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O'Mara ML, Rauscher S, Wetmore SD. Introduction to the RSC Advances themed collection on New insights into biomolecular systems from large-scale simulations. RSC Adv 2024; 14:6985-6986. [PMID: 38440778 PMCID: PMC10911406 DOI: 10.1039/d4ra90012j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Megan O'Mara, Sarah Rauscher and Stacey Wetmore introduce the RSC Advances themed collection on New insights into biomolecular systems from large-scale simulations.
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Affiliation(s)
- Megan L O'Mara
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Building 75, Cnr College Rd &, Cooper Rd St Lucia Queensland 4067 Australia
| | - Sarah Rauscher
- University of Toronto Mississauga, Chemical and Physical Sciences 3359 Mississauga Rd N Mississauga Ontario L5L 1C6 Canada
- University of Toronto, Department of Physics 60 St. George St Toronto Ontario M5S 3H6 Canada
- Department of Chemistry 80 St. George St Toronto Ontario M5S 3H6 Canada
| | - Stacey D Wetmore
- University of Lethbridge, Department of Chemistry and Biochemistry 4401 University Drive West Lethbridge Alberta T1K 3M4 Canada +1 (403) 329-2323
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2
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Thai LD, Fanelli J, Munaweera R, O'Mara ML, Barner-Kowollik C, Mutlu H. Main-chain Macromolecular Hydrazone Photoswitches. Angew Chem Int Ed Engl 2024; 63:e202315887. [PMID: 37988197 DOI: 10.1002/anie.202315887] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
Hydrazones-consisting of a dynamic imine bond and an acidic NH proton-have recently emerged as versatile photoswitches underpinned by their ability to form thermally bistable isomers, (Z) and (E), respectively. Herein, we introduce two photoresponsive homopolymers containing structurally different hydrazones as main-chain repeating units, synthesized via head-to-tail Acyclic Diene METathesis (ADMET) polymerization. Their key difference lies in the hydrazone design, specifically the location of the aliphatic arm connecting the rotor of the hydrazone photoswitch to the aliphatic polymer backbone. Critically, we demonstrate that their main photoresponsive property, i.e., their hydrodynamic volume, changes in opposite directions upon photoisomerization (λ=410 nm) in dilute solution. Further, the polymers-independent of the design of the individual hydrazone monomer-feature a photoswitchable glass transition temperature (Tg ) by close to 10 °C. The herein established design strategy allows to photochemically manipulate macromolecular properties by simple structural changes.
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Affiliation(s)
- Linh Duy Thai
- School of Chemistry and Physics, Queensland University of Technology (QUT), 2 George Street, 4000, Brisbane, QLD, Australia
- Centre for Materials Science, Queensland University of Technology (QUT), 2 George Street, 4000, Brisbane, QLD, Australia
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Julian Fanelli
- School of Chemistry and Physics, Queensland University of Technology (QUT), 2 George Street, 4000, Brisbane, QLD, Australia
- Centre for Materials Science, Queensland University of Technology (QUT), 2 George Street, 4000, Brisbane, QLD, Australia
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Soft Matter Synthesis Laboratory, Institute for Biological Interfaces 3, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Rangika Munaweera
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland (UQ), 4067, St Lucia, QLD, Australia
| | - Megan L O'Mara
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland (UQ), 4067, St Lucia, QLD, Australia
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics, Queensland University of Technology (QUT), 2 George Street, 4000, Brisbane, QLD, Australia
- Centre for Materials Science, Queensland University of Technology (QUT), 2 George Street, 4000, Brisbane, QLD, Australia
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Hatice Mutlu
- Institut de Science des Matériaux de Mulhouse (IS2M), UMR 7361 CNRS/, Université de Haute Alsace (UHA), 15 rue Jean Starcky, 68057, Mulhouse Cedex, France
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Chater RC, Quinn AS, Wilson K, Frangos ZJ, Sutton P, Jayakumar S, Cioffi CL, O'Mara ML, Vandenberg RJ. The efficacy of the analgesic GlyT2 inhibitor, ORG25543, is determined by two connected allosteric sites. J Neurochem 2023. [PMID: 38131125 DOI: 10.1111/jnc.16028] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/23/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Glycine Transporter 2 (GlyT2) inhibitors have shown considerable potential as analgesics for the treatment of neuropathic pain but also display considerable side effects. One potential source of side effects is irreversible inhibition. In this study, we have characterized the mechanism of ORG25543 inhibition of GlyT2 by first considering three potential ligand binding sites on GlyT2-the substrate site, the vestibule allosteric site and the lipid allosteric site. The three sites were tested using a combination of molecular dynamics simulations and analysis of the inhibition of glycine transport of a series point mutated GlyT2 using electrophysiological methods. We demonstrate that the lipid allosteric site on GlyT2 is the most likely binding site for ORG25543. We also demonstrate that cholesterol derived from the cell membrane can form specific interactions with inhibitor-bound transporters to form an allosteric network of regulatory sites. These observations will guide the future design of GlyT2 inhibitors with the objective of minimising on-target side effects and improving the therapeutic window for the treatment of patients suffering from neuropathic pain.
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Affiliation(s)
- Ryan Cantwell Chater
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ada S Quinn
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
| | - Katie Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Zachary J Frangos
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Patrick Sutton
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
| | - Srinivasan Jayakumar
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Christopher L Cioffi
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia
| | - Robert J Vandenberg
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
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4
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Chen S, Iannotta D, O'Mara ML, Goncalves JP, Wolfram J. Extracellular vesicle lipids in cancer immunoevasion. Trends Cancer 2023; 9:883-886. [PMID: 37666676 DOI: 10.1016/j.trecan.2023.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/29/2023] [Revised: 08/07/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
Recent studies have revealed that cancer cell-derived extracellular vesicles (EVs) modulate immunological responses. Lipids have diverse biological functions, and are known to promote tumor malignancy. However, the immunoevasive roles of EV lipids in cancer progression remain poorly understood. Nevertheless, the study of cancer cell-derived EV lipids holds great promise for diagnostic and therapeutic interventions.
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Affiliation(s)
- Siyu Chen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Building 75, Cnr College Rd & Cooper Rd, Brisbane, QLD 4072, Australia
| | - Dalila Iannotta
- School of Chemical Engineering, The University of Queensland, Andrew N. Liveris Building, 46 Staff House Rd, Brisbane, QLD 4072, Australia
| | - Megan L O'Mara
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Building 75, Cnr College Rd & Cooper Rd, Brisbane, QLD 4072, Australia.
| | - Jenifer Pendiuk Goncalves
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Building 75, Cnr College Rd & Cooper Rd, Brisbane, QLD 4072, Australia.
| | - Joy Wolfram
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Building 75, Cnr College Rd & Cooper Rd, Brisbane, QLD 4072, Australia; School of Chemical Engineering, The University of Queensland, Andrew N. Liveris Building, 46 Staff House Rd, Brisbane, QLD 4072, Australia; Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, TX 77030, USA.
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Zeng YC, Sobti M, Quinn A, Smith NJ, Brown SHJ, Vandenberg JI, Ryan RM, O'Mara ML, Stewart AG. Structural basis of promiscuous substrate transport by Organic Cation Transporter 1. Nat Commun 2023; 14:6374. [PMID: 37821493 PMCID: PMC10567722 DOI: 10.1038/s41467-023-42086-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Abstract
Organic Cation Transporter 1 (OCT1) plays a crucial role in hepatic metabolism by mediating the uptake of a range of metabolites and drugs. Genetic variations can alter the efficacy and safety of compounds transported by OCT1, such as those used for cardiovascular, oncological, and psychological indications. Despite its importance in drug pharmacokinetics, the substrate selectivity and underlying structural mechanisms of OCT1 remain poorly understood. Here, we present cryo-EM structures of full-length human OCT1 in the inward-open conformation, both ligand-free and drug-bound, indicating the basis for its broad substrate recognition. Comparison of our structures with those of outward-open OCTs provides molecular insight into the alternating access mechanism of OCTs. We observe that hydrophobic gates stabilize the inward-facing conformation, whereas charge neutralization in the binding pocket facilitates the release of cationic substrates. These findings provide a framework for understanding the structural basis of the promiscuity of drug binding and substrate translocation in OCT1.
