 19:1013-1021. [PMID: 37081311 PMCID: PMC10530065 DOI: 10.1038/s41589-023-01321-6] [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: 09/07/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
The relaxin family peptide receptor 1 (RXFP1) is the receptor for relaxin-2, an important regulator of reproductive and cardiovascular physiology. RXFP1 is a multi-domain G protein-coupled receptor (GPCR) with an ectodomain consisting of a low-density lipoprotein receptor class A (LDLa) module and leucine-rich repeats. The mechanism of RXFP1 signal transduction is clearly distinct from that of other GPCRs, but remains very poorly understood. In the present study, we determine the cryo-electron microscopy structure of active-state human RXFP1, bound to a single-chain version of the endogenous agonist relaxin-2 and the heterotrimeric Gs protein. Evolutionary coupling analysis and structure-guided functional experiments reveal that RXFP1 signals through a mechanism of autoinhibition. Our results explain how an unusual GPCR family functions, providing a path to rational drug development targeting the relaxin receptors.
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Affiliation(s)
- Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James Osei-Owusu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly P Brock
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xinyue Liu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Julian Mintseris
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiaojing Cong
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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11
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Park E, Rawson S, Schmoker A, Kim BW, Oh S, Song K, Jeon H, Eck MJ. Cryo-EM structure of a RAS/RAF recruitment complex. Nat Commun 2023; 14:4580. [PMID: 37516774 PMCID: PMC10387098 DOI: 10.1038/s41467-023-40299-6] [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: 09/29/2022] [Accepted: 07/19/2023] [Indexed: 07/31/2023] Open
Abstract
RAF-family kinases are activated by recruitment to the plasma membrane by GTP-bound RAS, whereupon they initiate signaling through the MAP kinase cascade. Prior structural studies of KRAS with RAF have focused on the isolated RAS-binding and cysteine-rich domains of RAF (RBD and CRD, respectively), which interact directly with RAS. Here we describe cryo-EM structures of a KRAS bound to intact BRAF in an autoinhibited state with MEK1 and a 14-3-3 dimer. Analysis of this KRAS/BRAF/MEK1/14-3-3 complex reveals KRAS bound to the RAS-binding domain of BRAF, captured in two orientations. Core autoinhibitory interactions in the complex are unperturbed by binding of KRAS and in vitro activation studies confirm that KRAS binding is insufficient to activate BRAF, absent membrane recruitment. These structures illustrate the separability of binding and activation of BRAF by RAS and suggest stabilization of this pre-activation intermediate as an alternative therapeutic strategy to blocking binding of KRAS.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Pfizer R&D Center, 3200 Walnut St, Boulder, CO, 80301, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anna Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Sehee Oh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA, 01605, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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12
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Duncan-Lowey B, Tal N, Johnson AG, Rawson S, Mayer ML, Doron S, Millman A, Melamed S, Fedorenko T, Kacen A, Brandis A, Mehlman T, Amitai G, Sorek R, Kranzusch PJ. Cryo-EM structure of the RADAR supramolecular anti-phage defense complex. Cell 2023; 186:987-998.e15. [PMID: 36764290 PMCID: PMC9994260 DOI: 10.1016/j.cell.2023.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 08/15/2022] [Revised: 12/02/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023]
Abstract
RADAR is a two-protein bacterial defense system that was reported to defend against phage by "editing" messenger RNA. Here, we determine cryo-EM structures of the RADAR defense complex, revealing RdrA as a heptameric, two-layered AAA+ ATPase and RdrB as a dodecameric, hollow complex with twelve surface-exposed deaminase active sites. RdrA and RdrB join to form a giant assembly up to 10 MDa, with RdrA docked as a funnel over the RdrB active site. Surprisingly, our structures reveal an RdrB active site that targets mononucleotides. We show that RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication. Our results define ATP mononucleotide deamination as a determinant of RADAR immunity and reveal supramolecular assembly of a nucleotide-modifying machine as a mechanism of anti-phage defense.
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Affiliation(s)
- Brianna Duncan-Lowey
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nitzan Tal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Shaun Rawson
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA 02115, USA
| | - Megan L Mayer
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA 02115, USA
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Taya Fedorenko
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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13
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Walsh RM, Mayer ML, Sun CH, Rawson S, Nair R, Sterling SM, Li Z. Practices for running a research-oriented shared cryo-EM facility. Front Mol Biosci 2022; 9:960940. [PMID: 36188224 PMCID: PMC9521047 DOI: 10.3389/fmolb.2022.960940] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The Harvard Cryo-Electron Microscopy Center for Structural Biology, which was formed as a consortium between Harvard Medical School, Boston Children’s Hospital, Dana-Farber Cancer Institute, and Massachusetts General Hospital, serves both academic and commercial users in the greater Harvard community. The facility strives to optimize research productivity while training users to become expert electron microscopists. These two tasks may be at odds and require careful balance to keep research projects moving forward while still allowing trainees to develop independence and expertise. This article presents the model developed at Harvard Medical School for running a research-oriented cryo-EM facility. Being a research-oriented facility begins with training in cryo-sample preparation on a trainee’s own sample, ideally producing grids that can be screened and optimized on the Talos Arctica via multiple established pipelines. The first option, staff assisted screening, requires no user experience and a staff member provides instant feedback about the suitability of the sample for cryo-EM investigation and discusses potential strategies for sample optimization. Another option, rapid access, allows users short sessions to screen samples and introductory training for basic microscope operation. Once a sample reaches the stage where data collection is warranted, new users are trained on setting up data collection for themselves on either the Talos Arctica or Titan Krios microscope until independence is established. By providing incremental training and screening pipelines, the bottleneck of sample preparation can be overcome in parallel with developing skills as an electron microscopist. This approach allows for the development of expertise without hindering breakthroughs in key research areas.
