1
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Kumar A, Sharma M, Katkar HH. Peripheral Linker Mediates Acyl Carrier Protein's Recognition of Dehydratase and Stabilizes Type-I Mycobacterium tuberculosis Fatty Acid Synthase. J Chem Inf Model 2024; 64:1347-1360. [PMID: 38346863 DOI: 10.1021/acs.jcim.3c01873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Incomplete structural details of Mycobacterium tuberculosis (Mtb) fatty acid synthase-I (FAS-I) at near-atomic resolution have limited our understanding of the shuttling mechanism of its mobile acyl carrier protein (ACP). Here, we have performed atomistic molecular dynamics simulation of Mtb FAS-I with a homology-modeled structure of ACP stalled at dehydratase (DH) and identified key residues that mediate anchoring of the recognition helix of ACP near DH. The observed distance between catalytic residues of ACP and DH agrees with that reported for fungal FAS-I. Further, the conformation of the peripheral linker is found to be crucial in stabilizing ACP near DH. Correlated interdomain motion is observed between DH, enoyl reductase, and malonyl/palmitoyl transferase, consistent with prior experimental reports of fungal and Mtb FAS-I.
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Affiliation(s)
- Akhil Kumar
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Manisha Sharma
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Harshwardhan H Katkar
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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2
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Buyachuihan L, Stegemann F, Grininger M. How Acyl Carrier Proteins (ACPs) Direct Fatty Acid and Polyketide Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202312476. [PMID: 37856285 DOI: 10.1002/anie.202312476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
Megasynthases, such as type I fatty acid and polyketide synthases (FASs and PKSs), are multienzyme complexes responsible for producing primary metabolites and complex natural products. Fatty acids (FAs) and polyketides (PKs) are built by assembling and modifying small acyl moieties in a stepwise manner. A central aspect of FA and PK biosynthesis involves the shuttling of substrates between the domains of the multienzyme complex. This essential process is mediated by small acyl carrier proteins (ACPs). The ACPs must navigate to the different catalytic domains within the multienzyme complex in a particular order to guarantee the fidelity of the biosynthesis pathway. However, the precise mechanisms underlying ACP-mediated substrate shuttling, particularly the factors contributing to the programming of the ACP movement, still need to be fully understood. This Review illustrates the current understanding of substrate shuttling, including concepts of conformational and specificity control, and proposes a confined ACP movement within type I megasynthases.
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Affiliation(s)
- Lynn Buyachuihan
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Franziska Stegemann
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
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3
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Samani EK, Chen AC, Lou JW, Dai DL, Keszei AFA, Tan G, Boone C, Grininger M, Mazhab-Jafari MT. Direct structural analysis of a single acyl carrier protein domain in fatty acid synthase from the fungus Saccharomyces cerevisiae. Commun Biol 2024; 7:92. [PMID: 38216676 PMCID: PMC10786820 DOI: 10.1038/s42003-024-05777-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
Acyl carrier protein (ACP) is the work horse of polyketide (PKS) and fatty acid synthases (FAS) and acts as a substrate shuttling domain in these mega enzymes. In fungi, FAS forms a 2.6 MDa symmetric assembly with six identical copies of FAS1 and FAS2 polypeptides. However, ACP spatial distribution is not restricted by symmetry owing to the long and flexible loops that tether the shuttling domain to its corresponding FAS2 polypeptide. This symmetry breaking has hampered experimental investigation of substrate shuttling route in fungal FAS. Here, we develop a protein engineering and expression method to isolate asymmetric fungal FAS proteins containing odd numbers of ACP domains. Electron cryomicroscopy (cryoEM) observation of the engineered complex reveals a non-uniform distribution of the substrate shuttling domain relative to its corresponding FAS2 polypeptide at 2.9 Å resolution. This work lays the methodological foundation for experimental study of ACP shuttling route in fungi.
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Affiliation(s)
| | - Amy C Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jennifer W Lou
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - David L Dai
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Alexander F A Keszei
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | | | - Charles Boone
- Donnelly Centre, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada.
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4
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Singh K, Bunzel G, Graf B, Yip KM, Neumann-Schaal M, Stark H, Chari A. Reconstruction of a fatty acid synthesis cycle from acyl carrier protein and cofactor structural snapshots. Cell 2023; 186:5054-5067.e16. [PMID: 37949058 DOI: 10.1016/j.cell.2023.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 07/21/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023]
Abstract
Fatty acids (FAs) play a central metabolic role in living cells as constituents of membranes, cellular energy reserves, and second messenger precursors. A 2.6 MDa FA synthase (FAS), where the enzymatic reactions and structures are known, is responsible for FA biosynthesis in yeast. Essential in the yeast FAS catalytic cycle is the acyl carrier protein (ACP) that actively shuttles substrates, biosynthetic intermediates, and products from one active site to another. We resolve the S. cerevisiae FAS structure at 1.9 Å, elucidating cofactors and water networks involved in their recognition. Structural snapshots of ACP domains bound to various enzymatic domains allow the reconstruction of a full yeast FA biosynthesis cycle. The structural information suggests that each FAS functional unit could accommodate exogenous proteins to incorporate various enzymatic activities, and we show proof-of-concept experiments where ectopic proteins are used to modulate FAS product profiles.