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Affiliation(s)
- Yi C Zeng
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Meghna Sobti
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ada Quinn
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Nicola J Smith
- School of Biomedical Sciences, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Simon H J Brown
- School of Chemistry and Molecular Bioscience, Molecular Horizons, and Australian Research Council Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia
| | - Jamie I Vandenberg
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Molecular Cardiology and Biophysics Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Renae M Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Megan L O'Mara
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
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6
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Frangos ZJ, Wilson KA, Aitken HM, Cantwell Chater R, Vandenberg RJ, O'Mara ML. Membrane cholesterol regulates inhibition and substrate transport by the glycine transporter, GlyT2. Life Sci Alliance 2023; 6:e202201708. [PMID: 36690444 PMCID: PMC9873984 DOI: 10.26508/lsa.202201708] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Membrane cholesterol binds to and modulates the function of various SLC6 neurotransmitter transporters, including stabilizing the outward-facing conformation of the dopamine and serotonin transporters. Here, we investigate how cholesterol binds to GlyT2 (SLC6A5), modulates glycine transport rate, and influences bioactive lipid inhibition of GlyT2. Bioactive lipid inhibitors are analgesics that bind to an allosteric site accessible from the extracellular solution when GlyT2 adopts an outward-facing conformation. Using molecular dynamics simulations, mutagenesis, and cholesterol depletion experiments, we show that bioactive lipid inhibition of glycine transport is modulated by the recruitment of membrane cholesterol to a binding site formed by transmembrane helices 1, 5, and 7. Recruitment involves cholesterol flipping from its membrane orientation, and insertion of the 3' hydroxyl group into the cholesterol binding cavity, close to the allosteric site. The synergy between cholesterol and allosteric inhibitors provides a novel mechanism of inhibition and a potential avenue for the development of potent GlyT2 inhibitors as alternative therapeutics for the treatment of neuropathic pain and therapeutics that target other SLC6 transporters.
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Affiliation(s)
- Zachary J Frangos
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australia
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Canada
| | - Heather M Aitken
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ryan Cantwell Chater
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Robert J Vandenberg
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
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7
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MacDermott-Opeskin HI, Wilson KA, O'Mara ML. The Impact of Antimicrobial Peptides on the Acinetobacter baumannii Inner Membrane Is Modulated by Lipid Polyunsaturation. ACS Infect Dis 2023; 9:815-826. [PMID: 36920795 DOI: 10.1021/acsinfecdis.2c00530] [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: 03/16/2023]
Abstract
The Gram-negative pathogen Acinetobacter baumannii is a primary contributor to nosocomial multi-drug-resistant (MDR) infections. To combat the rise of MDR infections, novel features of A. baumannii need to be considered for the development of new treatment options. One such feature is the preferential scavenging of exogenous lipids, including host-derived polyunsaturated fatty acids (PUFAs), for membrane phospholipid synthesis. These alterations in membrane composition impact both the lipid chemistry and the membrane biophysical properties. In this work we examine how antimicrobial peptides (AMPs) interact with the inner membranes of A. baumannii in the presence and absence of polyunsaturated phospholipids. Using coarse-grained molecular dynamics simulations of complex A. baumannii inner membrane models derived from lipidomes of bacteria grown in the presence and absence of PUFAs, we examine the impact of the adsorption of four prototypical AMPs (CAMEL, LL-37, pexiganan, and magainin-2) on the membrane biophysical properties. Our simulations reveal that the impact of AMP adsorption on the membrane biophysical properties was dependent on both the membrane composition and the specific AMP involved. Both lipid headgroup charge and tail unsaturation played important roles in driving the interactions that occurred both within the membrane and between the membrane and AMPs. The changes to the membrane biophysical properties also showed a complex relationship with the AMP's physical properties, such as AMP charge, chain length, and charge-to-mass ratio. Cumulatively, this work highlights the importance of studying AMPs using a complex membrane environment and provides insights into the mechanistic action of AMPs in polyunsaturated lipid-rich bacterial membranes.
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Affiliation(s)
- Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia.,Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1C 5S7 Canada
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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8
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Mundsinger K, Tuten BT, Wang L, Neubauer K, Kropf C, O'Mara ML, Barner-Kowollik C. Visible Light Reactive Single-Chain Nanoparticles. Angew Chem Int Ed Engl 2023; 62:e202302995. [PMID: 36882373 DOI: 10.1002/anie.202302995] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/09/2023]
Abstract
We introduce a single-chain nanoparticle (SCNP) system capable of catalyzing the photooxidation of nonpolar alkenes up to three times more efficiently than an equivalent small-molecule photosensitizer at an identical concentration. Specifically, we construct a polymer chain constituted of poly(ethylene glycol) methyl ether methacrylate and glycidyl methacrylate which we compact via multifunctional thiol-epoxide ligation and functionalize with Rose Bengal (RB) in a one pot reaction, affording SCNPs with a hydrophilic shell and hydrophobic photocatalytic regions. Photooxidation of the internal alkene in oleic acid proceeds under green light. RB confined within the SCNP is three times more effective for nonpolar alkenes than free RB in solution, which we hypothesize is due to the spatial proximity of the photosensitizing units to the substrate in the hydrophobic region. Our approach demonstrates that SCNP based catalysts can afford enhanced photocatalysis via confinement effects in a homogeneous reaction environment.
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Affiliation(s)
- Kai Mundsinger
- Queensland University of Technology, School of Chemistry and Physics, AUSTRALIA
| | - Bryan T Tuten
- Queensland University of Technology - Gardens Point Campus, School of Chemistry and Physics, AUSTRALIA
| | - Lily Wang
- Australian National University, Research School of Chemistry, AUSTRALIA
| | | | | | - Megan L O'Mara
- The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, AUSTRALIA
| | - Christopher Barner-Kowollik
- Queensland University of Technology, School of Chemistry and Physics, 2 George Street, 4000, Brisbane, AUSTRALIA
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9
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Mundsinger K, Tuten BT, Wang L, Neubauer K, Kropf C, O'Mara ML, Barner-Kowollik C. Visible Light Reactive Single‐Chain Nanoparticles. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202302995] [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: 03/09/2023]
Affiliation(s)
- Kai Mundsinger
- Queensland University of Technology School of Chemistry and Physics AUSTRALIA
| | - Bryan T. Tuten
- Queensland University of Technology - Gardens Point Campus School of Chemistry and Physics AUSTRALIA
| | - Lily Wang
- Australian National University Research School of Chemistry AUSTRALIA
| | | | | | - Megan L. O'Mara
- The University of Queensland Australian Institute of Bioengineering and Nanotechnology AUSTRALIA
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10
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MacDermott-Opeskin H, Wilson KA, Eijkelkamp B, O'Mara ML. Polyunsaturated lipids promote membrane phase separation and antimicrobial sensitivity. Biophys J 2023; 122:322a-323a. [PMID: 36783622 DOI: 10.1016/j.bpj.2022.11.1805] [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: 02/12/2023] Open
Affiliation(s)
| | - Katie A Wilson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Bart Eijkelkamp
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
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11
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Gallagher CI, Chang Lin Y, Kumar A, Ha D, Cioffi CL, Chakrapani S, O'Mara ML, Vandenberg RJ. Identification and characterisation of lipids that are positive allosteric modulators of glycine receptors. Biophys J 2023; 122:391a. [PMID: 36783988 DOI: 10.1016/j.bpj.2022.11.2138] [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: 02/12/2023] Open
Affiliation(s)
| | - Yie Chang Lin
- The Australian National University, Canberra, Australia
| | - Arvind Kumar
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Damian Ha
- School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Megan L O'Mara
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
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12
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MacDermott-Opeskin H, Clarke C, Wu X, Roseblade A, York E, Pacchini E, Roy R, Cranfield C, Gale PA, O'Mara ML, Murray M, Rawling T. Protonophoric and mitochondrial uncoupling activity of aryl-carbamate substituted fatty acids. Org Biomol Chem 2022; 21:132-139. [PMID: 36453203 DOI: 10.1039/d2ob02049a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Aryl-urea substituted fatty acids are protonophores and mitochondrial uncouplers that utilise a urea-based synthetic anion transport moiety to carry out the protonophoric cycle. Herein we show that replacement of the urea group with carbamate, a functional group not previously reported to possess anion transport activity, produces analogues that retain the activity of their urea counterparts. Thus, the aryl-carbamate substituted fatty acids uncouple oxidative phosphorylation and inhibit ATP production by collapsing the mitochondrial proton gradient. Proton transport proceeds via self-assembly of the deprotonated aryl-carbamates into membrane permeable dimeric species, formed by intermolecular binding of the carboxylate group to the carbamate moiety. These results highlight the anion transport capacity of the carbamate functional group.