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Affiliation(s)
- Richard M. Walsh
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Megan L. Mayer
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Christopher H. Sun
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Shaun Rawson
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Remya Nair
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Sarah M. Sterling
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Zongli Li
- Harvard Cryo-EM Center for Structural Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
- *Correspondence: Zongli Li,
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14
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Schnell HM, Walsh RM, Rawson S, Hanna J. Chaperone-mediated assembly of the proteasome core particle - recent developments and structural insights. J Cell Sci 2022; 135:275096. [PMID: 35451017 PMCID: PMC9080555 DOI: 10.1242/jcs.259622] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Much of cellular activity is mediated by large multisubunit complexes. However, many of these complexes are too complicated to assemble spontaneously. Instead, their biogenesis is facilitated by dedicated chaperone proteins, which are themselves excluded from the final product. This is the case for the proteasome, a ubiquitous and highly conserved cellular regulator that mediates most selective intracellular protein degradation in eukaryotes. The proteasome consists of two subcomplexes: the core particle (CP), where proteolysis occurs, and the regulatory particle (RP), which controls substrate access to the CP. Ten chaperones function in proteasome biogenesis. Here, we review the pathway of CP biogenesis, which requires five of these chaperones and proceeds through a highly ordered multistep pathway. We focus on recent advances in our understanding of CP assembly, with an emphasis on structural insights. This pathway of CP biogenesis represents one of the most dramatic examples of chaperone-mediated assembly and provides a paradigm for understanding how large multisubunit complexes can be produced.
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Affiliation(s)
- Helena M Schnell
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Richard M Walsh
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.,Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
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15
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Schnell HM, Ang J, Rawson S, Walsh RM, Micoogullari Y, Hanna J. Mechanism of Proteasome Gate Modulation by Assembly Chaperones Pba1 and Pba2. J Biol Chem 2022; 298:101906. [PMID: 35398095 PMCID: PMC9065996 DOI: 10.1016/j.jbc.2022.101906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/04/2022] Open
Abstract
The active sites of the proteasome are housed within its central core particle (CP), a barrel-shaped chamber of four stacked heptameric rings, and access of substrates to the CP interior is mediated by gates at either axial end. These gates are constitutively closed and may be opened by the regulatory particle (RP), which binds the CP and facilitates substrate degradation. We recently showed that the heterodimeric CP assembly chaperones Pba1/2 also mediate gate opening through an unexpected structural arrangement that facilitates the insertion of the N terminus of Pba1 into the CP interior; however, the full mechanism of Pba1/2-mediated gate opening is unclear. Here, we report a detailed analysis of CP gate modulation by Pba1/2. The clustering of key residues at the interface between neighboring α-subunits is a critical feature of RP-mediated gate opening, and we find that Pba1/2 recapitulate this strategy. Unlike RP, which inserts at six α-subunit interfaces, Pba1/2 insert at only two α-subunit interfaces. Nevertheless, Pba1/2 are able to regulate six of the seven interfacial clusters, largely through direct interactions. The N terminus of Pba1 also physically interacts with the center of the gate, disrupting the intersubunit contacts that maintain the closed state. This novel mechanism of gate modulation appears to be unique to Pba1/2 and therefore likely occurs only during proteasome assembly. Our data suggest that release of Pba1/2 at the conclusion of assembly is what allows the nascent CP to assume its mature gate conformation, which is primarily closed, until activated by RP.
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16
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Zheng W, Shen C, Wang L, Rawson S, Xie WJ, Nist-Lund C, Wu J, Shen Z, Xia S, Holt JR, Wu H, Fu TM. pH regulates potassium conductance and drives a constitutive proton current in human TMEM175. Sci Adv 2022; 8:eabm1568. [PMID: 35333573 PMCID: PMC8956256 DOI: 10.1126/sciadv.abm1568] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/03/2022] [Indexed: 06/01/2023]
Abstract
Human TMEM175, a noncanonical potassium (K+) channel in endolysosomes, contributes to their pH stability and is implicated in the pathogenesis of Parkinson's disease (PD). Structurally, the TMEM175 family exhibits an architecture distinct from canonical potassium channels, as it lacks the typical TVGYG selectivity filter. Here, we show that human TMEM175 not only exhibits pH-dependent structural changes that reduce K+ permeation at acidic pH but also displays proton permeation. TMEM175 constitutively conducts K+ at pH 7.4 but displays reduced K+ permeation at lower pH. In contrast, proton current through TMEM175 increases with decreasing pH because of the increased proton gradient. Molecular dynamics simulation, structure-based mutagenesis, and electrophysiological analysis suggest that K+ ions and protons share the same permeation pathway. The M393T variant of human TMEM175 associated with PD shows reduced function in both K+ and proton permeation. Together, our structural and electrophysiological analysis reveals a mechanism of TMEM175 regulation by pH.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology and Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Shen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Wen Jun Xie
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Carl Nist-Lund
- Departments of Otolaryngology and Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Wu
- Departments of Otolaryngology and Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Shiyu Xia
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jeffrey R. Holt
- Departments of Otolaryngology and Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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17
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Andreeva L, David L, Rawson S, Shen C, Pasricha T, Pelegrin P, Wu H. NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation. Cell 2021; 184:6299-6312.e22. [PMID: 34861190 PMCID: PMC8763037 DOI: 10.1016/j.cell.2021.11.011] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/17/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022]
Abstract
The NACHT-, leucine-rich-repeat- (LRR), and pyrin domain-containing protein 3 (NLRP3) is emerging to be a critical intracellular inflammasome sensor of membrane integrity and a highly important clinical target against chronic inflammation. Here, we report that an endogenous, stimulus-responsive form of full-length mouse NLRP3 is a 12- to 16-mer double-ring cage held together by LRR-LRR interactions with the pyrin domains shielded within the assembly to avoid premature activation. Surprisingly, this NLRP3 form is predominantly membrane localized, which is consistent with previously noted localization of NLRP3 at various membrane organelles. Structure-guided mutagenesis reveals that trans-Golgi network dispersion into vesicles, an early event observed for many NLRP3-activating stimuli, requires the double-ring cages of NLRP3. Double-ring-defective NLRP3 mutants abolish inflammasome punctum formation, caspase-1 processing, and cell death. Thus, our data uncover a physiological NLRP3 oligomer on the membrane that is poised to sense diverse signals to induce inflammasome activation.
