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Chen JZ, Church WB, Bastard K, Duff AP, Balle T. Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit. Molecules 2023; 28:molecules28104108. [PMID: 37241849 DOI: 10.3390/molecules28104108] [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] [Received: 04/05/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Encephalopathies are brain dysfunctions that lead to cognitive, sensory, and motor development impairments. Recently, the identification of several mutations within the N-methyl-D-aspartate receptor (NMDAR) have been identified as significant in the etiology of this group of conditions. However, a complete understanding of the underlying molecular mechanism and changes to the receptor due to these mutations has been elusive. We studied the molecular mechanisms by which one of the first mutations within the NMDAR GluN1 ligand binding domain, Ser688Tyr, causes encephalopathies. We performed molecular docking, randomly seeded molecular dynamics simulations, and binding free energy calculations to determine the behavior of the two major co-agonists: glycine and D-serine, in both the wild-type and S688Y receptors. We observed that the Ser688Tyr mutation leads to the instability of both ligands within the ligand binding site due to structural changes associated with the mutation. The binding free energy for both ligands was significantly more unfavorable in the mutated receptor. These results explain previously observed in vitro electrophysiological data and provide detailed aspects of ligand association and its effects on receptor activity. Our study provides valuable insight into the consequences of mutations within the NMDAR GluN1 ligand binding domain.
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Affiliation(s)
- Jake Zheng Chen
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
| | - William Bret Church
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Karine Bastard
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Anthony P Duff
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Thomas Balle
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
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2
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Taylor JE, Chow JY, Jeffries CM, Kwan AH, Duff AP, Hamilton WA, Trewhella J. Calmodulin Binds a Highly Extended HIV-1 MA Protein That Refolds Upon Its Release. Biophys J 2023; 122:1734. [PMID: 37031681 PMCID: PMC10183364 DOI: 10.1016/j.bpj.2023.04.004] [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: 04/11/2023] Open
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3
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Tsai WJ, Lai YH, Shi YA, Hammel M, Duff AP, Whitten AE, Wilde KL, Wu CM, Knott R, Jeng US, Kang CY, Hsu CY, Wu JL, Tsai PJ, Chiang-Ni C, Wu JJ, Lin YS, Liu CC, Senda T, Wang S. Structural basis underlying the synergism of NADase and SLO during group A Streptococcus infection. Commun Biol 2023; 6:124. [PMID: 36721030 PMCID: PMC9887584 DOI: 10.1038/s42003-023-04502-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/18/2023] [Indexed: 02/02/2023] Open
Abstract
Group A Streptococcus (GAS) is a strict human pathogen possessing a unique pathogenic trait that utilizes the cooperative activity of NAD+-glycohydrolase (NADase) and Streptolysin O (SLO) to enhance its virulence. How NADase interacts with SLO to synergistically promote GAS cytotoxicity and intracellular survival is a long-standing question. Here, the structure and dynamic nature of the NADase/SLO complex are elucidated by X-ray crystallography and small-angle scattering, illustrating atomic details of the complex interface and functionally relevant conformations. Structure-guided studies reveal a salt-bridge interaction between NADase and SLO is important to cytotoxicity and resistance to phagocytic killing during GAS infection. Furthermore, the biological significance of the NADase/SLO complex in GAS virulence is demonstrated in a murine infection model. Overall, this work delivers the structure-functional relationship of the NADase/SLO complex and pinpoints the key interacting residues that are central to the coordinated actions of NADase and SLO in the pathogenesis of GAS infection.
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Affiliation(s)
- Wei-Jiun Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Hsin Lai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yong-An Shi
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Karyn L Wilde
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Chun-Ming Wu
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, Taiwan
| | - Robert Knott
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Yu Kang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Yu Hsu
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, Tainan, Taiwan
| | - Jian-Li Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Chuan Chiang-Ni
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Orthopedic Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jiunn-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yee-Shin Lin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Shuying Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
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4
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Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland TE, Cowieson N, Crossett B, Duff AP, Franke D, Gabel F, Gillilan RE, Graewert M, Grishaev A, Guss JM, Hammel M, Hopkins J, Huang Q, Hub JS, Hura GL, Irving TC, Jeffries CM, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg DJ, Ryan TM, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss TM, Whitten AE, Wood K, Zuo X. A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking. Acta Crystallogr D Struct Biol 2022; 78:1315-1336. [PMID: 36322416 PMCID: PMC9629491 DOI: 10.1107/s2059798322009184] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022] Open
Abstract
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0-1 Å-1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to <0.5 Å-1, but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H2O and in D2O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å-1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Paris, 91198 Gif-sur-Yvette, France
| | - Jan Bierma
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Clement Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Emre Brookes
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Srinivas Chakravarthy
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Leonie Chatzimagas
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123 Saarbrücken, Germany
| | - Thomas E. Cleveland
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Nathan Cowieson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Frank Gabel
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoblé Alpes, 41 Rue Jules Horowitz, 38027 Grenoble, France
| | - Richard E. Gillilan
- Cornell High-Energy Synchrotron Source, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Melissa Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jesse Hopkins
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Qingqui Huang
- Cornell High-Energy Synchrotron Source, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123 Saarbrücken, Germany
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas C. Irving
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Cy Michael Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Cheol Jeong
- Department of Physics, Wesleyan University, Middletown, CT 06459, USA
| | - Nigel Kirby
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3158, Australia
| | - Susan Krueger
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Anne Martel
- Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9, France
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Na Li
- National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Road No. 333, Haike Road, Shanghai 201210, People’s Republic of China
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Lionel Porcar
- Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9, France
| | - Thierry Prangé
- CITCoM (UMR 8038 CNRS), Faculté de Pharmacie, 4 Avenue de l’Observatoire, 75006 Paris, France
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mattia Rocco
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy
| | - Daniel J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Timothy M. Ryan
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3158, Australia
| | - Soenke Seifert
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Hiroshi Sekiguchi
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyōgo 679-5198, Japan
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Susana Teixeira
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Aurelien Thureau
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
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Duff AP, Cagnes M, Darwish TA, Krause-Heuer AM, Moir M, Recsei C, Rekas A, Russell RA, Wilde KL, Yepuri NR. Deuteration for biological SANS: Case studies, success and challenges in chemistry and biology. Methods Enzymol 2022; 677:85-126. [DOI: 10.1016/bs.mie.2022.08.030] [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: 11/05/2022]
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Separovic F, Hofferek V, Duff AP, McConville MJ, Sani MA. In-cell DNP NMR reveals multiple targeting effect of antimicrobial peptide. J Struct Biol X 2022; 6:100074. [PMID: 36147732 PMCID: PMC9486116 DOI: 10.1016/j.yjsbx.2022.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Abstract
DNP NMR allowed simultaneous monitoring of lipids, proteins and nucleic acids of E. coli cells. The bacterial stress response against an antimicrobial peptide was measured in situ. The antimicrobial peptide maculatin 1.1 significantly compacted nucleic acids in bacteria. Maculatin 1.1 prevented salt bridges forming between membrane lipids.