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Affiliation(s)
- Hugo MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT, 0200, Australia
| | - Callum Clarke
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Xin Wu
- School of Chemistry, The University of Sydney, NSW, 2006, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Ariane Roseblade
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Edward York
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Ethan Pacchini
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Ritik Roy
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia.
| | - Charles Cranfield
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Philip A Gale
- School of Chemistry, The University of Sydney, NSW, 2006, Australia.,The University of Sydney Nano Institute (SydneyNano), The University of Sydney, NSW, 2006, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT, 0200, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Michael Murray
- Discipline of Pharmacology, School of Medical Sciences, The University of Sydney, NSW 2006, Australia
| | - Tristan Rawling
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia.
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13
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MacDermott-Opeskin HI, Panizza A, Eijkelkamp BA, O'Mara ML. Dynamics of the Acinetobacter baumannii inner membrane under exogenous polyunsaturated fatty acid stress. Biochim Biophys Acta Biomembr 2022; 1864:183908. [PMID: 35276227 DOI: 10.1016/j.bbamem.2022.183908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/11/2022] [Accepted: 03/05/2022] [Indexed: 01/04/2023]
Abstract
Exogenous polyunsaturated fatty acids (PUFAs) are readily incorporated into the synthesis pathways of A. baumannii membrane phospholipids, where they contribute to reduced bacterial fitness and increased antimicrobial susceptibility. Here we examine the impact of PUFA membrane modification on membrane organisation and biophysical properties using coarse grained MARTINI simulations of chemically representative membrane models developed from mass-spectrometry datasets of an untreated, arachidonic acid (AA) treated and docosahexaenoic acid (DHA) treated A. baumannii membranes. Enzymatic integration of AA or DHA into phospholipids of the A. baumannii membrane resulted in modulation of membrane biophysical properties. Membrane thickness decreased slightly following PUFA treatment, concomitant with changes in the lateral area per lipid of each lipid headgroup class. PUFA treatment resulted in a decrease in membrane ordering and an increase in lipid lateral diffusion. Changes in lateral membrane organisation were observed in the PUFA treated membranes, with a concurrent increase in ordered cardiolipin domains and disordered PUFA-containing domains. Notably, separation between ordered and disordered domains was enhanced and was more pronounced for DHA relative to AA, providing a possible mechanism for greater antimicrobial action of DHA relative to AA observed experimentally. Furthermore, the membrane active antimicrobial, pentamidine, preferentially adsorbs to cardiolipin domains of the A. baumannii model membranes. This interaction, and membrane penetration of pentamidine, was enhanced following PUFA treatment. Cumulatively, this work explores the wide-ranging effects of PUFA incorporation on the A. baumannii membrane and provides a molecular basis for bacterial inner membrane disruption by PUFAs.
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Affiliation(s)
- Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Alessandra Panizza
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Bart A Eijkelkamp
- Molecular Science and Technology, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT, 2601, Australia.
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14
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Goodwin RJ, Docker A, MacDermott‐Opeskin HI, Aitken HM, O'Mara ML, Beer PD, White NG. Hydroxy Groups Enhance [2]Rotaxane Anion Binding Selectivity. Chemistry 2022; 28:e202200389. [PMID: 35293643 PMCID: PMC9321576 DOI: 10.1002/chem.202200389] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 11/25/2022]
Abstract
We report the synthesis of two [2]rotaxanes containing an interlocked three dimensional binding cavity formed from a pyridinium bis(amide) axle component containing two phenol donors, and an isophthalamide based macrocycle. In the competitive solvent mixture 1 : 1 CDCl3 : CD3OD, one of the receptors exhibits a much higher selectivity preference for chloride than an analogous rotaxane without the hydroxy groups. X‐ray crystal structures reveal the chloride anion guest encapsulated within the interlocked binding cavity, though not all of the hydrogen bond donors are utilised. Computational semi‐empirical simulations indicate that secondary intermolecular interactions occur between the axle hydroxy hydrogen bond donors and the [2]rotaxane macrocycle components, contributing to a more preorganised binding pocket, which may be responsible for the observed enhanced selectivity.
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Affiliation(s)
- Rosemary J. Goodwin
- Research School of Chemistry Australian National University Canberra ACT Australia
| | - Andrew Docker
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | | | - Heather M. Aitken
- Research School of Chemistry Australian National University Canberra ACT Australia
| | - Megan L. O'Mara
- Research School of Chemistry Australian National University Canberra ACT Australia
| | - Paul D. Beer
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Nicholas G. White
- Research School of Chemistry Australian National University Canberra ACT Australia
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15
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Adamson LSR, Tasneem N, Andreas MP, Close W, Jenner EN, Szyszka TN, Young R, Cheah LC, Norman A, MacDermott-Opeskin HI, O'Mara ML, Sainsbury F, Giessen TW, Lau YH. Pore structure controls stability and molecular flux in engineered protein cages. Sci Adv 2022. [PMID: 35119930 DOI: 10.1101/2021.01.27.428512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the Thermotoga maritima encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux.
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Affiliation(s)
- Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Nuren Tasneem
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William Close
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Reginald Young
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Li Chen Cheah
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander Norman
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Frank Sainsbury
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, QLD 4102, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Campderdown, NSW 2006, Australia
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16
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Qin J, Wilson KA, Sarkar S, Heras B, O'Mara ML, Totsika M. Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function. Comput Struct Biotechnol J 2022; 20:4532-4541. [PMID: 36090810 PMCID: PMC9428848 DOI: 10.1016/j.csbj.2022.08.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022] Open
Abstract
The binding of the type 1 fimbrial adhesin FimH to mannosylated receptors is allosterically regulated to enhance the fitness of uropathogenic Escherichia coli (UPEC) during urinary tract infection (UTI). Mutations in the two FimH domains (pilin and lectin) located outside the mannose binding pocket have been shown to influence mannose binding affinity, yet the details of the allostery mechanism are not fully elucidated. Here we characterised different FimH conformational states (termed low-affinity tense and high-affinity relaxed conformations) of natural FimH variants using molecular dynamics (MD) simulation techniques and report key structural dynamics differences between them. The clinically dominant FimH30 variant from the pandemic multidrug resistant E. coli ST131 lineage contains an R166H mutation that weakens FimH interdomain interactions and allows enhanced mannose interactions with pre-existing high-affinity relaxed conformations. When expressed in an isogenic ST131 strain background, FimH30 mediated high human cell adhesion and invasion, and enhanced biofilm formation over other variants. Collectively, our computational and experimental findings support a model of FimH protein allostery that is mediated by shifts in the pre-existing conformational equilibrium of FimH, additional to the sequential step-wise process of structural perturbations transmitted from one site to another within the protein. Importantly, it is the first study to shed light into how natural mutations in a clinically dominant FimH variant influence the protein’s conformational landscape optimising its function for ST131 fitness at intestinal and extraintestinal niches.
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17
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Kumar A, Nothling MD, Aitken HM, Xiao Z, Lam M, Bell CA, O'Mara ML, Connal LA. Simple synthetic route to an enzyme-inspired transesterification catalyst. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00744d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembling transesterification catalyst inspired by the catalytic triad.
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Affiliation(s)
- Ashwani Kumar
- Research School of Chemistry, Australian National University, Canberra, ACT, 2600, Australia
| | | | - Heather M. Aitken
- Research School of Chemistry, Australian National University, Canberra, ACT, 2600, Australia
| | - Zeyun Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Matthew Lam
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Craig A. Bell
- Centre for Advanced Imaging and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Megan L. O'Mara
- Research School of Chemistry, Australian National University, Canberra, ACT, 2600, Australia
| | - Luke A. Connal
- Research School of Chemistry, Australian National University, Canberra, ACT, 2600, Australia
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18
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Wang L, O'Mara ML. Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein. J Chem Theory Comput 2021; 17:6491-6508. [PMID: 34506133 DOI: 10.1021/acs.jctc.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has grown from simulation studies that have employed various simulation conditions and parameters, including AMBER, CHARMM, OPLS, GROMOS, and coarse-grained force fields, drawing conclusions from simulations spanning hundreds of nanoseconds. Each force field is typically parametrized and validated on different data and observables, usually of small molecules and peptides; there have been few comparisons of force field performance on large protein-membrane systems. Here we compare the conformational ensembles of P-gp embedded in a POPC/cholesterol bilayer generated over 500 ns of replicate simulation with five force fields from popular biomolecular families: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, and MARTINI. We find considerable differences among the ensembles with little conformational overlap, although they correspond to similar extents to structural data obtained from electron paramagnetic resonance and cross-linking studies. Moreover, each trajectory was still sampling new conformations at a high rate after 500 ns of simulation, suggesting the need for more sampling. This work highlights the need to consider known limitations of the force field used (e.g., biases toward certain secondary structures) and the simulation itself (e.g., whether sufficient sampling has been achieved) when interpreting accumulated results of simulation studies of P-gp and other transport proteins.