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Affiliation(s)
- Kashish Singh
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Georg Bunzel
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Benjamin Graf
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany; Research Group Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ka Man Yip
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Ashwin Chari
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany; Research Group Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
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5
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Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Fallah S, Sanchez H, Skulska I, Ušaj MM, Safizadeh H, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras AC, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, Cowen LE. Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity. Cell Chem Biol 2023; 30:795-810.e8. [PMID: 37369212 PMCID: PMC11016341 DOI: 10.1016/j.chembiol.2023.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 04/17/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
Rising drug resistance among pathogenic fungi, paired with a limited antifungal arsenal, poses an increasing threat to human health. To identify antifungal compounds, we screened the RIKEN natural product depository against representative isolates of four major human fungal pathogens. This screen identified NPD6433, a triazenyl indole with broad-spectrum activity against all screening strains, as well as the filamentous mold Aspergillus fumigatus. Mechanistic studies indicated that NPD6433 targets the enoyl reductase domain of fatty acid synthase 1 (Fas1), covalently inhibiting its flavin mononucleotide-dependent NADPH-oxidation activity and arresting essential fatty acid biosynthesis. Robust Fas1 inhibition kills Candida albicans, while sublethal inhibition impairs diverse virulence traits. At well-tolerated exposures, NPD6433 extended the lifespan of nematodes infected with azole-resistant C. albicans. Overall, identification of NPD6433 provides a tool with which to explore lipid homeostasis as a therapeutic target in pathogenic fungi and reveals a mechanism by which Fas1 function can be inhibited.
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Affiliation(s)
- Kali R Iyer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sheena C Li
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada; RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Nicole M Revie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer W Lou
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Dustin Duncan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sara Fallah
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Iwona Skulska
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Mojca Mattiazzi Ušaj
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, Canada
| | - Hamid Safizadeh
- Department of Computer Science and Engineering and Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Brett Larsen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Cassandra Wong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mami Yoshimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiromi Kimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | | | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Japan.
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada; RIKEN Center for Sustainable Resource Science, Wako, Japan.
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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6
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Hasan SMN, Lou JW, Keszei AFA, Dai DL, Mazhab-Jafari MT. Atomic model for core modifying region of human fatty acid synthase in complex with Denifanstat. Nat Commun 2023; 14:3460. [PMID: 37308485 DOI: 10.1038/s41467-023-39266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
Fatty acid synthase (FASN) catalyzes the de novo synthesis of palmitate, a 16-carbon chain fatty acid that is the primary precursor of lipid metabolism and an important intracellular signaling molecule. FASN is an attractive drug target in diabetes, cancer, fatty liver diseases, and viral infections. Here, we develop an engineered full-length human FASN (hFASN) that enables isolation of the condensing and modifying regions of the protein post-translation. The engineered protein enables electron cryo-microscopy (cryoEM) structure determination of the core modifying region of hFASN to 2.7 Å resolution. Examination of the dehydratase dimer within this region reveals that unlike its close homolog, porcine FASN, the catalytic cavity is close-ended and is accessible only through one opening in the vicinity of the active site. The core modifying region exhibits two major global conformational variabilities that describe long-range bending and twisting motions of the complex in solution. Finally, we solved the structure of this region bound to an anti-cancer drug, Denifanstat (i.e., TVB-2640), demonstrating the utility of our approach as a platform for structure guided design of future hFASN small molecule inhibitors.
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Affiliation(s)
- S M Naimul Hasan
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer W Lou
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - David L Dai
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
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7
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Abstract
Fatty acid (FA) biosynthesis plays a central role in the metabolism of living cells as building blocks of biological membranes, energy reserves of the cell, and precursors to second messenger molecules. In keeping with its central metabolic role, FA biosynthesis impacts several cellular functions and its misfunction is linked to disease, such as cancer, obesity, and non-alcoholic fatty liver disease. Cellular FA biosynthesis is conducted by fatty acid synthases (FAS). All FAS enzymes catalyze similar biosynthetic reactions, but the functional architectures adopted by these cellular catalysts can differ substantially. This variability in FAS structure amongst various organisms and the essential role played by FA biosynthetic pathways makes this metabolic route a valuable target for the development of antibiotics. Beyond cellular FA biosynthesis, the quest for renewable energy sources has piqued interest in FA biosynthetic pathway engineering to generate biofuels and fatty acid derived chemicals. For these applications, based on FA biosynthetic pathways, to succeed, detailed metabolic, functional and structural insights into FAS are required, along with an intimate knowledge into the regulation of FAS. In this review, we summarize our present knowledge about the functional, structural, and regulatory aspects of FAS.
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Affiliation(s)
- Aybeg N Günenc
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Benjamin Graf
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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8
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Snowden JS, Alzahrani J, Sherry L, Stacey M, Rowlands DJ, Ranson NA, Stonehouse NJ. Structural insight into Pichia pastoris fatty acid synthase. Sci Rep 2021; 11:9773. [PMID: 33963233 PMCID: PMC8105331 DOI: 10.1038/s41598-021-89196-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022] Open
Abstract
Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identified FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purified from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identified several differences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classification, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further efforts to engineer yeast FAS for synthesis of alternate products.
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Affiliation(s)
- Joseph S Snowden
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jehad Alzahrani
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Lee Sherry
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Stacey
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Nicola J Stonehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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