Dynamic nuclear polarization NMR spectroscopy was used to investigate the effect of the antimicrobial peptide (AMP) maculatin 1.1 on E. coli cells. The enhanced 15N NMR signals from nucleic acids, proteins and lipids identified a number of unanticipated physiological responses to peptide stress, revealing that membrane-active AMPs can have a multi-target impact on E. coli cells. DNP-enhanced 15N-observed 31P-dephased REDOR NMR allowed monitoring how Mac1 induced DNA condensation and prevented intermolecular salt bridges between the main E. coli lipid phosphatidylethanolamine (PE) molecules. The latter was supported by similar results obtained using E. coli PE lipid systems. Overall, the ability to monitor the action of antimicrobial peptides in situ will provide greater insight into their mode of action.
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Affiliation(s)
- Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vinzenz Hofferek
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anthony P. Duff
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia
| | - Malcom J. McConville
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Corresponding author.
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Yang HC, Lin SW, Ge YC, Huang MY, Yang CH, Liu WM, Duff AP, Wu CM, Lan YK, Su AC, Yeh YQ, Jeng US, Chou PT. Probing protein structures in solution by molecular dynamics simulation and small-angle X-ray scattering. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Chen Z, Church WB, Bastard K, Duff AP, Balle T. Effects of mutations in the NMDA receptor GluN1 subunit on binding and dynamics: a computational approach. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321090000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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9
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Ding Y, Chow SH, Chen J, Brun APL, Wu CM, Duff AP, Wang Y, Song J, Wang JH, Wong VH, Zhao D, Nishimura T, Lee TH, Conn CE, Hsu HY, Bui BV, Liu GS, Shen HH. Targeted delivery of LM22A-4 by cubosomes protects retinal ganglion cells in an experimental glaucoma model. Acta Biomater 2021; 126:433-444. [PMID: 33774200 DOI: 10.1016/j.actbio.2021.03.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 02/08/2023]
Abstract
Glaucoma, a major cause of irreversible blindness worldwide, is associated with elevated intraocular pressure (IOP) and progressive loss of retinal ganglion cells (RGCs) that undergo apoptosis. A mechanism for RGCs injury involves impairment of neurotrophic support and exogenous supply of neurotrophic factors has been shown to be beneficial. However, neurotrophic factors can have widespread effects on neuronal tissues, thus targeting neurotrophic support to injured neurons may be a better neuroprotective strategy. In this study, we have encapsulated LM22A-4, a small neurotrophic factor mimetic, into Annexin V-conjugated cubosomes (L4-ACs) for targeted delivery to injured RGCs in a model of acute IOP elevation, which is induced by acute IOP elevation. We have tested cubosomes formulations that encapsulate from 9% to 33% LM22A-4. Our data indicated that cubosomes encapsulating 9% and 17% LM22A-4 exhibited a mixture of Pn3m/Im3m cubic phase, whereas 23% and 33% showed a pure Im3m cubic phase. We found that 17% L4-ACs with Pn3m/Im3m symmetries showed better in-situ and in-vitro lipid membrane interactions than the 23% and 33% L4-ACs with Im3m symmetry. In vivo experiments showed that 17% L4-ACs targeted the posterior retina and the optic nerve head, which prevented RGCs loss and improved functional outcomes in a mouse model of acute IOP elevation. These results provide evidence that Annexin V-conjugated cubosomes-based LM22A-4 delivery may be a useful targeted approach to prevent the progression of RGCs loss in glaucoma. STATEMENT OF SIGNIFICANCE: Recent studies suggest that the therapy of effectively delivering neurotrophic factors to the injured retinal ganglion cells (RGCs) could promote the survival of RGCs in glaucoma. Our present work has for the first time used cubosomes as an active targeted delivery system and have successfully delivered a neuroprotective drug to the damaged RGCs in vivo. Our new cubosomal formulation can protect apoptotic cell death in vitro and in vivo, showing that cubosomes are a promising drug carrier system for ocular drug delivery and glaucoma treatment. We have further found that by controlling cubosomes in Pn3m phase we can facilitate delivery of neuroprotective drug through apoptotic membranes. This data, we believe, has important implications for future design and formulation of cubosomes for therapeutic applications.
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10
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Chen X, Ding Y, Bamert RS, Le Brun AP, Duff AP, Wu CM, Hsu HY, Shiota T, Lithgow T, Shen HH. Substrate-dependent arrangements of the subunits of the BAM complex determined by neutron reflectometry. Biochim Biophys Acta Biomembr 2021; 1863:183587. [PMID: 33639106 DOI: 10.1016/j.bbamem.2021.183587] [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] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/22/2022]
Abstract
In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex catalyses the assembly of β-barrel proteins into the outer membrane, and is composed of five subunits: BamA, BamB, BamC, BamD and BamE. Once assembled, - β-barrel proteins can be involved in various functions including uptake of nutrients, export of toxins and mediating host-pathogen interactions, but the precise mechanism by which these ubiquitous and often essential β-barrel proteins are assembled is yet to be established. In order to determine the relative positions of BAM subunits in the membrane environment we reconstituted each subunit into a biomimetic membrane, characterizing their interaction and structural changes by Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) and neutron reflectometry. Our results suggested that the binding of BamE, or a BamDE dimer, to BamA induced conformational changes in the polypeptide transported-associated (POTRA) domains of BamA, but that BamB or BamD alone did not promote any such changes. As monitored by neutron reflectometry, addition of an unfolded substrate protein extended the length of POTRA domains further away from the membrane interface as part of the mechanism whereby the substrate protein was folded into the membrane.