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Affiliation(s)
- Lily Wang
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
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19
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Neville SL, Sjöhamn J, Watts JA, MacDermott-Opeskin H, Fairweather SJ, Ganio K, Hulyer AC, Hayes AJ, McGrath AP, Malcolm TR, Davies MR, Nomura N, So I, O'Mara ML, McDevitt CA, Maher MJ. The structure of the ABC transporter PsaBC shows that bacterial manganese import is achieved by unique architectural features that are conserved across the kingdoms of life. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321095799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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20
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Neville SL, Sjöhamn J, Watts JA, MacDermott-Opeskin H, Fairweather SJ, Ganio K, Carey Hulyer A, McGrath AP, Hayes AJ, Malcolm TR, Davies MR, Nomura N, Iwata S, O'Mara ML, Maher MJ, McDevitt CA. The structural basis of bacterial manganese import. Sci Adv 2021; 7:7/32/eabg3980. [PMID: 34362732 PMCID: PMC8346216 DOI: 10.1126/sciadv.abg3980] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/10/2021] [Indexed: 05/23/2023]
Abstract
Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined. Here, we present the crystal structure of the manganese transporter PsaBC from Streptococcus pneumoniae in an open-inward conformation. The type II transporter has a tightly closed transmembrane channel due to "extracellular gating" residues that prevent water permeation or ion reflux. Below these residues, the channel contains a hitherto unreported metal coordination site, which is essential for manganese translocation. Mutagenesis of the extracellular gate perturbs manganese uptake, while coordination site mutagenesis abolishes import. These structural features are highly conserved in metal-specific ABC transporters and are represented throughout the kingdoms of life. Collectively, our results define the structure of PsaBC and reveal the features required for divalent cation transport.
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Affiliation(s)
- Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennie Sjöhamn
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jacinta A Watts
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Stephen J Fairweather
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alex Carey Hulyer
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aaron P McGrath
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tess R Malcolm
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Acceleration Program, Membrane Protein Crystallography Project, Japan Science and Technology Agency, Kyoto, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Megan J Maher
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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21
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Wilson KA, Fairweather SJ, MacDermott-Opeskin HI, Wang L, Morris RA, O'Mara ML. The role of plasmalogens, Forssman lipids, and sphingolipid hydroxylation in modulating the biophysical properties of the epithelial plasma membrane. J Chem Phys 2021; 154:095101. [PMID: 33685172 DOI: 10.1063/5.0040887] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A coarse-grain model of the epithelial plasma membrane was developed from high-resolution lipidomic data and simulated using the MARTINI force field to characterize its biophysical properties. Plasmalogen lipids, Forssman glycosphingolipids, and hydroxylated Forssman glycosphingolipids and sphingomyelin were systematically added to determine their structural effects. Plasmalogen lipids have a minimal effect on the overall biophysical properties of the epithelial plasma membrane. In line with the hypothesized role of Forssman lipids in the epithelial apical membrane, the introduction of Forssman lipids initiates the formation of glycosphingolipid-rich nanoscale lipid domains, which also include phosphatidylethanolamine (PE), sphingomyelin (SM), and cholesterol (CHOL). This decreases the lateral diffusion in the extracellular leaflet, as well as the area per lipid of domain forming lipids, most notably PE. Finally, hydroxylation of the Forssman glycosphingolipids and sphingomyelin further modulates the lateral organization of the membrane. Through comparison to the previously studied average and neuronal plasma membranes, the impact of membrane lipid composition on membrane properties was characterized. Overall, this study furthers our understanding of the biophysical properties of complex membranes and the impact of lipid diversity in modulating membrane properties.
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Affiliation(s)
- Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Stephen J Fairweather
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Lily Wang
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Richard A Morris
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
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22
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Bhaskaran A, Aitken HM, Xiao Z, Blyth M, Nothling MD, Kamdar S, O'Mara ML, Connal LA. Enzyme inspired polymer functionalized with an artificial catalytic triad. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Wilson KA, Mostyn SN, Frangos ZJ, Shimmon S, Rawling T, Vandenberg RJ, O'Mara ML. The allosteric inhibition of glycine transporter 2 by bioactive lipid analgesics is controlled by penetration into a deep lipid cavity. J Biol Chem 2021; 296:100282. [PMID: 33450225 PMCID: PMC7949037 DOI: 10.1016/j.jbc.2021.100282] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/25/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/07/2023] Open
Abstract
The role of lipids in modulating membrane protein function is an emerging and rapidly growing area of research. The rational design of lipids that target membrane proteins for the treatment of pathological conditions is a novel extension in this field and provides a step forward in our understanding of membrane transporters. Bioactive lipids show considerable promise as analgesics for the treatment of chronic pain and bind to a high-affinity allosteric-binding site on the human glycine transporter 2 (GlyT2 or SLC6A5). Here, we use a combination of medicinal chemistry, electrophysiology, and computational modeling to develop a rational structure-activity relationship for lipid inhibitors and demonstrate the key role of the lipid tail interactions for GlyT2 inhibition. Specifically, we examine how lipid inhibitor head group stereochemistry, tail length, and double-bond position promote enhanced inhibition. Overall, the l-stereoisomer is generally a better inhibitor than the d-stereoisomer, longer tail length correlates with greater potency, and the position of the double bond influences the activity of the inhibitor. We propose that the binding of the lipid inhibitor deep into the allosteric-binding pocket is critical for inhibition. Furthermore, this provides insight into the mechanism of inhibition of GlyT2 and highlights how lipids can modulate the activity of membrane proteins by binding to cavities between helices. The principles identified in this work have broader implications for the development of a larger class of compounds that could target SLC6 transporters for disease treatment.
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Affiliation(s)
- Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT, Australia
| | - Shannon N Mostyn
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Zachary J Frangos
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Susan Shimmon
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Tristan Rawling
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Robert J Vandenberg
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT, Australia.
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24
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Wilson KA, Wang L, Lin YC, O'Mara ML. Investigating the lipid fingerprint of SLC6 neurotransmitter transporters: a comparison of dDAT, hDAT, hSERT, and GlyT2. BBA Advances 2021; 1:100010. [PMID: 37082011 PMCID: PMC10074915 DOI: 10.1016/j.bbadva.2021.100010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The local lipid annulus, or "fingerprint", of four SLC6 transporters (dDAT, hDAT, hSERT, and GlyT2) embedded in a complex neuronal membrane were compared and characterised using molecular dynamics. Our analysis included the development of new tools to improve membrane leaflet detection and the analysis of leaflet-dependent properties. Overall, the lipid fingerprints of the four transporters are comprised of similar lipids when grouped by headgroup or tail saturation. The enrichment and depletion of specific lipids, including sites of cholesterol contacts, varies between transporters. The subtle differences in lipid fingerprints results in varying membrane biophysical properties near the transporter. Our results highlight that the lipid-fingerprint of SLC6 transporters in complex membranes is highly dependent on membrane composition. Our results further characterize how the presence and identity of membrane proteins affects the complex interplay of lipid-protein interactions, influencing the local lipid environment and membrane biophysical properties.
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25
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Rawling T, MacDermott-Opeskin H, Roseblade A, Pazderka C, Clarke C, Bourget K, Wu X, Lewis W, Noble B, Gale PA, O'Mara ML, Cranfield C, Murray M. Aryl urea substituted fatty acids: a new class of protonophoric mitochondrial uncoupler that utilises a synthetic anion transporter. Chem Sci 2020; 11:12677-12685. [PMID: 34094462 PMCID: PMC8163295 DOI: 10.1039/d0sc02777d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/10/2020] [Indexed: 01/21/2023] Open
Abstract
Respiring mitochondria establish a proton gradient across the mitochondrial inner membrane (MIM) that is used to generate ATP. Protein-independent mitochondrial uncouplers collapse the proton gradient and disrupt ATP production by shuttling protons back across the MIM in a protonophoric cycle. Continued cycling relies on the formation of MIM-permeable anionic species that can return to the intermembrane space after deprotonation in the mitochondrial matrix. Previously described protonophores contain acidic groups that are part of delocalised π-systems that provide large surfaces for charge delocalisation and facilitate anion permeation across the MIM. Here we present a new class of protonophoric uncoupler based on aryl-urea substituted fatty acids in which an acidic group and a π-system are separated by a long alkyl chain. The aryl-urea group in these molecules acts as a synthetic anion receptor that forms intermolecular hydrogen bonds with the fatty acid carboxylate after deprotonation. Dispersal of the negative charge across the aryl-urea system produces lipophilic dimeric complexes that can permeate the MIM and facilitate repeated cycling. Substitution of the aryl-urea group with lipophilic electron withdrawing groups is critical to complex lipophilicity and uncoupling activity. The aryl-urea substituted fatty acids represent the first biological example of mitochondrial uncoupling mediated by the interaction of a fatty acid and an anion receptor moiety, via self-assembly.