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Affiliation(s)
- Liudmila Andreeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Cryo-EM Center for Structural Biology, Boston, MA 02115, USA
| | - Chen Shen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Teerithveen Pasricha
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Northeastern University, Boston, MA 02115, USA
| | - Pablo Pelegrin
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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18
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Cai Y, Zhang J, Xiao T, Lavine CL, Rawson S, Peng H, Zhu H, Anand K, Tong P, Gautam A, Lu S, Sterling SM, Walsh RM, Rits-Volloch S, Lu J, Wesemann DR, Yang W, Seaman MS, Chen B. Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants. Science 2021; 373:642-648. [PMID: 34168070 PMCID: PMC9245151 DOI: 10.1126/science.abi9745] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022]
Abstract
As battles to contain the COVID-19 pandemic continue, attention is focused on emerging variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that have been deemed variants of concern because they are resistant to antibodies elicited by infection or vaccination or they increase transmissibility or disease severity. Three papers used functional and structural studies to explore how mutations in the viral spike protein affect its ability to infect host cells and to evade host immunity. Gobeil et al. looked at a variant spike protein involved in transmission between minks and humans, as well as the B1.1.7 (alpha), B.1.351 (beta), and P1 (gamma) spike variants; Cai et al. focused on the alpha and beta variants; and McCallum et al. discuss the properties of the spike protein from the B1.1.427/B.1.429 (epsilon) variant. Together, these papers show a balance among mutations that enhance stability, those that increase binding to the human receptor ACE2, and those that confer resistance to neutralizing antibodies. —VV Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains in the COVID-19 pandemic. We report here cryo–electron microscopy structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Amino acid substitutions in the B.1.1.7 protein increase both the accessibility of its receptor binding domain and the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement may account for the increased transmissibility. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, making it resistant to some potent neutralizing antibodies. These findings provide structural details on how SARS-CoV-2 has evolved to enhance viral fitness and immune evasion.
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Affiliation(s)
- Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Street, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Street, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Street, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Shaun Rawson
- SBGrid Consortium, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Street, Boston, MA 02115, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, 4 Blackfan Circle, Boston, MA 02115, USA
| | - Krishna Anand
- Institute for Protein Innovation, Harvard Institutes of Medicine, 4 Blackfan Circle, Boston, MA 02115, USA
| | - Pei Tong
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Avneesh Gautam
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Shen Lu
- Codex BioSolutions, Inc., 401 Professional Drive, Gaithersburg, MD 20879, USA
| | - Sarah M Sterling
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Richard M Walsh
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sophia Rits-Volloch
- Division of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Street, Boston, MA 02115, USA
| | - Jianming Lu
- Codex BioSolutions, Inc., 401 Professional Drive, Gaithersburg, MD 20879, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, 3900 Reservoir Road, NW, Washington, DC 20057, USA
| | - Duane R Wesemann
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Wei Yang
- Institute for Protein Innovation, Harvard Institutes of Medicine, 4 Blackfan Circle, Boston, MA 02115, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, 3 Blackfan Street, Boston, MA 02115, USA. .,Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, USA
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19
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Cai Y, Zhang J, Xiao T, Lavine CL, Rawson S, Peng H, Zhu H, Anand K, Tong P, Gautam A, Lu S, Sterling SM, Walsh RM, Rits-Volloch S, Lu J, Wesemann DR, Yang W, Seaman MS, Chen B. Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants. bioRxiv 2021. [PMID: 33880477 DOI: 10.1101/2021.04.13.439709] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains that continue to fuel the COVID-19 pandemic despite intensive vaccination efforts throughout the world. We report here cryo-EM structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Mutations in the B.1.1.7 protein increase the accessibility of its receptor binding domain and also the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement can account for the increased transmissibility and risk of mortality as the variant may begin to infect efficiently infect additional cell types expressing low levels of ACE2. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, rendering complete resistance to some potent neutralizing antibodies. These findings provide structural details on how the wide spread of SARS-CoV-2 enables rapid evolution to enhance viral fitness and immune evasion. They may guide intervention strategies to control the pandemic.
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20
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Schnell HM, Walsh RM, Rawson S, Kaur M, Bhanu MK, Tian G, Prado MA, Guerra-Moreno A, Paulo JA, Gygi SP, Roelofs J, Finley D, Hanna J. Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis. Nat Struct Mol Biol 2021; 28:418-425. [PMID: 33846632 DOI: 10.1038/s41594-021-00583-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022]
Abstract
The proteasome mediates most selective protein degradation. Proteolysis occurs within the 20S core particle (CP), a barrel-shaped chamber with an α7β7β7α7 configuration. CP biogenesis proceeds through an ordered multistep pathway requiring five chaperones, Pba1-4 and Ump1. Using Saccharomyces cerevisiae, we report high-resolution structures of CP assembly intermediates by cryogenic-electron microscopy. The first structure corresponds to the 13S particle, which consists of a complete α-ring, partial β-ring (β2-4), Ump1 and Pba1/2. The second structure contains two additional subunits (β5-6) and represents a later pre-15S intermediate. These structures reveal the architecture and positions of Ump1 and β2/β5 propeptides, with important implications for their functions. Unexpectedly, Pba1's N terminus extends through an open CP pore, accessing the CP interior to contact Ump1 and the β5 propeptide. These results reveal how the coordinated activity of Ump1, Pba1 and the active site propeptides orchestrate key aspects of CP assembly.