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Affiliation(s)
- Xiaoyu Chen
- Department of Materials Science & Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Yue Ding
- Department of Materials Science & Engineering, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Rebecca S Bamert
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Anthony P Duff
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Chun-Ming Wu
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia; National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hsien-Yi Hsu
- School of Energy and Environment & Department of Materials Science and Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, PR China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China
| | - Takuya Shiota
- Institute for Tenure Track Promotion, Organization for Promotion of Career Management, University of Miyazaki, Miyazaki, Japan
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
| | - Hsin-Hui Shen
- Department of Materials Science & Engineering, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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11
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Whitten AE, Jarrott RJ, Hu SH, Duff AP, King GJ, Martin JL, Christie MP. Studying Munc18:Syntaxin Interactions Using Small-Angle Scattering. Methods Mol Biol 2019; 1860:115-144. [PMID: 30317501 DOI: 10.1007/978-1-4939-8760-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The interaction between the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein syntaxin (Sx) and regulatory partner Sec/Munc18 (SM) protein is a critical step in vesicle fusion. The exact role played by SM proteins, whether positive or negative, has been the topic of much debate. High-resolution structures of the SM:Sx complex have shown that SM proteins can bind syntaxin in a closed fusion incompetent state. However, in vitro and in vivo experiments also point to a positive regulatory role for SM proteins that is inconsistent with binding syntaxin in a closed conformation. Here we present protocols we used for the expression and purification of the SM proteins Munc18a and Munc18c and syntaxins 1 and 4 along with procedures used for small-angle X-ray and neutron scattering that showed that syntaxins can bind in an open conformation to SM proteins. We also describe methods for chemical cross-linking experiments and detail how this information can be combined with scattering data to obtain low-resolution structural models for SM:Sx protein complexes.
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Affiliation(s)
- Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Russell J Jarrott
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Shu-Hong Hu
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Gordon J King
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia, QLD, Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Michelle P Christie
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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12
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Rath EM, Cheng YY, Pinese M, Sarun KH, Hudson AL, Weir C, Wang YD, Håkansson AP, Howell VM, Liu GJ, Reid G, Knott RB, Duff AP, Church WB. BAMLET kills chemotherapy-resistant mesothelioma cells, holding oleic acid in an activated cytotoxic state. PLoS One 2018; 13:e0203003. [PMID: 30157247 PMCID: PMC6114908 DOI: 10.1371/journal.pone.0203003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022] Open
Abstract
Malignant pleural mesothelioma is an aggressive cancer with poor prognosis. Here we have investigated in vitro efficacy of BAMLET and BLAGLET complexes (anti-cancer complexes consisting of oleic acid and bovine α-lactalbumin or β-lactoglobulin respectively) in killing mesothelioma cells, determined BAMLET and BLAGLET structures, and investigated possible biological mechanisms. We performed cell viability assays on 16 mesothelioma cell lines. BAMLET and BLAGLET having increasing oleic acid content inhibited human and rat mesothelioma cell line proliferation at decreasing doses. Most of the non-cancer primary human fibroblasts were more resistant to BAMLET than were human mesothelioma cells. BAMLET showed similar cytotoxicity to cisplatin-resistant, pemetrexed-resistant, vinorelbine-resistant, and parental rat mesothelioma cells, indicating the BAMLET anti-cancer mechanism may be different to drugs currently used to treat mesothelioma. Cisplatin, pemetrexed, gemcitabine, vinorelbine, and BAMLET, did not demonstrate a therapeutic window for mesothelioma compared with immortalised non-cancer mesothelial cells. We demonstrated by quantitative PCR that ATP synthase is downregulated in mesothelioma cells in response to regular dosing with BAMLET. We sought structural insight for BAMLET and BLAGLET activity by performing small angle X-ray scattering, circular dichroism, and scanning electron microscopy. Our results indicate the structural mechanism by which BAMLET and BLAGLET achieve increased cytotoxicity by holding increasing amounts of oleic acid in an active cytotoxic state encapsulated in increasingly unfolded protein. Our structural studies revealed similarity in the molecular structure of the protein components of these two complexes and in their encapsulation of the fatty acid, and differences in the microscopic structure and structural stability. BAMLET forms rounded aggregates and BLAGLET forms long fibre-like aggregates whose aggregation is more stable than that of BAMLET due to intermolecular disulphide bonds. The results reported here indicate that BAMLET and BLAGLET may be effective second-line treatment options for mesothelioma.
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Affiliation(s)
- Emma M. Rath
- Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
| | - Yuen Yee Cheng
- Asbestos Diseases Research Institute (ADRI), Concord, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Mark Pinese
- Kinghorn Cancer Centre and Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kadir H. Sarun
- Asbestos Diseases Research Institute (ADRI), Concord, NSW, Australia
| | - Amanda L. Hudson
- Bill Walsh Translational Cancer Research Laboratory, Kolling Institute, University of Sydney, Sydney, NSW, Australia
| | - Christopher Weir
- Northern Blood Research Centre, Kolling Institute, University of Sydney, Sydney, NSW, Australia
| | - Yiwei D. Wang
- Burns Research, ANZAC Research Institute, Concord Hospital, University of Sydney, Concord, NSW, Australia
| | | | - Viive M. Howell
- Bill Walsh Translational Cancer Research Laboratory, Kolling Institute, University of Sydney, Sydney, NSW, Australia
| | - Guo Jun Liu
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, Australia
- Brain and Mind Centre and Faculty of Health Sciences, University of Sydney, Sydney, NSW, Australia
| | - Glen Reid
- Asbestos Diseases Research Institute (ADRI), Concord, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Robert B. Knott
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, Australia
| | - Anthony P. Duff
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, Australia
| | - W. Bret Church
- Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
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13
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Baker MAB, Tuckwell AJ, Berengut JF, Bath J, Benn F, Duff AP, Whitten AE, Dunn KE, Hynson RM, Turberfield AJ, Lee LK. Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering. ACS Nano 2018; 12:5791-5799. [PMID: 29812934 DOI: 10.1021/acsnano.8b01669] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.