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Affiliation(s)
- Tristan Rawling
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney Sydney NSW 2007 Australia +61-2-9514-7956
| | - Hugo MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University Canberra ACT 0200 Australia
| | - Ariane Roseblade
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney Sydney NSW 2007 Australia +61-2-9514-7956
| | - Curtis Pazderka
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney Sydney NSW 2007 Australia +61-2-9514-7956
| | - Callum Clarke
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney Sydney NSW 2007 Australia +61-2-9514-7956
| | - Kirsi Bourget
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney Sydney NSW 2006 Australia
| | - Xin Wu
- School of Chemistry, University of Sydney Sydney NSW 2006 Australia
| | - William Lewis
- School of Chemistry, University of Sydney Sydney NSW 2006 Australia
| | - Benjamin Noble
- Research School of Chemistry, College of Science, The Australian National University Canberra ACT 0200 Australia
- School of Engineering, College of Science, Engineering and Health, RMIT University Melbourne VIC 3001 Australia
| | - Philip A Gale
- School of Chemistry, University of Sydney Sydney NSW 2006 Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University Canberra ACT 0200 Australia
| | - Charles Cranfield
- School of Life Sciences, Faculty of Science, University of Technology Sydney Sydney NSW 2007 Australia
| | - Michael Murray
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney Sydney NSW 2006 Australia
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26
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Ou A, Schmidberger JW, Wilson KA, Evans CW, Hargreaves JA, Grigg M, O'Mara ML, Iyer KS, Bond CS, Smith NM. High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A π-stacking interactions for small-molecule recognition. Nucleic Acids Res 2020; 48:5766-5776. [PMID: 32313953 PMCID: PMC7261167 DOI: 10.1093/nar/gkaa262] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 12/13/2022] Open
Abstract
Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 Å) of a KRAS G-quadruplex as a 5'-head-to-head dimer with extensive poly-A π-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A π-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5'-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.
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Affiliation(s)
- Arnold Ou
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Jason W Schmidberger
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Katie A Wilson
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Cameron W Evans
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Jessica A Hargreaves
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Melanie Grigg
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
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27
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Wilson KA, MacDermott-Opeskin HI, Riley E, Lin Y, O'Mara ML. Understanding the Link between Lipid Diversity and the Biophysical Properties of the Neuronal Plasma Membrane. Biochemistry 2020; 59:3010-3018. [PMID: 32786397 DOI: 10.1021/acs.biochem.0c00524] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cell membranes contain incredible diversity in the chemical structures of their individual lipid species and the ratios in which these lipids are combined to make membranes. Nevertheless, our current understanding of how each of these components affects the properties of the cell membrane remains elusive, in part due to the difficulties in studying the dynamics of membranes at high spatiotemporal resolution. In this work, we use coarse-grained molecular dynamics simulations to investigate how individual lipid species contribute to the biophysical properties of the neuronal plasma membrane. We progress through eight membranes of increasing chemical complexity, ranging from a simple POPC/CHOL membrane to a previously published neuronal plasma membrane [Ingólfsson, H. I., et al. (2017) Biophys. J. 113 (10), 2271-2280] containing 49 distinct lipid species. Our results show how subtle chemical changes can affect the properties of the membrane and highlight the lipid species that give the neuronal plasma membrane its unique biophysical properties. This work has potential far-reaching implications for furthering our understanding of cell membranes.
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Affiliation(s)
- Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Eden Riley
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Yiechang Lin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
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28
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Carey Hulyer AR, Briggs DA, O'Mara ML, Kerr ID, Harmer JR, Callaghan R. Cross-linking, DEER-spectroscopy and molecular dynamics confirm the inward facing state of P-glycoprotein in a lipid membrane. J Struct Biol 2020; 211:107513. [PMID: 32339763 DOI: 10.1016/j.jsb.2020.107513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
The drug efflux pump P-glycoprotein (P-gp) displays a complex transport mechanism involving multiple drug binding sites and two centres for nucleotide hydrolysis. Elucidating the molecular mechanism of transport remains elusive and the availability of P-gp structures in distinct natural and ligand trapped conformations will accelerate our understanding. The present investigation sought to provide biochemical data to validate specific features of these structures; with particular focus on the transmembrane domain that provides the transport conduit. Hence our focus was on transmembrane helices six and twelve (TM6/TM12), which are believed to participate in drug binding, as they line the central transport conduit and provide a direct link to the catalytic centres. A series of P-gp mutants were generated with a single cysteine in both TM6 and TM12 to facilitate measurement of inter-helical distances using cross-linking and DEER strategies. Experimental results were compared to published structures per se and those refined by MD simulations. This analysis revealed that the refined inward-facing murine structure (4M1M) of P-gp provides a good representation of the proximity, topography and relative motions of TM6 and TM12 in reconstituted human P-gp.
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Affiliation(s)
- Alex R Carey Hulyer
- Research School of Biology, and the Medical School, Australian National University, Canberra, ACT 2601, Australia
| | - Deborah A Briggs
- Centre for Biochemistry and Cell Biology, School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Ian D Kerr
- Centre for Biochemistry and Cell Biology, School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Jeffrey R Harmer
- The Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Richard Callaghan
- Research School of Biology, and the Medical School, Australian National University, Canberra, ACT 2601, Australia.
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29
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MacDermott-Opeskin H, McDevitt CA, O'Mara ML. Comparing Nonbonded Metal Ion Models in the Divalent Cation Binding Protein PsaA. J Chem Theory Comput 2020; 16:1913-1923. [PMID: 32059108 DOI: 10.1021/acs.jctc.9b01180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Divalent metal cations are essential for many biological processes; however, accurately modeling divalent metal ions has proved a significant challenge for molecular dynamics force fields. Here we show that the choice of ion model influences the observed dynamics in PsaA, a metal binding protein from Streptococcus pneumoniae. We conduct extensive unbiased simulations and free energy calculations of PsaA bound to its cognate ligand Mn2+ and inhibitory ligand Zn2+ using three nonbonded ion models: a 12-6 model, a 12-6-4 model, and a multisite model. The observed coordination geometries and metal binding dynamics are sensitive to the choice of ion model, with the most dramatic differences observed in free energy calculations of ion release. We show that the conformational ensemble of Mn-bound PsaA is more similar to the crystallographic metal bound open state. This work extends the current model of PsaA metal binding and provides a framework for the rationalization of experimentally determined metal binding behavior. Our findings support the use of the 12-6-4 ion model for further simulations of divalent cation binding proteins.
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Affiliation(s)
- Hugo MacDermott-Opeskin
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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30
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Wilson KA, Wang L, MacDermott-Opeskin H, O'Mara ML. The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane. Aust J Chem 2020. [DOI: 10.1071/ch19353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools and techniques, the role of the major lipid species, insights gained into lipid bilayer structure and function from molecular dynamics simulations, and recent progress towards the computational modelling of the physiological complexity of eukaryotic lipid bilayers.
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31
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Mostyn SN, Wilson KA, Schumann-Gillett A, Frangos ZJ, Shimmon S, Rawling T, Ryan RM, O'Mara ML, Vandenberg RJ. Identification of an allosteric binding site on the human glycine transporter, GlyT2, for bioactive lipid analgesics. eLife 2019; 8:e47150. [PMID: 31621581 PMCID: PMC6797481 DOI: 10.7554/elife.47150] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 03/26/2019] [Accepted: 09/30/2019] [Indexed: 01/01/2023] Open
Abstract
The treatment of chronic pain is poorly managed by current analgesics, and there is a need for new classes of drugs. We recently developed a series of bioactive lipids that inhibit the human glycine transporter GlyT2 (SLC6A5) and provide analgesia in animal models of pain. Here, we have used functional analysis of mutant transporters combined with molecular dynamics simulations of lipid-transporter interactions to understand how these bioactive lipids interact with GlyT2. This study identifies a novel extracellular allosteric modulator site formed by a crevice between transmembrane domains 5, 7, and 8, and extracellular loop 4 of GlyT2. Knowledge of this site could be exploited further in the development of drugs to treat pain, and to identify other allosteric modulators of the SLC6 family of transporters.