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Affiliation(s)
- Helena M Schnell
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Mandeep Kaur
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Meera K Bhanu
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Angel Guerra-Moreno
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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21
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Susa KJ, Rawson S, Kruse AC, Blacklow SC. Cryo-EM structure of the B cell co-receptor CD19 bound to the tetraspanin CD81. Science 2021; 371:300-305. [PMID: 33446559 DOI: 10.1126/science.abd9836] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022]
Abstract
Signaling through the CD19-CD81 co-receptor complex, in combination with the B cell receptor, is a critical determinant of B cell development and activation. It is unknown how CD81 engages CD19 to enable co-receptor function. Here, we report a 3.8-angstrom structure of the CD19-CD81 complex bound to a therapeutic antigen-binding fragment, determined by cryo-electron microscopy (cryo-EM). The structure includes both the extracellular domains and the transmembrane helices of the complex, revealing a contact interface between the ectodomains that drives complex formation. Upon binding to CD19, CD81 opens its ectodomain to expose a hydrophobic CD19-binding surface and reorganizes its transmembrane helices to occlude a cholesterol binding pocket present in the apoprotein. Our data reveal the structural basis for CD19-CD81 complex assembly, providing a foundation for rational design of therapies for B cell dysfunction.
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Affiliation(s)
- Katherine J Susa
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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22
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Cai Y, Zhang J, Xiao T, Peng H, Sterling SM, Walsh RM, Rawson S, Rits-Volloch S, Chen B. Distinct conformational states of SARS-CoV-2 spike protein. Science 2020; 369:1586-1592. [PMID: 32694201 PMCID: PMC7464562 DOI: 10.1126/science.abd4251] [Citation(s) in RCA: 772] [Impact Index Per Article: 193.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Intervention strategies are urgently needed to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The trimeric viral spike (S) protein catalyzes fusion between viral and target cell membranes to initiate infection. Here, we report two cryo-electron microscopy structures derived from a preparation of the full-length S protein, representing its prefusion (2.9-angstrom resolution) and postfusion (3.0-angstrom resolution) conformations, respectively. The spontaneous transition to the postfusion state is independent of target cells. The prefusion trimer has three receptor-binding domains clamped down by a segment adjacent to the fusion peptide. The postfusion structure is strategically decorated by N-linked glycans, suggesting possible protective roles against host immune responses and harsh external conditions. These findings advance our understanding of SARS-CoV-2 entry and may guide the development of vaccines and therapeutics.
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Affiliation(s)
- Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sarah M Sterling
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Richard M Walsh
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- SBGrid Consortium, Harvard Medical School, Boston, MA 02115, USA
| | - Sophia Rits-Volloch
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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23
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Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Baslé A, Ranson NA, Potempa J, van den Berg B. Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis. Nat Microbiol 2020; 5:1016-1025. [PMID: 32393857 PMCID: PMC7610489 DOI: 10.1038/s41564-020-0716-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 09/02/2019] [Accepted: 03/31/2020] [Indexed: 12/30/2022]
Abstract
Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.
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Affiliation(s)
- Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Joshua B R White
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- The Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
| | - Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Shaun Rawson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- The Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
| | - Carsten Scavenius
- Interdisciplinary Nanoscience Center (iNANO) and the Department of Molecular Biology, Aarhus University, Aarhus, Denmark
| | - Jan J Enghild
- Interdisciplinary Nanoscience Center (iNANO) and the Department of Molecular Biology, Aarhus University, Aarhus, Denmark
| | - Grzegorz P Bereta
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karunakar Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | | | - Arnaud Baslé
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA.
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK.
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24
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Tomasek D, Rawson S, Lee J, Wzorek JS, Harrison SC, Li Z, Kahne D. Structure of a nascent membrane protein as it folds on the BAM complex. Nature 2020; 583:473-478. [PMID: 32528179 PMCID: PMC7367713 DOI: 10.1038/s41586-020-2370-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [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: 11/18/2019] [Accepted: 03/25/2020] [Indexed: 11/09/2022]
Abstract
Mitochondria, chloroplasts, and Gram-negative bacteria are encased in a double layer of membranes. The outer membrane contains proteins with a β-barrel structure1,2. β-barrels are sheets of β-strands wrapped into a cylinder with the first strand hydrogen-bonded to the last strand. Conserved multi-subunit molecular machines fold and insert these proteins into the outer membrane3–5. One subunit of the machines is itself a β-barrel protein that plays a central role in folding other β-barrels. In Gram-negative bacteria, the β-barrel assembly machine (Bam) consists of the β-barrel protein BamA and four lipoproteins5–8. To understand how the Bam complex accelerates folding without using exogenous energy (e.g., ATP)9, we trapped folding intermediates on the machine. We report here the structure of the Bam complex folding BamA itself. The BamA catalyst (BamAM, for BamAmachine) forms an asymmetric hybrid β-barrel with the BamA substrate (BamAS). The N-terminal edge of BamAM has an antiparallel hydrogen-bonded interface with the C-terminal edge of BamAS, consistent with previous crosslinking studies10–12; the other edges of BamAM and BamAS are close to each other but curl inward and do not pair. Six hydrogen bonds in a membrane environment make the interface between the two proteins very stable. This stability allows folding but creates a high kinetic barrier to substrate release once folding has finished. Features at each end of the substrate overcome the barrier and promote release by stepwise exchange of hydrogen bonds. This mechanism of substrate-assisted product release explains how the Bam complex can stably associate with the substrate during folding and then turn over rapidly when folding is complete.