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Affiliation(s)
- Matthew A B Baker
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
| | - Andrew J Tuckwell
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
| | - Jonathan Bath
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Florence Benn
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation , Lucas Heights 2234 , Australia
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation , Lucas Heights 2234 , Australia
| | - Katherine E Dunn
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Robert M Hynson
- Structural and Computational Biology Division , The Victor Chang Cardiac Research Institute , Darlinghurst 2010 , Australia
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
- Structural and Computational Biology Division , The Victor Chang Cardiac Research Institute , Darlinghurst 2010 , Australia
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14
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Furlong EJ, Choudhury HG, Kurth F, Duff AP, Whitten AE, Martin JL. Disulfide isomerase activity of the dynamic, trimeric Proteus mirabilis ScsC protein is primed by the tandem immunoglobulin-fold domain of ScsB. J Biol Chem 2018; 293:5793-5805. [PMID: 29491145 DOI: 10.1074/jbc.ra118.001860] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 01/12/2018] [Revised: 02/15/2018] [Indexed: 11/06/2022] Open
Abstract
Correct disulfide bond formation is essential for proper folding of many proteins, including bacterial virulence factors. The suppressor of copper sensitivity (Scs) proteins have roles in dithiol/disulfide interchange and the bacterial response to copper stress. Encoded in a four-gene cassette (ScsABCD) present in many Gram-negative bacteria, the Scs proteins are enigmatic and poorly characterized. Here, we show that the periplasmic α-domain of the membrane protein ScsB in the Gram-negative bacterium Proteus mirabilis forms a redox relay with the soluble periplasmic protein PmScsC. We also found that the periplasmic α-domain is sufficient to activate the disulfide isomerase activity of PmScsC. The crystal structure of PmScsBα at a resolution of 1.54 Å revealed that it comprises two structurally similar immunoglobulin-like folds, one of which includes a putative redox-active site with the sequence CXXXC. We confirmed the importance of these cysteine residues for PmScsBα function, and in addition, we engineered cysteine variants that produced a stable complex between PmScsC and PmScsBα. Using small-angle X-ray and neutron scattering analyses with contrast variation, we determined a low-resolution structure of the PmScsC-PmScsBα complex. The structural model of this complex suggested that PmScsBα uses both of its immunoglobulin-like folds to interact with PmScsC and revealed that the highly dynamic PmScsC becomes ordered upon PmScsBα binding. These findings add to our understanding of the poorly characterized Scs proteins.
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Affiliation(s)
- Emily J Furlong
- From the Institute for Molecular Bioscience, University of Queensland, St, Lucia, Queensland 4072, Australia.,Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111 Australia, and
| | - Hassanul G Choudhury
- From the Institute for Molecular Bioscience, University of Queensland, St, Lucia, Queensland 4072, Australia
| | - Fabian Kurth
- From the Institute for Molecular Bioscience, University of Queensland, St, Lucia, Queensland 4072, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Jennifer L Martin
- From the Institute for Molecular Bioscience, University of Queensland, St, Lucia, Queensland 4072, Australia, .,Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111 Australia, and
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15
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Ding Y, Chow SH, Liu GS, Wang B, Lin TW, Hsu HY, Duff AP, Le Brun AP, Shen HH. Annexin V-containing cubosomes for targeted early detection of apoptosis in degenerative retinal tissue. J Mater Chem B 2018; 6:7652-7661. [DOI: 10.1039/c8tb02465k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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
ANX–PS–Phy cubosomes could be applied as a safe and robust drug delivery vehicle for targeting damaged, apoptotic cells in ocular diseases.
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Affiliation(s)
- Yue Ding
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
| | - Seong Hoong Chow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania
- Australia
- Ophthalmology, Department of Surgery, University of Melbourne
- Victoria
- Australia
| | - Bo Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Anatomy and Developmental Biology, Monash University
- Clayton
- Australia
| | - Tsung-Wu Lin
- Department of Chemistry, Tunghai University
- Taichung City
- Taiwan
| | - Hsien-Yi Hsu
- School of Energy and Environment, City University of Hong Kong
- Kowloon Tong
- China
- Shenzhen Research Institute of City University of Hong Kong
- Shenzhen 518057
| | - Anthony P. Duff
- Australian Nuclear Science and Technology Organisation (ANSTO)
- Lucas Heights
- Australia
| | - Anton P. Le Brun
- Australian Nuclear Science and Technology Organisation (ANSTO)
- Lucas Heights
- Australia
| | - Hsin-Hui Shen
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
- Department of Materials Science and Engineering
- Faculty of Engineering
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16
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Liew CW, Hynson RM, Ganuelas LA, Shah-Mohammadi N, Duff AP, Kojima S, Homma M, Lee LK. Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering. Biochem Biophys Res Commun 2017; 495:1614-1619. [PMID: 29197577 DOI: 10.1016/j.bbrc.2017.11.194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/18/2023]
Abstract
The bacterial flagellar motor drives the rotation of helical flagellar filaments to propel bacteria through viscous media. It consists of a dynamic population of mechanosensitive stators that are embedded in the inner membrane and activate in response to external load. This entails assembly around the rotor, anchoring to the peptidoglycan layer to counteract torque from the rotor and opening of a cation channel to facilitate an influx of cations, which is converted into mechanical rotation. Stator complexes are comprised of four copies of an integral membrane A subunit and two copies of a B subunit. Each B subunit includes a C-terminal OmpA-like peptidoglycan-binding (PGB) domain. This is thought to be linked to a single N-terminal transmembrane helix by a long unstructured peptide, which allows the PGB domain to bind to the peptidoglycan layer during stator anchoring. The high-resolution crystal structures of flagellar motor PGB domains from Salmonella enterica (MotBC2) and Vibrio alginolyticus (PomBC5) have previously been elucidated. Here, we use small-angle X-ray scattering (SAXS). We show that unlike MotBC2, the dimeric conformation of the PomBC5 in solution differs to its crystal structure, and explore the functional relevance by characterising gain-of-function mutants as well as wild-type constructs of various lengths. These provide new insight into the conformational diversity of flagellar motor PGB domains and experimental verification of their overall topology.
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Affiliation(s)
- C W Liew
- School of Medical Sciences, The University of New South Wales, Australia
| | - R M Hynson
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - L A Ganuelas
- School of Medical Sciences, The University of New South Wales, Australia
| | - N Shah-Mohammadi
- Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia; Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - A P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - S Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - M Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
| | - L K Lee
- School of Medical Sciences, The University of New South Wales, Australia; Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.