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Affiliation(s)
- Shannon N Mostyn
- School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
| | - Katie A Wilson
- Research School of Chemistry, College of ScienceThe Australian National UniversityCanberraAustralia
| | | | - Zachary J Frangos
- School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
| | - Susan Shimmon
- School of Mathematical and Physical SciencesUniversity of Technology SydneySydneyAustralia
| | - Tristan Rawling
- School of Mathematical and Physical SciencesUniversity of Technology SydneySydneyAustralia
| | - Renae M Ryan
- School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
| | - Megan L O'Mara
- Research School of Chemistry, College of ScienceThe Australian National UniversityCanberraAustralia
| | - Robert J Vandenberg
- School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
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32
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Chiou TT, Long P, Schumann-Gillett A, Kanamarlapudi V, Haas SA, Harvey K, O'Mara ML, De Blas AL, Kalscheuer VM, Harvey RJ. Mutation p.R356Q in the Collybistin Phosphoinositide Binding Site Is Associated With Mild Intellectual Disability. Front Mol Neurosci 2019; 12:60. [PMID: 30914922 PMCID: PMC6422930 DOI: 10.3389/fnmol.2019.00060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 10/02/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
The recruitment of inhibitory GABAA receptors to neuronal synapses requires a complex interplay between receptors, neuroligins, the scaffolding protein gephyrin and the GDP-GTP exchange factor collybistin (CB). Collybistin is regulated by protein-protein interactions at the N-terminal SH3 domain, which can bind neuroligins 2/4 and the GABAAR α2 subunit. Collybistin also harbors a RhoGEF domain which mediates interactions with gephyrin and catalyzes GDP-GTP exchange on Cdc42. Lastly, collybistin has a pleckstrin homology (PH) domain, which binds phosphoinositides, such as phosphatidylinositol 3-phosphate (PI3P/PtdIns3P) and phosphatidylinositol 4-monophosphate (PI4P/PtdIns4P). PI3P located in early/sorting endosomes has recently been shown to regulate the postsynaptic clustering of gephyrin and GABAA receptors and consequently the strength of inhibitory synapses in cultured hippocampal neurons. This process is disrupted by mutations in the collybistin gene (ARHGEF9), which cause X-linked intellectual disability (XLID) by a variety of mechanisms converging on disrupted gephyrin and GABAA receptor clustering at central synapses. Here we report a novel missense mutation (chrX:62875607C>T, p.R356Q) in ARHGEF9 that affects one of the two paired arginine residues in the PH domain that were predicted to be vital for binding phosphoinositides. Functional assays revealed that recombinant collybistin CB3SH3- R356Q was deficient in PI3P binding and was not able to translocate EGFP-gephyrin to submembrane microaggregates in an in vitro clustering assay. Expression of the PI3P-binding mutants CB3SH3- R356Q and CB3SH3- R356N/R357N in cultured hippocampal neurones revealed that the mutant proteins did not accumulate at inhibitory synapses, but instead resulted in a clear decrease in the overall number of synaptic gephyrin clusters compared to controls. Molecular dynamics simulations suggest that the p.R356Q substitution influences PI3P binding by altering the range of structural conformations adopted by collybistin. Taken together, these results suggest that the p.R356Q mutation in ARHGEF9 is the underlying cause of XLID in the probands, disrupting gephyrin clustering at inhibitory GABAergic synapses via loss of collybistin PH domain phosphoinositide binding.
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Affiliation(s)
- Tzu-Ting Chiou
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Philip Long
- Department of Pharmacology, UCL School of Pharmacy, London, United Kingdom
| | | | | | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kirsten Harvey
- Department of Pharmacology, UCL School of Pharmacy, London, United Kingdom
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, Australia
| | - Angel L De Blas
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Vera M Kalscheuer
- Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert J Harvey
- School of Health and Sport Sciences, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Sunshine Coast Health Institute, Birtinya, QLD, Australia
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33
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Schumann-Gillett A, O'Mara ML. The effects of oxidised phospholipids and cholesterol on the biophysical properties of POPC bilayers. Biochimica et Biophysica Acta (BBA) - Biomembranes 2019; 1861:210-219. [DOI: 10.1016/j.bbamem.2018.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/04/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
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34
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Abstract
E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.
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Affiliation(s)
- Alexandra Schumann-Gillett
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2061, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia
- The Institute for Molecular Biosciences (IMB), University of Queensland, Brisbane, QLD, 4072, Australia
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia.
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2061, Australia.
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, 6102, Australia.
| | - Megan L O'Mara
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia. megan.o'
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2061, Australia. megan.o'
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35
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Thomas M, Anglim Lagones T, Judd M, Morshedi M, O'Mara ML, White NG. Hydrogen bond-Driven Self-Assembly between Amidinium Cations and Carboxylate Anions: A Combined Molecular Dynamics, NMR Spectroscopy, and Single Crystal X-ray Diffraction Study. Chem Asian J 2017; 12:1587-1597. [PMID: 28544634 DOI: 10.1002/asia.201700406] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/18/2017] [Indexed: 11/06/2022]
Abstract
A combination of molecular dynamics (MD), NMR spectroscopy, and single crystal X-ray diffraction (SCXRD) techniques was used to probe the self-assembly of para- and meta-bis(amidinium) compounds with para-, meta-, and ortho-dicarboxylates. Good concordance was observed between the MD and experimental results. In DMSO solution, the systems form several rapidly exchanging assemblies, in part because a range of hydrogen bonding interactions is possible between the amidinium and carboxylate moieties. Upon crystallization, the majority of the systems form 1D supramolecular polymers, which are held together by short N-H⋅⋅⋅O hydrogen bonds.
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Affiliation(s)
- Michael Thomas
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Thomas Anglim Lagones
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Martyna Judd
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Mahbod Morshedi
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nicholas G White
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
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36
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Nothling MD, Ganesan A, Condic-Jurkic K, Pressly E, Davalos A, Gotrik MR, Xiao Z, Khoshdel E, Hawker CJ, O'Mara ML, Coote ML, Connal LA. Simple Design of an Enzyme-Inspired Supported Catalyst Based on a Catalytic Triad. Chem 2017. [DOI: 10.1016/j.chempr.2017.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Kretzmann JA, Ho D, Evans CW, Plani-Lam JHC, Garcia-Bloj B, Mohamed AE, O'Mara ML, Ford E, Tan DEK, Lister R, Blancafort P, Norret M, Iyer KS. Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA. Chem Sci 2017; 8:2923-2930. [PMID: 28451358 PMCID: PMC5376716 DOI: 10.1039/c7sc00097a] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/26/2017] [Indexed: 01/10/2023] Open
Abstract
Tools for editing the genome and epigenome have revolutionised the field of molecular biology and represent a new frontier in targeted therapeutic intervention. Although efficiencies and specificities of genome editing technologies have improved with the development of TALEs and CRISPR platforms, intracellular delivery of these larger constructs still remains a challenge using existing delivery agents. Viral vectors, including lentiviruses and adeno-associated viruses, as well as some non-viral strategies, such as cationic polymers and liposomes, are limited by packaging capacity, poor delivery, toxicity, and immunogenicity. We report a highly controlled synthetic strategy to engineer a flexible dendritic polymer using click chemistry to overcome the aforementioned delivery challenges associated with genome engineering technologies. Using a systematic approach, we demonstrate that high transfection efficiencies and packaging capacity can be achieved using this non-viral delivery methodology to deliver zinc fingers, TALEs and CRISPR/dCas9 platforms.