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Affiliation(s)
- David Tomasek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Lee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY, USA
| | - Joseph S Wzorek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston, MA, USA.
| | - Zongli Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston, MA, USA.
| | - Daniel Kahne
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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25
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Cai Y, Zhang J, Xiao T, Peng H, Sterling SM, Walsh RM, Rawson S, Rits-Volloch S, Chen B. Distinct conformational states of SARS-CoV-2 spike protein. bioRxiv 2020. [PMID: 32511405 DOI: 10.1101/2020.05.16.099317] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ongoing SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic has created urgent needs for intervention strategies to control the crisis. The spike (S) protein of the virus forms a trimer and catalyzes fusion between viral and target cell membranes - the first key step of viral infection. Here we report two cryo-EM structures, both derived from a single preparation of the full-length S protein, representing the prefusion (3.1Å resolution) and postfusion (3.3Å resolution) conformations, respectively. The spontaneous structural transition to the postfusion state under mild conditions is independent of target cells. The prefusion trimer forms a tightly packed structure with three receptor-binding domains clamped down by a segment adjacent to the fusion peptide, significantly different from recently published structures of a stabilized S ectodomain trimer. The postfusion conformation is a rigid tower-like trimer, but decorated by N-linked glycans along its long axis with almost even spacing, suggesting possible involvement in a mechanism protecting the virus from host immune responses and harsh external conditions. These findings advance our understanding of how SARS-CoV-2 enters a host cell and may guide development of vaccines and therapeutics.
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26
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Erlandson SC, Rawson S, Kruse AC. Characterization of a Leucine‐Rich Repeat‐Containing G Protein‐Coupled Receptor. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.09325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Park E, Rawson S, Li K, Kim BW, Ficarro SB, Pino GGD, Sharif H, Marto JA, Jeon H, Eck MJ. Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes. Nature 2019; 575:545-550. [PMID: 31581174 PMCID: PMC7014971 DOI: 10.1038/s41586-019-1660-y] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival1–3. RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer4–6. At present, the structural basis for RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo electron microscopy (cryo-EM). A 4.1Å resolution cryo-EM reconstruction reveals an inactive BRAF/MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kunhua Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonzalo Gonzalez-Del Pino
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Humayun Sharif
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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28
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Winkler MBL, Kidmose RT, Szomek M, Thaysen K, Rawson S, Muench SP, Wüstner D, Pedersen BP. Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins. Cell 2019; 179:485-497.e18. [PMID: 31543266 DOI: 10.1016/j.cell.2019.08.038] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/05/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022]
Abstract
Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, using a combination of crystallography, cryo-electron microscopy, and biochemical and in vivo studies on the Saccharomyces cerevisiae NPC system (NCR1 and NPC2), we present a framework for sterol membrane integration. Sterols are transferred between hydrophobic pockets of vacuolar NPC2 and membrane-protein NCR1. NCR1 has its N-terminal domain (NTD) positioned to deliver a sterol to a tunnel connecting NTD to the luminal membrane leaflet 50 Å away. A sterol is caught inside this tunnel during transport, and a proton-relay network of charged residues in the transmembrane region is linked to this tunnel supporting a proton-driven transport mechanism. We propose a model for sterol integration that clarifies the role of NPC proteins in this essential eukaryotic pathway and that rationalizes mutations in patients with Niemann-Pick disease type C.
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Affiliation(s)
- Mikael B L Winkler
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark
| | - Rune T Kidmose
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Shaun Rawson
- School of Biomedical Sciences and The Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences and The Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Bjørn Panyella Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Aarhus C 8000, Denmark.
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29
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Thompson RF, Iadanza MG, Hesketh EL, Rawson S, Ranson NA. Collection, pre-processing and on-the-fly analysis of data for high-resolution, single-particle cryo-electron microscopy. Nat Protoc 2019; 14:100-118. [PMID: 30487656 DOI: 10.1038/s41596-018-0084-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dramatic growth in the use of cryo-electron microscopy (cryo-EM) to generate high-resolution structures of macromolecular complexes has changed the landscape of structural biology. The majority of structures deposited in the Electron Microscopy Data Bank (EMDB) at higher than 4-Å resolution were collected on Titan Krios microscopes. Although the pipeline for single-particle data collection is becoming routine, there is much variation in how sessions are set up. Furthermore, when collection is under way, there are a range of approaches for efficiently moving and pre-processing these data. Here, we present a standard operating procedure for single-particle data collection with Thermo Fisher Scientific EPU software, using the two most common direct electron detectors (the Thermo Fisher Scientific Falcon 3 (F3EC) and the Gatan K2), as well as a strategy for structuring these data to enable efficient pre-processing and on-the-fly monitoring of data collection. This protocol takes 3-6 h to set up a typical automated data collection session.
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Affiliation(s)
- Rebecca F Thompson
- The Astbury Biostructure Laboratory, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Matthew G Iadanza
- The Astbury Biostructure Laboratory, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Emma L Hesketh
- The Astbury Biostructure Laboratory, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Shaun Rawson
- The Astbury Biostructure Laboratory, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,The Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
| | - Neil A Ranson
- The Astbury Biostructure Laboratory, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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30
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Johnson R, Rawson S, McPhillie M, Fishwick C, Muench S. The Growing Role of Electron Microscopy in Anti-parasitic Drug Discovery. Curr Med Chem 2019; 25:5279-5290. [DOI: 10.2174/0929867324666171109120526] [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] [Received: 08/06/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 11/22/2022]
Abstract
Background:
Parasite diseases are a huge burden on human health causing significant
morbidity and mortality. However, parasite structure based drug discovery programmes
have been hindered by a lack of high resolution structural information from parasite
derived proteins and have often relied upon homology models from mammalian systems.
The recent renaissance in electron microscopy (EM) has caused a dramatic rise in the
number of structures being determined at high resolution and subsequently enabled it to be
thought of as a tool in drug discovery.
Results:
In this review, we discuss the challenges associated with the structural determination
of parasite proteins including the difficulties in obtaining sufficient quantities of protein.