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17
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Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017; 73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [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: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022] Open
Abstract
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- ANSTO, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale (IBS), and Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A. Jacques
- University of Technology Sydney, ithree Institute, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Nigel M. Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette CEDEX, France
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Nokestrasse 85, 22607 Hamburg, Germany
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - John A. Tainer
- Basic Science Research Division, Molecular and Cellular Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 07102, USA
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18
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Rath EM, Duff AP, Gilbert EP, Doherty G, Knott RB, Church WB. Cover Image, Volume 85, Issue 7. Proteins 2017. [DOI: 10.1002/prot.25320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emma M. Rath
- Faculty of Pharmacy; University of Sydney; Sydney New South Wales Australia
| | - Anthony P. Duff
- Australian Nuclear Science and Technology Organisation (ANSTO); Lucas Heights New South Wales Australia
| | - Elliot P. Gilbert
- Australian Nuclear Science and Technology Organisation (ANSTO); Lucas Heights New South Wales Australia
| | - Greg Doherty
- Australian Nuclear Science and Technology Organisation (ANSTO); Lucas Heights New South Wales Australia
| | - Robert B. Knott
- Australian Nuclear Science and Technology Organisation (ANSTO); Lucas Heights New South Wales Australia
| | - W. Bret Church
- Faculty of Pharmacy; University of Sydney; Sydney New South Wales Australia
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19
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Rath EM, Duff AP, Gilbert EP, Doherty G, Knott RB, Church WB. Neutron scattering shows a droplet of oleic acid at the center of the BAMLET complex. Proteins 2017; 85:1371-1378. [PMID: 28380660 DOI: 10.1002/prot.25298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/10/2017] [Accepted: 03/27/2017] [Indexed: 01/13/2023]
Abstract
The anti-cancer complex, Bovine Alpha-lactalbumin Made LEthal to Tumors (BAMLET), has intriguing broad-spectrum anti-cancer activity. Although aspects of BAMLET's anti-cancer mechanism are still not known, it is understood that it involves the oleic acid or oleate component of BAMLET being preferentially released into cancer cell membranes leading to increased membrane permeability and lysis. The structure of the protein component of BAMLET has previously been elucidated by small angle X-ray scattering (SAXS) to be partially unfolded and dramatically enlarged. However, the structure of the oleic acid component of BAMLET and its disposition with respect to the protein component was not revealed as oleic acid has the same X-ray scattering length density (SLD) as water. Employing the difference in the neutron SLDs of hydrogen and deuterium, we carried out solvent contrast variation small angle neutron scattering (SANS) experiments of hydrogenated BAMLET in deuterated water buffers, to reveal the size, shape, and disposition of the oleic acid component of BAMLET. Our resulting analysis and models generated from SANS and SAXS data indicate that oleic acid forms a spherical droplet of oil incompletely encapsulated by the partially unfolded protein component. This model provides insight into the anti-cancer mechanism of this cache of lipid. The model also reveals a protein component "tail" not associated with the oleic acid component that is able to interact with the tail of other BAMLET molecules, providing a plausible explanation of how BAMLET readily forms aggregates. Proteins 2017; 85:1371-1378. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Emma M Rath
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, New South Wales, Australia
| | - Elliot P Gilbert
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, New South Wales, Australia
| | - Greg Doherty
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, New South Wales, Australia
| | - Robert B Knott
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, New South Wales, Australia
| | - W Bret Church
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, Australia
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20
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Al-Zyoud WA, Hynson RMG, Ganuelas LA, Coster ACF, Duff AP, Baker MAB, Stewart AG, Giannoulatou E, Ho JWK, Gaus K, Liu D, Lee LK, Böcking T. Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Res 2016; 44:1411-20. [PMID: 26681693 PMCID: PMC4756830 DOI: 10.1093/nar/gkv1466] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022] Open
Abstract
Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR-DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR-DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites/genetics
- Chromatography, Gel
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon/genetics
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Multimerization
- Protein Structure, Tertiary
- Scattering, Small Angle
- Sequence Homology, Nucleic Acid
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/metabolism
- X-Ray Diffraction
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Affiliation(s)
- Walid A Al-Zyoud
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Robert M G Hynson
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Lorraine A Ganuelas
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Adelle C F Coster
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Matthew A B Baker
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Alastair G Stewart
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Eleni Giannoulatou
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Joshua W K Ho
- The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia
| | - Katharina Gaus
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Lawrence K Lee
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
| | - Till Böcking
- School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia
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21
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Baker MAB, Hynson RMG, Ganuelas LA, Mohammadi NS, Liew CW, Rey AA, Duff AP, Whitten AE, Jeffries CM, Delalez NJ, Morimoto YV, Stock D, Armitage JP, Turberfield AJ, Namba K, Berry RM, Lee LK. Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor. Nat Struct Mol Biol 2016; 23:197-203. [PMID: 26854663 DOI: 10.1038/nsmb.3172] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/13/2016] [Indexed: 01/02/2023]
Abstract
Large protein complexes assemble spontaneously, yet their subunits do not prematurely form unwanted aggregates. This paradox is epitomized in the bacterial flagellar motor, a sophisticated rotary motor and sensory switch consisting of hundreds of subunits. Here we demonstrate that Escherichia coli FliG, one of the earliest-assembling flagellar motor proteins, forms ordered ring structures via domain-swap polymerization, which in other proteins has been associated with uncontrolled and deleterious protein aggregation. Solution structural data, in combination with in vivo biochemical cross-linking experiments and evolutionary covariance analysis, revealed that FliG exists predominantly as a monomer in solution but only as domain-swapped polymers in assembled flagellar motors. We propose a general structural and thermodynamic model for self-assembly, in which a structural template controls assembly and shapes polymer formation into rings.
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Affiliation(s)
- Matthew A B Baker
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Robert M G Hynson
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Lorraine A Ganuelas
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Nasim Shah Mohammadi
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Chu Wai Liew
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Anthony A Rey
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Anthony P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Andrew E Whitten
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Cy M Jeffries
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | | | - Yusuke V Morimoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Daniela Stock
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | | | | | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Lawrence K Lee
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
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22
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Rath EM, Duff AP, Håkansson AP, Vacher CS, Liu GJ, Knott RB, Church WB. Structure and Potential Cellular Targets of HAMLET-like Anti-Cancer Compounds made from Milk Components. J Pharm Pharm Sci 2015; 18:773-824. [DOI: 10.18433/j3g60c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The HAMLET family of compounds (Human Alpha-lactalbumin Made Lethal to Tumours) was discovered during studies on the properties of human milk, and is a class of protein-lipid complexes having broad spectrum anti-cancer, and some specific anti-bacterial properties. The structure of HAMLET-like compounds consists of an aggregation of partially unfolded protein making up the majority of the compound's mass, with fatty acid molecules bound in the hydrophobic core. This is a novel protein-lipid structure and has only recently been derived by small-angle X-ray scattering analysis. The structure is the basis of a novel cytotoxicity mechanism responsible for anti-cancer activity to all of the around 50 different cancer cell types for which the HAMLET family has been trialled. Multiple cytotoxic mechanisms have been hypothesised for the HAMLET-like compounds, but it is not yet clear which of those are the initiating cytotoxic mechanism(s) and which are subsequent activities triggered by the initiating mechanism(s). In addition to the studies into the structure of these compounds, this review presents the state of knowledge of the anti-cancer aspects of HAMLET-like compounds, the HAMLET-induced cytotoxic activities to cancer and non-cancer cells, and the several prospective cell membrane and intracellular targets of the HAMLET family. The emerging picture is that HAMLET-like compounds initiate their cytotoxic effects on what may be a cancer-specific target in the cell membrane that has yet to be identified. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.