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Affiliation(s)
- Jessica A Kretzmann
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
| | - Diwei Ho
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
| | - Cameron W Evans
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
| | - Janice H C Plani-Lam
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
| | - Benjamin Garcia-Bloj
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
| | - A Elaaf Mohamed
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Megan L O'Mara
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Ethan Ford
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- ARC Centre of Excellence in Plant Energy Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Dennis E K Tan
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- ARC Centre of Excellence in Plant Energy Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Ryan Lister
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- ARC Centre of Excellence in Plant Energy Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- School of Anatomy, Physiology and Human Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Marck Norret
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
| | - K Swaminathan Iyer
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
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Mittra R, Pavy M, Subramanian N, George AM, O'Mara ML, Kerr ID, Callaghan R. Location of contact residues in pharmacologically distinct drug binding sites on P-glycoprotein. Biochem Pharmacol 2017; 123:19-28. [DOI: 10.1016/j.bcp.2016.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
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39
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Mohamed AE, Condic-Jurkic K, Ahmed FH, Yuan P, O'Mara ML, Jackson CJ, Coote ML. Hydrophobic Shielding Drives Catalysis of Hydride Transfer in a Family of F 420H 2-Dependent Enzymes. Biochemistry 2016; 55:6908-6918. [PMID: 27951661 DOI: 10.1021/acs.biochem.6b00683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A family of flavin/deazaflavin-dependent oxidoreductases (FDORs) from mycobacteria has been recently characterized and found to play a variety of catalytic roles, including the activation of prodrugs such as the candidate anti-tuberculosis drug pretomanid (PA-824). However, our understanding of the catalytic mechanism used by these enzymes is relatively limited. To address this, we have used a combination of quantum mechanics and molecular dynamics calculations to study the catalytic mechanism of the activation of pretomanid by the deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis. The preferred pathway involves an initial hydride transfer step from the deprotonated cofactor (i.e., F420H-), with subsequent protonation, before a series of spontaneous intramolecular reactions to form the final reactive nitrogen species. The most likely proton source is a hydroxonium ion within the solvent accessible active site. Intriguingly, catalysis of the rate-determining hydride transfer step is aided by three tyrosine residues that form a hydrophobic barrier around the active site that, upon reaction, is then disrupted to allow increased water accessibility to facilitate the subsequent proton transfer step. The catalytic mechanism we propose is consistent with previous experimental observations of the Ddn enzyme and will inform the design of improved prodrugs in the future.
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Affiliation(s)
- A Elaaf Mohamed
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Karmen Condic-Jurkic
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - F Hafna Ahmed
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Peng Yuan
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Michelle L Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
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40
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Subramanian N, Scopelliti AJ, Carland JE, Ryan RM, O'Mara ML, Vandenberg RJ. Correction: Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2. PLoS One 2016; 11:e0159896. [PMID: 27434127 PMCID: PMC4951049 DOI: 10.1371/journal.pone.0159896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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41
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Ahmed FH, Mohamed AE, Carr PD, Lee BM, Condic-Jurkic K, O'Mara ML, Jackson CJ. Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Sci 2016; 25:1692-709. [PMID: 27364382 DOI: 10.1002/pro.2975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 05/11/2016] [Accepted: 06/29/2016] [Indexed: 12/12/2022]
Abstract
Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F420 H2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immuno-evasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.
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Affiliation(s)
- F Hafna Ahmed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - A Elaaf Mohamed
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Paul D Carr
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Brendon M Lee
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
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42
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Subramanian N, Condic-Jurkic K, O'Mara ML. Structural and dynamic perspectives on the promiscuous transport activity of P-glycoprotein. Neurochem Int 2016; 98:146-52. [PMID: 27180050 DOI: 10.1016/j.neuint.2016.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 11/25/2022]
Abstract
The multidrug transporter P-glycoprotein (P-gp) is expressed in the blood-brain barrier endothelium where it effluxes a range of drug substrates, preventing their accumulation within the brain. P-gp has been studied extensively for 40 years because of its crucial role in the absorption, distribution, metabolism and elimination of a range of pharmaceutical compounds. Despite this, many aspects of the structure-function mechanism of P-gp are unresolved. Here we review the emerging role of molecular dynamics simulation techniques in our understanding of the membrane-embedded conformation of P-gp. We discuss its conformational plasticity in the presence and absence of ATP, and recent efforts to characterize the drug binding sites and uptake pathways.
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Affiliation(s)
- Nandhitha Subramanian
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia
| | - Megan L O'Mara
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2601, Australia. megan.o'
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43
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Subramanian N, Schumann-Gillett A, Mark AE, O'Mara ML. Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning. Biochimica et Biophysica Acta (BBA) - Biomembranes 2016; 1858:776-82. [DOI: 10.1016/j.bbamem.2015.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/18/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022]
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44
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Fairweather SJ, Bröer A, Subramanian N, Tumer E, Cheng Q, Schmoll D, O'Mara ML, Bröer S. Molecular basis for the interaction of the mammalian amino acid transporters B0AT1 and B0AT3 with their ancillary protein collectrin. J Biol Chem 2015; 290:24308-25. [PMID: 26240152 PMCID: PMC4591816 DOI: 10.1074/jbc.m115.648519] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/19/2015] [Indexed: 12/19/2022] Open
Abstract
Many solute carrier 6 (SLC6) family transporters require ancillary subunits to modify their expression and activity. The main apical membrane neutral amino acid transporters in mouse intestine and kidney, B(0)AT1 and B(0)AT3, require the ancillary protein collectrin or ACE2 for plasma membrane expression. Expression and activity of SLC6 neurotransmitter transporters are modulated by interaction with syntaxin 1A. Utilizing monocarboxylate-B(0)AT1/3 fusion constructs, we discovered that collectrin is also necessary for B(0)AT1 and B(0)AT3 catalytic function. Syntaxin 1A and syntaxin 3 inhibit the membrane expression of B(0)AT1 by competing with collectrin for access. A mutagenesis screening approach identified residues on trans-membrane domains 1α, 5, and 7 on one face of B(0)AT3 as a key region involved in interaction with collectrin. Mutant analysis established residues that were involved in collectrin-dependent functions as follows: plasma membrane expression of B(0)AT3, catalytic activation, or both. These results identify a potential binding site for collectrin and other SLC6 ancillary proteins.
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Affiliation(s)
| | | | - Nandhitha Subramanian
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia and
| | | | - Qi Cheng
- From the Research School of Biology and
| | - Dieter Schmoll
- the Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, Frankfurt am Main 65926, Germany
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia and
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45
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Deplazes E, Begg SL, van Wonderen JH, Campbell R, Kobe B, Paton JC, MacMillan F, McDevitt CA, O'Mara ML. Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy. Biophys Chem 2015; 207:51-60. [PMID: 26379256 DOI: 10.1016/j.bpc.2015.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 07/11/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022]
Abstract
Prokaryotic metal-ion receptor proteins, or solute-binding proteins, facilitate the acquisition of metal ions from the extracellular environment. Pneumococcal surface antigen A (PsaA) is the primary Mn(2+)-recruiting protein of the human pathogen Streptococcus pneumoniae and is essential for its in vivo colonization and virulence. The recently reported high-resolution structures of metal-free and metal-bound PsaA have provided the first insights into the mechanism of PsaA-facilitated metal binding. However, the conformational dynamics of metal-free PsaA in solution remain unknown. Here, we use continuous wave electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations to study the relative flexibility of the structural domains in metal-free PsaA and its distribution of conformations in solution. The results show that the crystal structure of metal-free PsaA is a good representation of the dominant conformation in solution, but the protein also samples structurally distinct conformations that are not captured by the crystal structure. Further, these results suggest that the metal binding site is both larger and more solvent exposed than indicated by the metal-free crystal structure. Collectively, this study provides atomic-resolution insight into the conformational dynamics of PsaA prior to metal binding and lays the groundwork for future EPR and MD based studies of PsaA in solution.
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Affiliation(s)
- Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Stephanie L Begg
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Jessica H van Wonderen
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Rebecca Campbell
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Fraser MacMillan
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia.
| | - Megan L O'Mara
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Research School of Chemistry, The Australian National University, Canberra, Australia. megan.o'
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46
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Subramanian N, Condic-Jurkic K, Mark AE, O'Mara ML. Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques. J Chem Inf Model 2015; 55:1202-17. [PMID: 25938863 DOI: 10.1021/ci5007382] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The multidrug transporter P-glycoprotein (P-gp) is central to the development of multidrug resistance in cancer. While residues essential for transport and binding have been identified, the location, composition, and specificity of potential drug binding sites are uncertain. Here molecular dynamics simulations are used to calculate the free energy profile for the binding of morphine and nicardipine to P-gp. We show that morphine and nicardipine primarily interact with key residues implicated in binding and transport from mutational studies, binding at different but overlapping sites within the transmembrane pore. Their permeation pathways were distinct but involved overlapping sets of residues. The results indicate that the binding location and permeation pathways of morphine and nicardipine are not well separated and cannot be considered as unique. This has important implications for our understanding of substrate uptake and transport by P-gp. Our results are independent of the choice of starting structure and consistent with a range of experimental studies.