We then discuss the reasons behind the resurgence in EM, how it may overcome some of
these challenges and provide examples of EM derived parasite protein structures. Finally,
we discuss the challenges which EM needs to overcome before it is used as a mainstream
technique in anti-parasite drug discovery.
Conclusions:
This review reports the progress that has been made in obtaining sufficient
quantities of proteins for structural studies and the role EM may play in future structure
based drug design programs. The outlook for future structure based drug design programs
against some of the most devastating parasite diseases looks promising.
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Affiliation(s)
- R.M. Johnson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - S. Rawson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - M.J. McPhillie
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - C.W.G. Fishwick
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - S.P. Muench
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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31
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Shearer T, Rawson S, Castro S, Lowe T, Vila-Comamala J, Lee P, Cartmell S. X-ray computed tomography of the anterior cruciate ligament and patellar tendon. Muscles Ligaments Tendons J 2019. [DOI: 10.32098/mltj.02.2014.26] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- T. Shearer
- School of Mathematics, University of Manchester,UK
| | - S. Rawson
- School of Materials, University of Manchester, UK
| | - S.J. Castro
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, UK
| | - T. Lowe
- Henry Mosely X-ray Imaging Facility, School of Materials, University of Manchester, UK
| | | | - P.D. Lee
- School of Materials, University of Manchester, UK
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32
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Affiliation(s)
- S. Rawson
- Material’s Science Centre, University of Manchester, UK
| | - S. Cartmell
- Material’s Science Centre, University of Manchester, UK
| | - J. Wong
- Plastic Surgery Research, University of Manchester, UK
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33
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Agip ANA, Blaza JN, Bridges HR, Viscomi C, Rawson S, Muench SP, Hirst J. Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states. Nat Struct Mol Biol 2018; 25:548-556. [PMID: 29915388 PMCID: PMC6054875 DOI: 10.1038/s41594-018-0073-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [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: 03/07/2018] [Accepted: 04/26/2018] [Indexed: 02/02/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-complete models of all 45 subunits in the bovine, ovine and porcine complexes and have identified two states relevant to complex I in ischemia-reperfusion injury. Here, we describe the 3.3-Å structure of complex I from mouse heart mitochondria, a biomedically relevant model system, in the 'active' state. We reveal a nucleotide bound in subunit NDUFA10, a nucleoside kinase homolog, and define mechanistically critical elements in the mammalian enzyme. By comparisons with a 3.9-Å structure of the 'deactive' state and with known bacterial structures, we identify differences in helical geometry in the membrane domain that occur upon activation or that alter the positions of catalytically important charged residues. Our results demonstrate the capability of cryo-EM analyses to challenge and develop mechanistic models for mammalian complex I.
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Affiliation(s)
- Ahmed-Noor A Agip
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - James N Blaza
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Hannah R Bridges
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Carlo Viscomi
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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34
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Amporndanai K, Johnson RM, O’Neill PM, Fishwick CWG, Jamson AH, Rawson S, Muench SP, Hasnain SS, Antonyuk SV. X-ray and cryo-EM structures of inhibitor-bound cytochrome bc1 complexes for structure-based drug discovery. IUCrJ 2018; 5:200-210. [PMID: 29765610 PMCID: PMC5947725 DOI: 10.1107/s2052252518001616] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/26/2018] [Indexed: 05/10/2023]
Abstract
Cytochrome bc1, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry, University of Leeds, Leeds LS2 9JT, England
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, England
| | - Colin W. G. Fishwick
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry, University of Leeds, Leeds LS2 9JT, England
| | - Alexander H. Jamson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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35
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Parmar M, Rawson S, Scarff CA, Goldman A, Dafforn TR, Muench SP, Postis VLG. Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure. Biochim Biophys Acta Biomembr 2018; 1860:378-383. [PMID: 28993151 PMCID: PMC5780298 DOI: 10.1016/j.bbamem.2017.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 01/10/2023]
Abstract
The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine receptor, TRPV1 and the Glutamate receptor. Further developments in the EM field hold the promise of even greater progress in terms of greater resolution, which for membrane proteins is still typically within the 4-7Å range. One advantage of a cryo-EM approach is the ability to study membrane proteins in more "native" like environments for example proteoliposomes, amphipols and nanodiscs. Recently, styrene maleic acid co-polymers (SMA) have been used to extract membrane proteins surrounded by native lipids (SMALPs) maintaining a more natural environment. We report here the structure of the Escherichia coli multidrug efflux transporter AcrB in a SMALP scaffold to sub-nm resolution, with the resulting map being consistent with high resolution crystal structures and other EM derived maps. However, both the C-terminal helix (TM12) and TM7 are poorly defined in the map. These helices are at the exterior of the helical bundle and form the greater interaction with the native lipids and SMA polymer and may represent a more dynamic region of the protein. This work shows the promise of using an SMA approach for single particle cryo-EM studies to provide sub-nm structures.
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Affiliation(s)
- Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Charlotte A Scarff
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK; Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.
| | - Vincent L G Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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Snaith RP, Dove E, Marlowe J, Pemberton S, Price DJ, Rawson S, Wright JF, Butler A, Coughlan AK, Hird M, Trigwell P. Psychosurgery: description and outcome study of a regional service. Psychiatr bull 2018. [DOI: 10.1192/pb.21.2.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The report indicates that a psychosurgery service can be established on a regional basis. The outcome study of the Yorkshire Regional Psychosurgery Service indicates that the treatment should retain a place in the treatment of patients who have failed to respond to other available approaches. For such patients (and their carers) life is a state of persisting torment. Some psychiatrists consider psychosurgery as a procedure not to be countenanced, or outmoded, but patients have a right to know what may be achieved by the treatment and at what cost in terms of possible failure to improve and adverse effects. An audit of the Regional Psychosurgery Service indicates a favourable result of the Intervention. All patients improved to some extent, some very remarkably, and no adverse effects were encountered.