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23
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Tarahi Tabrizi S, Langley DB, Harrop SJ, Duff AP, Willows RD. Structure of GUN4 from Chlamydomonas reinhardtii. Acta Crystallogr F Struct Biol Commun 2015; 71:1094-9. [PMID: 26249706 PMCID: PMC4528948 DOI: 10.1107/s2053230x15012248] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/26/2015] [Indexed: 11/10/2022] Open
Abstract
The genomes uncoupled 4 (GUN4) protein stimulates chlorophyll biosynthesis by increasing the activity of Mg-chelatase, the enzyme that inserts magnesium into protoporphyrin IX (PPIX) in the chlorophyll biosynthesis pathway. One of the roles of GUN4 is in binding PPIX and Mg-PPIX. In eukaryotes, GUN4 also participates in plastid-to-nucleus signalling, although the mechanism for this is unclear. Here, the first crystal structure of a eukaryotic GUN4, from Chlamydomonas reinhardtii, is presented. The structure is in broad agreement with those of previously solved cyanobacterial structures. Most interestingly, conformational divergence is restricted to several loops which cover the porphyrin-binding cleft. The conformational dynamics suggested by this ensemble of structures lend support to the understanding of how GUN4 binds PPIX or Mg-PPIX.
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Affiliation(s)
- Shabnam Tarahi Tabrizi
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - David B. Langley
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Stephen J. Harrop
- Australian Synchrotron, 800 Blackburn, Clayton, Melbourne, VIC 3168, Australia
| | | | - Robert D. Willows
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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24
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Golden E, Attwood PV, Duff AP, Meilleur F, Vrielink A. Production and characterization of recombinant perdeuterated cholesterol oxidase. Anal Biochem 2015; 485:102-8. [PMID: 26073659 DOI: 10.1016/j.ab.2015.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
Cholesterol oxidase (CO) is a FAD (flavin adenine dinucleotide) containing enzyme that catalyzes the oxidization and isomerization of cholesterol. Studies directed toward elucidating the catalytic mechanism of CO will provide an important general understanding of Flavin-assisted redox catalysis. Hydrogen atoms play an important role in enzyme catalysis; however, they are not readily visualized in protein X-ray diffraction structures. Neutron crystallography is an ideal method for directly visualizing hydrogen positions at moderate resolutions because hydrogen and deuterium have comparable neutron scattering lengths to other heavy atoms present in proteins. The negative coherent and large incoherent scattering lengths of hydrogen atoms in neutron diffraction experiments can be circumvented by replacing hydrogen atoms with its isotope, deuterium. The perdeuterated form of CO was successfully expressed from minimal medium, purified, and crystallized. X-ray crystallographic structures of the enzyme in the perdeuterated and hydrogenated states confirm that there are no apparent structural differences between the two enzyme forms. Kinetic assays demonstrate that perdeuterated and hydrogenated enzymes are functionally identical. Together, structural and functional studies indicate that the perdeuterated protein is suitable for structural studies by neutron crystallography directed at understanding the role of hydrogen atoms in enzyme catalysis.
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Affiliation(s)
- Emily Golden
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - Paul V Attwood
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - Anthony P Duff
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Alice Vrielink
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia.
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25
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Kim E, Rath EM, Tsang VHM, Duff AP, Robinson BG, Church WB, Benn DE, Dwight T, Clifton-Bligh RJ. Structural and functional consequences of succinate dehydrogenase subunit B mutations. Endocr Relat Cancer 2015; 22:387-97. [PMID: 25972245 DOI: 10.1530/erc-15-0099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mitochondrial dysfunction, due to mutations of the gene encoding succinate dehydrogenase (SDH), has been implicated in the development of adrenal phaeochromocytomas, sympathetic and parasympathetic paragangliomas, renal cell carcinomas, gastrointestinal stromal tumours and more recently pituitary tumours. Underlying mechanisms behind germline SDH subunit B (SDHB) mutations and their associated risk of disease are not clear. To investigate genotype-phenotype correlation of SDH subunit B (SDHB) variants, a homology model for human SDH was developed from a crystallographic structure. SDHB mutations were mapped, and biochemical effects of these mutations were predicted in silico. Results of structural modelling indicated that many mutations within SDHB are predicted to cause either failure of functional SDHB expression (p.Arg27*, p.Arg90*, c.88delC and c.311delAinsGG), or disruption of the electron path (p.Cys101Tyr, p.Pro197Arg and p.Arg242His). GFP-tagged WT SDHB and mutant SDHB constructs were transfected (HEK293) to determine biological outcomes of these mutants in vitro. According to in silico predictions, specific SDHB mutations resulted in impaired mitochondrial localisation and/or SDH enzymatic activity. These results indicated strong genotype-functional correlation for SDHB variants. This study reveals new insights into the effects of SDHB mutations and the power of structural modelling in predicting biological consequences. We predict that our functional assessment of SDHB mutations will serve to better define specific consequences for SDH activity as well as to provide a much needed assay to distinguish pathogenic mutations from benign variants.
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Affiliation(s)
- E Kim
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - E M Rath
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - V H M Tsang
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - A P Duff
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - B G Robinson
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - W B Church
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - D E Benn
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - T Dwight
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - R J Clifton-Bligh
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
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26
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Hynson RMG, Duff AP, Kirby N, Mudie S, Lee LK. Differential ultracentrifugation coupled to small-angle X-ray scattering on macromolecular complexes. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715005051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) can provide accurate structural information and low-resolution shapes of macromolecules in solution. The technique is particularly amenable to large protein assemblies, which produce a strong scattering signal. Hence, SAXS can be a powerful tool to elucidate quaternary structure, especially when used in combination with high-resolution structural techniques such as X-ray crystallography and NMR. Sample requirements for SAXS experiments are stringent and only monodispersed samples can be satisfactorily analysed. Often, it is not possible to obtain a stable monodispersed sample of the protein of interest, in particular for multi-subunit protein complexes. In these circumstances, when the complex is less than approximately 1 MDa, size exclusion chromatography (SEC) coupled with SAXS (SEC-SAXS) can facilitate the separation of monodispersed protein from a polydispersed sample for a sufficient amount of time to collect useful SAXS data. However, many very large multi-subunit macromolecular assemblies have not been successfully purified with SEC, and hence despite being well suited to SAXS there is often no way to produce sample of sufficient quality. Rather than SEC, differential ultracentrifugation (DU) is the method of choice for the final step in the purification of large macromolecular protein complexes. Here, a new method is described for collecting SAXS data on samples directly from the fractionated elution of ultracentrifuge tubes after DU. It is demonstrated using apoferritin as a model protein that, like SEC-SAXS, DU-coupled SAXS can facilitate simultaneous purification and data collection. It is envisaged that this new method will enable high-quality SAXS data to be collected on a host of large macromolecular protein complex assemblies for the first time.