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Affiliation(s)
- Nandhitha Subramanian
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Karmen Condic-Jurkic
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan E Mark
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Megan L O'Mara
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
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47
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Begg SL, Eijkelkamp BA, Luo Z, Couñago RM, Morey JR, Maher MJ, Ong CLY, McEwan AG, Kobe B, O'Mara ML, Paton JC, McDevitt CA. Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae. Nat Commun 2015; 6:6418. [PMID: 25731976 PMCID: PMC4366526 DOI: 10.1038/ncomms7418] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [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: 10/22/2014] [Accepted: 01/27/2015] [Indexed: 11/30/2022] Open
Abstract
Cadmium is a transition metal ion that is highly toxic in biological systems. Although relatively rare in the Earth’s crust, anthropogenic release of cadmium since industrialization has increased biogeochemical cycling and the abundance of the ion in the biosphere. Despite this, the molecular basis of its toxicity remains unclear. Here we combine metal-accumulation assays, high-resolution structural data and biochemical analyses to show that cadmium toxicity, in Streptococcus pneumoniae, occurs via perturbation of first row transition metal ion homeostasis. We show that cadmium uptake reduces the millimolar cellular accumulation of manganese and zinc, and thereby increases sensitivity to oxidative stress. Despite this, high cellular concentrations of cadmium (~17 mM) are tolerated, with negligible impact on growth or sensitivity to oxidative stress, when manganese and glutathione are abundant. Collectively, this work provides insight into the molecular basis of cadmium toxicity in prokaryotes, and the connection between cadmium accumulation and oxidative stress. The molecular basis for the high toxicity of cadmium is unclear. Here, Begg et al. use the bacterium Streptococcus pneumoniae as a model system, and show that cadmium uptake increases sensitivity to oxidative stress by reducing intracellular concentrations of manganese and zinc through different mechanisms.
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Affiliation(s)
- Stephanie L Begg
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 4072, Australia
| | - Bart A Eijkelkamp
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 4072, Australia
| | - Zhenyao Luo
- 1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia [3] Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rafael M Couñago
- 1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia [3] Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacqueline R Morey
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 4072, Australia
| | - Megan J Maher
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Cheryl-Lynn Y Ong
- 1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alastair G McEwan
- 1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bostjan Kobe
- 1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia [3] Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Megan L O'Mara
- 1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] School of Mathematics and Physics, University of Queensland, Brisbane, Queensland 4072, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 4072, Australia
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 4072, Australia
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48
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Brooks AJ, Dai W, O'Mara ML, Abankwa D, Chhabra Y, Pelekanos RA, Gardon O, Tunny KA, Blucher KM, Morton CJ, Parker MW, Sierecki E, Gambin Y, Gomez GA, Alexandrov K, Wilson IA, Doxastakis M, Mark AE, Waters MJ. Mechanism of activation of protein kinase JAK2 by the growth hormone receptor. Science 2014; 344:1249783. [PMID: 24833397 DOI: 10.1126/science.1249783] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Signaling from JAK (Janus kinase) protein kinases to STAT (signal transducers and activators of transcription) transcription factors is key to many aspects of biology and medicine, yet the mechanism by which cytokine receptors initiate signaling is enigmatic. We present a complete mechanistic model for activation of receptor-bound JAK2, based on an archetypal cytokine receptor, the growth hormone receptor. For this, we used fluorescence resonance energy transfer to monitor positioning of the JAK2 binding motif in the receptor dimer, substitution of the receptor extracellular domains with Jun zippers to control the position of its transmembrane (TM) helices, atomistic modeling of TM helix movements, and docking of the crystal structures of the JAK2 kinase and its inhibitory pseudokinase domain with an opposing kinase-pseudokinase domain pair. Activation of the receptor dimer induced a separation of its JAK2 binding motifs, driven by a ligand-induced transition from a parallel TM helix pair to a left-handed crossover arrangement. This separation leads to removal of the pseudokinase domain from the kinase domain of the partner JAK2 and pairing of the two kinase domains, facilitating trans-activation. This model may well generalize to other class I cytokine receptors.
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Affiliation(s)
- Andrew J Brooks
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia.
| | - Wei Dai
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA
| | - Megan L O'Mara
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
| | - Daniel Abankwa
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Yash Chhabra
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Rebecca A Pelekanos
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Olivier Gardon
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Kathryn A Tunny
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Kristopher M Blucher
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Craig J Morton
- Biota Structural Biology Laboratory and Australian Cancer Research Foundation (ACRF) Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Michael W Parker
- Biota Structural Biology Laboratory and Australian Cancer Research Foundation (ACRF) Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia. Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Emma Sierecki
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Yann Gambin
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Guillermo A Gomez
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Kirill Alexandrov
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Ian A Wilson
- Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA
| | - Alan E Mark
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia. The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
| | - Michael J Waters
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia.
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49
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van Wonderen JH, McMahon RM, O'Mara ML, McDevitt CA, Thomson AJ, Kerr ID, MacMillan F, Callaghan R. The central cavity of ABCB1 undergoes alternating access during ATP hydrolysis. FEBS J 2014; 281:2190-2201. [PMID: 24597976 DOI: 10.1111/febs.12773] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/18/2014] [Accepted: 02/28/2014] [Indexed: 02/06/2023]
Abstract
Understanding the process that underlies multidrug recognition and efflux by P-glycoprotein (ABCB1) remains a key biological challenge. Structural data have recently become available for the murine and Caenorhabditis elegans homologues of ABCB1; however all structures were obtained in the absence of nucleotide. A feature of these structures was the presence of a central cavity that is inaccessible from the extracellular face of the protein. To determine the conformational dynamics of this region several residues in transmembrane helices TM6 (331, 343 and 354) and TM12 (980) were mutated to cysteine. Based upon structural predictions, these residues are proposed to line, or reside proximal to, the central cavity. The mutant isoforms were labelled with a paramagnetic probe enabling the application of EPR spectroscopic methods. Power saturation EPR spectra were recorded in the presence of hydrophobic (O2 ) or hydrophilic (NiEDDA) quenching agents to study the local environment of each residue. ABCB1 was trapped in both its nucleotide-bound and post-hydrolytic conformations and EPR spectra were again recorded in the presence and absence of quenching agents. The EPR line shapes provide information on the movements of these residues within TM6 and TM12 during ATP hydrolysis. Rationalization of the data with molecular dynamic simulations indicates that the cavity is converted to a configuration open to the aqueous phase following nucleotide binding, thereby suggesting alternating access to the cavity on opposite sides of the membrane during translocation.
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Affiliation(s)
- Jessica H van Wonderen
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Róisin M McMahon
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.,Institute for Molecular Bioscience, Chemistry and Structural Biology Division, University of Queensland 4072, Australia
| | - Megan L O'Mara
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christopher A McDevitt
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Andrew J Thomson
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Ian D Kerr
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH.UK
| | - Fraser MacMillan
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Richard Callaghan
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.,Division of Biomedical Science & Biochemistry, Research School of Biology, College of Medicine, Biology & Environment, The Australian National University, Canberra ACT 0200 Australia
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50
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Plumptre CD, Eijkelkamp BA, Morey JR, Behr F, Couñago RM, Ogunniyi AD, Kobe B, O'Mara ML, Paton JC, McDevitt CA. AdcA and AdcAII employ distinct zinc acquisition mechanisms and contribute additively to zinc homeostasis inStreptococcus pneumoniae. Mol Microbiol 2014; 91:834-51. [DOI: 10.1111/mmi.12504] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Charles D. Plumptre
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Bart A. Eijkelkamp
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Jacqueline R. Morey
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Felix Behr
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Rafael M. Couñago
- School of Chemistry and Molecular Biosciences; University of Queensland; Brisbane Queensland Australia
- Australian Infectious Diseases Research Centre; University of Queensland; Brisbane Queensland Australia
- Institute for Molecular Bioscience; University of Queensland; Brisbane Queensland Australia
| | - Abiodun D. Ogunniyi
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences; University of Queensland; Brisbane Queensland Australia
- Australian Infectious Diseases Research Centre; University of Queensland; Brisbane Queensland Australia
- Institute for Molecular Bioscience; University of Queensland; Brisbane Queensland Australia
| | - Megan L. O'Mara
- School of Chemistry and Molecular Biosciences; University of Queensland; Brisbane Queensland Australia
- School of Mathematics and Physics; University of Queensland; Brisbane Queensland Australia
| | - James C. Paton
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
| | - Christopher A. McDevitt
- Research Centre for Infectious Diseases; School of Molecular and Biomedical Science; University of Adelaide; Adelaide South Australia Australia
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