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37
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Rawson S, McPhillie MJ, Johnson RM, Fishwick CWG, Muench SP. The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design. Acta Crystallogr D Struct Biol 2017; 73:534-540. [PMID: 28580915 PMCID: PMC5458495 DOI: 10.1107/s2059798317004077] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/13/2017] [Indexed: 12/14/2022] Open
Abstract
Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice. There are still significant challenges to be overcome using an EM approach, not least the speed of structure determination, difficulties with low-occupancy ligands and the modest resolution that is available. However, with the anticipated developments in the field of EM, the potential of EM to become a key tool for structure-based drug design, often complementing X-ray and NMR studies, seems promising.
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Affiliation(s)
- S. Rawson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - M. J. McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - R. M. Johnson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - C. W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - S. P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
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38
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Abstract
Membrane proteins are ubiquitous in biology and are key targets for therapeutic development. Despite this, our structural understanding has lagged behind that of their soluble counterparts. This review provides an overview of this important field, focusing in particular on the recent resurgence of electron microscopy (EM) and the increasing role it has to play in the structural studies of membrane proteins, and illustrating this through several case studies. In addition, we examine some of the challenges remaining in structural determination, and what steps are underway to enhance our knowledge of these enigmatic proteins.
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Affiliation(s)
- Shaun Rawson
- a School of Biomedical Sciences, Faculty of Biological Sciences , University of Leeds , Leeds , UK
| | - Simon Davies
- a School of Biomedical Sciences, Faculty of Biological Sciences , University of Leeds , Leeds , UK
| | - Jonathan D Lippiat
- a School of Biomedical Sciences, Faculty of Biological Sciences , University of Leeds , Leeds , UK
| | - Stephen P Muench
- a School of Biomedical Sciences, Faculty of Biological Sciences , University of Leeds , Leeds , UK
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39
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Rawson S, Iadanza MG, Ranson NA, Muench SP. Methods to account for movement and flexibility in cryo-EM data processing. Methods 2016; 100:35-41. [PMID: 27016144 PMCID: PMC4854228 DOI: 10.1016/j.ymeth.2016.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 12/02/2022] Open
Abstract
Recent advances in direct electron detectors and improved CMOS cameras have been accompanied by the development of a range of software to take advantage of the data they produce. In particular they allow for the correction of two types of motion in cryo electron microscopy samples: motion correction for movements of the sample particles in the ice, and differential masking to account for heterogeneity caused by flexibility within protein complexes. Here we provide several scripts that allow users to move between RELION and standalone motion correction and centring programs. We then compare the computational cost and improvements in data quality with each program. We also describe our masking procedures to account for conformational flexibility. For the different elements of this study we have used three samples; a high symmetry virus, flexible protein complex (∼1 MDa) and a relatively small protein complex (∼550 kDa), to benchmark four widely available motion correction packages. Using these as test cases we demonstrate how motion correction and differential masking, as well as an additional particle re-centring protocol can improve final reconstructions when used within the RELION image-processing package.
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Affiliation(s)
- S Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - M G Iadanza
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - N A Ranson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - S P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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40
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Rawson S, Phillips C, Huss M, Tiburcy F, Wieczorek H, Trinick J, Harrison MA, Muench SP. Structure of the vacuolar H+-ATPase rotary motor reveals new mechanistic insights. Structure 2015; 23:461-471. [PMID: 25661654 PMCID: PMC4353692 DOI: 10.1016/j.str.2014.12.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 01/08/2023]
Abstract
Vacuolar H(+)-ATPases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. Here we report a ∼ 1 nm resolution reconstruction of a V-ATPase in a different conformational state from that previously reported for a lower-resolution yeast model. The stator network of the V-ATPase (and by implication that of other rotary ATPases) does not change conformation in different catalytic states, and hence must be relatively rigid. We also demonstrate that a conserved bearing in the catalytic domain is electrostatic, contributing to the extraordinarily high efficiency of rotary ATPases. Analysis of the rotor axle/membrane pump interface suggests how rotary ATPases accommodate different c ring stoichiometries while maintaining high efficiency. The model provides evidence for a half channel in the proton pump, supporting theoretical models of ion translocation. Our refined model therefore provides new insights into the structure and mechanics of the V-ATPases.
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Affiliation(s)
- Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Clair Phillips
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Markus Huss
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
| | - Felix Tiburcy
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
| | - Helmut Wieczorek
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
| | - John Trinick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael A Harrison
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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41
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Postis V, Rawson S, Mitchell JK, Lee SC, Parslow RA, Dafforn TR, Baldwin SA, Muench SP. The use of SMALPs as a novel membrane protein scaffold for structure study by negative stain electron microscopy. Biochim Biophys Acta 2014; 1848:496-501. [PMID: 25450810 PMCID: PMC4331651 DOI: 10.1016/j.bbamem.2014.10.018] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [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: 07/19/2014] [Revised: 10/06/2014] [Accepted: 10/15/2014] [Indexed: 12/17/2022]
Abstract
Despite the great progress recently made in resolving their structures, investigation of the structural biology of membrane proteins still presents major challenges. Even with new technical advances such as lipidic cubic phase crystallisation, obtaining well-ordered crystals remains a significant hurdle in membrane protein X-ray crystallographic studies. As an alternative, electron microscopy has been shown to be capable of resolving > 3.5 Å resolution detail in membrane proteins of modest (~ 300 kDa) size, without the need for crystals. However, the conventional use of detergents for either approach presents several issues, including the possible effects on structure of removing the proteins from their natural membrane environment. As an alternative, it has recently been demonstrated that membrane proteins can be effectively isolated, in the absence of detergents, using a styrene maleic acid co-polymer (SMA). This approach yields SMA lipid particles (SMALPs) in which the membrane proteins are surrounded by a small disk of lipid bilayer encircled by polymer. Here we use the Escherichia coli secondary transporter AcrB as a model membrane protein to demonstrate how a SMALP scaffold can be used to visualise membrane proteins, embedded in a near-native lipid environment, by negative stain electron microscopy, yielding structures at a modest resolution in a short (days) timeframe. Moreover, we show that AcrB within a SMALP scaffold is significantly more active than the equivalent DDM stabilised form. The advantages of SMALP scaffolds within electron microscopy are discussed and we conclude that they may prove to be an important tool in studying membrane protein structure and function. Maintaining membrane proteins in a native-like environment is difficult. SMALP scaffolds efficiently extract AcrB from the membrane. We show SMALP scaffolds to be a robust tool for rapid structural analysis by EM.