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27
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Rath EM, Duff AP, Håkansson AP, Knott RB, Church WB. Small-angle X-ray scattering of BAMLET at pH 12: a complex of α-lactalbumin and oleic acid. Proteins 2014; 82:1400-8. [PMID: 24408789 DOI: 10.1002/prot.24508] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 06/28/2013] [Revised: 12/04/2013] [Accepted: 12/26/2013] [Indexed: 11/11/2022]
Abstract
BAMLET (Bovine Alpha-lactalbumin Made LEthal to Tumors) is a member of the family of the HAMLET-like complexes, a novel class of protein-based anti-cancer complexes that incorporate oleic acid and deliver it to cancer cells. Small angle X-ray scattering (SAXS) was performed on the complex at pH 12, examining the high pH structure as a function of oleic acid added. The SAXS data for BAMLET species prepared with a range of oleic acid concentrations indicate extended, irregular, partially unfolded protein conformations that vary with the oleic acid concentration. Increases in oleic acid concentration correlate with increasing radius of gyration without an increase in maximum particle dimension, indicating decreasing protein density. The models for the highest oleic acid content BAMLET indicate an unusual coiled elongated structure that contrasts with apo-α-lactalbumin at pH 12, which is an elongated globular molecule, suggesting that oleic acid inhibits the folding or collapse of the protein component of BAMLET to the globular form. Circular dichroism of BAMLET and apo-α-lactalbumin was performed and the results suggest that α-lactalbumin and BAMLET unfold in a continuum of increasing degree of unfolded states. Taken together, these results support a model in which BAMLET retains oleic acid by non-specific association in the core of partially unfolded protein, and represent a new type of lipoprotein structure.
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Affiliation(s)
- Emma M Rath
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, 2006, Australia
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28
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Jiang L, Phang JM, Yu J, Harrop SJ, Sokolova AV, Duff AP, Wilk KE, Alkhamici H, Breit SN, Valenzuela SM, Brown LJ, Curmi PMG. CLIC proteins, ezrin, radixin, moesin and the coupling of membranes to the actin cytoskeleton: a smoking gun? Biochim Biophys Acta 2013; 1838:643-57. [PMID: 23732235 DOI: 10.1016/j.bbamem.2013.05.025] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 12/20/2022]
Abstract
The CLIC proteins are a highly conserved family of metazoan proteins with the unusual ability to adopt both soluble and integral membrane forms. The physiological functions of CLIC proteins may include enzymatic activity in the soluble form and anion channel activity in the integral membrane form. CLIC proteins are associated with the ERM proteins: ezrin, radixin and moesin. ERM proteins act as cross-linkers between membranes and the cortical actin cytoskeleton. Both CLIC and ERM proteins are controlled by Rho family small GTPases. CLIC proteins, ERM and Rho GTPases act in a concerted manner to control active membrane processes including the maintenance of microvillar structures, phagocytosis and vesicle trafficking. All of these processes involve the interaction of membranes with the underlying cortical actin cytoskeleton. The relationships between Rho GTPases, CLIC proteins, ERM proteins and the membrane:actin cytoskeleton interface are reviewed. Speculative models are proposed involving the formation of localised multi-protein complexes on the membrane surface that assemble via multiple weak interactions. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé.
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Affiliation(s)
- Lele Jiang
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW 2010, Australia
| | - Juanita M Phang
- School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jiang Yu
- School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Stephen J Harrop
- School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna V Sokolova
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - Krystyna E Wilk
- School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Heba Alkhamici
- School of Medical and Molecular Biosciences, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Samuel N Breit
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW 2010, Australia
| | - Stella M Valenzuela
- School of Medical and Molecular Biosciences, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Louise J Brown
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Paul M G Curmi
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital, Sydney, NSW 2010, Australia; School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia.
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29
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Lee LK, Bryant KJ, Bouveret R, Lei PW, Duff AP, Harrop SJ, Huang EP, Harvey RP, Gelb MH, Gray PP, Curmi PM, Cunningham AM, Church WB, Scott KF. Selective inhibition of human group IIA-secreted phospholipase A2 (hGIIA) signaling reveals arachidonic acid metabolism is associated with colocalization of hGIIA to vimentin in rheumatoid synoviocytes. J Biol Chem 2013; 288:15269-79. [PMID: 23482564 PMCID: PMC3663547 DOI: 10.1074/jbc.m112.397893] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/06/2013] [Indexed: 11/06/2022] Open
Abstract
Human group IIA secreted phospholipase A2 (hGIIA) promotes tumor growth and inflammation and can act independently of its well described catalytic lipase activity via an alternative poorly understood signaling pathway. With six chemically diverse inhibitors we show that it is possible to selectively inhibit hGIIA signaling over catalysis, and x-ray crystal structures illustrate that signaling involves a pharmacologically distinct surface to the catalytic site. We demonstrate in rheumatoid fibroblast-like synoviocytes that non-catalytic signaling is associated with rapid internalization of the enzyme and colocalization with vimentin. Trafficking of exogenous hGIIA was monitored with immunofluorescence studies, which revealed that vimentin localization is disrupted by inhibitors of signaling that belong to a rare class of small molecule inhibitors that modulate protein-protein interactions. This study provides structural and pharmacological evidence for an association between vimentin, hGIIA, and arachidonic acid metabolism in synovial inflammation, avenues for selective interrogation of hGIIA signaling, and new strategies for therapeutic hGIIA inhibitor design.