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Affiliation(s)
- Vincent Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Jennifer K Mitchell
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Rosemary A Parslow
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Stephen A Baldwin
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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42
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Muench SP, Rawson S, Eyraud V, Delmas AF, Da Silva P, Phillips C, Trinick J, Harrison MA, Gressent F, Huss M. PA1b inhibitor binding to subunits c and e of the vacuolar ATPase reveals its insecticidal mechanism. J Biol Chem 2014; 289:16399-408. [PMID: 24795045 PMCID: PMC4047407 DOI: 10.1074/jbc.m113.541250] [Citation(s) in RCA: 23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 04/14/2014] [Indexed: 12/03/2022] Open
Abstract
The vacuolar ATPase (V-ATPase) is a 1MDa transmembrane proton pump that operates via a rotary mechanism fuelled by ATP. Essential for eukaryotic cell homeostasis, it plays central roles in bone remodeling and tumor invasiveness, making it a key therapeutic target. Its importance in arthropod physiology also makes it a promising pesticide target. The major challenge in designing lead compounds against the V-ATPase is its ubiquitous nature, such that any therapeutic must be capable of targeting particular isoforms. Here, we have characterized the binding site on the V-ATPase of pea albumin 1b (PA1b), a small cystine knot protein that shows exquisitely selective inhibition of insect V-ATPases. Electron microscopy shows that PA1b binding occurs across a range of equivalent sites on the c ring of the membrane domain. In the presence of Mg·ATP, PA1b localizes to a single site, distant from subunit a, which is predicted to be the interface for other inhibitors. Photoaffinity labeling studies show radiolabeling of subunits c and e. In addition, weevil resistance to PA1b is correlated with bafilomycin resistance, caused by mutation of subunit c. The data indicate a binding site to which both subunits c and e contribute and inhibition that involves locking the c ring rotor to a static subunit e and not subunit a. This has implications for understanding the V-ATPase mechanism and that of inhibitors with therapeutic or pesticidal potential. It also provides the first evidence for the position of subunit e within the complex.
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Affiliation(s)
- Stephen P Muench
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom,
| | - Shaun Rawson
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom
| | - Vanessa Eyraud
- Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées-Lyon, Université de Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Batiment Louis-Pasteur 20, avenue Albert Einstein, F-69621 Villeurbanne, France
| | - Agnès F Delmas
- the Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique Unité Propre de Recherche 4301, Rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Pedro Da Silva
- Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées-Lyon, Université de Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Batiment Louis-Pasteur 20, avenue Albert Einstein, F-69621 Villeurbanne, France
| | - Clair Phillips
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom
| | - John Trinick
- the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom, and
| | - Michael A Harrison
- From the School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, West Yorkshire, United Kingdom
| | - Frédéric Gressent
- Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées-Lyon, Université de Lyon, IFR 41, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Batiment Louis-Pasteur 20, avenue Albert Einstein, F-69621 Villeurbanne, France
| | - Markus Huss
- Abteilung Tierphysiologie, Fachbereich Biologie/Chemie Universität Osnabrück, 49069 Osnabrück, Germany
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43
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Wilkinson C, McPhillie MJ, Zhou Y, Woods S, Afanador GA, Rawson S, Khaliq F, Prigge ST, Roberts CW, Rice DW, McLeod R, Fishwick CW, Muench SP. The benzimidazole based drugs show good activity against T. gondii but poor activity against its proposed enoyl reductase enzyme target. Bioorg Med Chem Lett 2014; 24:911-6. [PMID: 24398298 PMCID: PMC3966656 DOI: 10.1016/j.bmcl.2013.12.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 11/08/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 01/22/2023]
Abstract
The enoyl acyl-carrier protein reductase (ENR) enzyme of the apicomplexan parasite family has been intensely studied for antiparasitic drug design for over a decade, with the most potent inhibitors targeting the NAD(+) bound form of the enzyme. However, the higher affinity for the NADH co-factor over NAD(+) and its availability in the natural environment makes the NADH complex form of ENR an attractive target. Herein, we have examined a benzimidazole family of inhibitors which target the NADH form of Francisella ENR, but despite good efficacy against Toxoplasma gondii, the IC50 for T. gondii ENR is poor, with no inhibitory activity at 1 μM. Moreover similar benzimidazole scaffolds are potent against fungi which lack the ENR enzyme and as such we believe that there may be significant off target effects for this family of inhibitors.
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Affiliation(s)
- Craig Wilkinson
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Martin J McPhillie
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, Pediatrics (Infectious Diseases), Committees on Genetics, Immunology, and Molecular Medicine, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, IL 60637, United States
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Gustavo A Afanador
- Johns Hopkins School of Public Health, Rm. E5132, 615 N. Wolfe St., Baltimore, MD 21205, United States
| | - Shaun Rawson
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Farzana Khaliq
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Sean T Prigge
- Johns Hopkins School of Public Health, Rm. E5132, 615 N. Wolfe St., Baltimore, MD 21205, United States
| | - Craig W Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - David W Rice
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, Pediatrics (Infectious Diseases), Committees on Genetics, Immunology, and Molecular Medicine, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, IL 60637, United States
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