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Affiliation(s)
- Lawrence K. Lee
- From the Faculty of Pharmacy, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Medical Sciences
| | | | - Romaric Bouveret
- St. Vincent's Hospital Clinical School, and
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
| | | | - Anthony P. Duff
- The Australian Nuclear Science and Technology Organisation, Sydney, New South Wales 2234, Australia
| | - Stephen J. Harrop
- School of Physics, Faculty of Science, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | | | - Richard P. Harvey
- St. Vincent's Hospital Clinical School, and
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
| | - Michael H. Gelb
- the Departments of Chemistry and Biochemistry, University of Washington, Seattle, Washington 98195
| | | | - Paul M. Curmi
- School of Physics, Faculty of Science, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital, Sydney, New South Wales 2010, Australia, and
| | | | - W. Bret Church
- From the Faculty of Pharmacy, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Medical Sciences
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30
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Morris VK, Linser R, Wilde KL, Duff AP, Sunde M, Kwan AH. Festkörper-NMR-Spektroskopie an funktionellen Amyloiden eines Pilz-Hydrophobins: Hinweise auf einen geordneten β-Faltblattkern bei genereller struktureller Heterogenität. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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31
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Morris VK, Linser R, Wilde KL, Duff AP, Sunde M, Kwan AH. Solid-state NMR spectroscopy of functional amyloid from a fungal hydrophobin: a well-ordered β-sheet core amidst structural heterogeneity. Angew Chem Int Ed Engl 2012; 51:12621-5. [PMID: 23125123 DOI: 10.1002/anie.201205625] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Indexed: 11/12/2022]
Abstract
GrEASy fibrils: Hydrophobins are fungal proteins that assemble into an amphipathic fibrillar monolayer with amyloid properties and a hydrophobic face as water-resistant as Teflon. Solid-state NMR studies on EAS hydrophobin fibrils reveal direct evidence of a partial molecular rearrangement on assembly and an ordered β-sheet-rich core in the context of a whole protein in this functional amyloid.
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Affiliation(s)
- Vanessa K Morris
- School of Medical Sciences and School of Molecular Bioscience, University of Sydney, Sydney, Australia
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32
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Taylor JEN, Chow JYH, Jeffries CM, Kwan AH, Duff AP, Hamilton WA, Trewhella J. Calmodulin binds a highly extended HIV-1 MA protein that refolds upon its release. Biophys J 2012; 103:541-549. [PMID: 22947870 PMCID: PMC3414894 DOI: 10.1016/j.bpj.2012.06.042] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/15/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022] Open
Abstract
Calmodulin (CaM) expression is upregulated upon HIV-1 infection and interacts with proteins involved in viral processing, including the multifunctional HIV-1 MA protein. We present here the results of studies utilizing small-angle neutron scattering with contrast variation that, when considered in the light of earlier fluorescence and NMR data, show CaM binds MA in an extended open-clamp conformation via interactions with two tryptophans that are widely spaced in sequence and space. The interaction requires a disruption of the MA tertiary fold such that MA becomes highly extended in a long snakelike conformation. The CaM-MA interface is extensive, covering ~70% of the length of the MA such that regions known to be important in MA interactions with critical binding partners would be impacted. The CaM conformation is semiextended and as such is distinct from the classical CaM-collapse about short α-helical targets. NMR data show that upon dissociation of the CaM-MA complex, either by the removal of Ca(2+) or increasing ionic strength, MA reforms its native tertiary contacts. Thus, we observe a high level of structural plasticity in MA that may facilitate regulation of its activities via intracellular Ca(2+)-signaling during viral processing.
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Affiliation(s)
- James E N Taylor
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New South Wales, Australia; School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - John Y H Chow
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - Cy M Jeffries
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - Ann H Kwan
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - Anthony P Duff
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - William A Hamilton
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia.
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Chen X, Wilde KL, Wang H, Lake V, Holden PJ, Middelberg AP, He L, Duff AP. High yield expression and efficient purification of deuterated human protein galectin-2. Food and Bioproducts Processing 2012. [DOI: 10.1016/j.fbp.2011.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Langley DB, Trambaiolo DM, Duff AP, Dooley DM, Freeman HC, Guss JM. Complexes of the copper-containing amine oxidase from Arthrobacter globiformis with the inhibitors benzylhydrazine and tranylcypromine. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:577-83. [PMID: 18607080 PMCID: PMC2443983 DOI: 10.1107/s174430910801556x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 05/23/2008] [Indexed: 11/10/2022]
Abstract
Complexes of Arthrobacter globiformis amine oxidase (AGAO) with the inhibitors benzylhydrazine and tranylcypromine (an antidepressant drug) have been refined at 1.86 and 1.65 A resolution, respectively. Both inhibitors form covalent adducts with the TPQ cofactor. A tyrosine residue, proposed to act as a gate to the AGAO active site, is in its open conformation.
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Affiliation(s)
- David B Langley
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
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35
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Langley DB, Brown DE, Cheruzel LE, Contakes SM, Duff AP, Hilmer KM, Dooley DM, Gray HB, Guss JM, Freeman HC. Enantiomer-specific binding of ruthenium(II) molecular wires by the amine oxidase of Arthrobacter globiformis. J Am Chem Soc 2008; 130:8069-78. [PMID: 18507382 PMCID: PMC2518534 DOI: 10.1021/ja801289f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The copper amine oxidase from Arthrobacter globiformis (AGAO) is reversibly inhibited by molecular wires comprising a Ru(II) complex head group and an aromatic tail group joined by an alkane linker. The crystal structures of a series of Ru(II)-wire-AGAO complexes differing with respect to the length of the alkane linker have been determined. All wires lie in the AGAO active-site channel, with their aromatic tail group in contact with the trihydroxyphenylalanine quinone (TPQ) cofactor of the enzyme. The TPQ cofactor is consistently in its active ("off-Cu") conformation, and the side chain of the so-called "gate" residue Tyr296 is consistently in the "gate-open" conformation. Among the wires tested, the most stable complex is produced when the wire has a -(CH2)4- linker. In this complex, the Ru(II)(phen)(bpy)2 head group is level with the protein molecular surface. Crystal structures of AGAO in complex with optically pure forms of the C4 wire show that the linker and head group in the two enantiomers occupy slightly different positions in the active-site channel. Both the Lambda and Delta isomers are effective competitive inhibitors of amine oxidation. Remarkably, inhibition by the C4 wire shows a high degree of selectivity for AGAO in comparison with other copper-containing amine oxidases.
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Affiliation(s)
- David B. Langley
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Doreen E. Brown
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Lionel E. Cheruzel
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen M. Contakes
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Kimberly M. Hilmer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - David M. Dooley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - J. Mitchell Guss
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Hans C. Freeman
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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36
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Duff AP, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM. A C-terminal disulfide bond in the copper-containing amine oxidase from pea seedlings violates the twofold symmetry of the molecular dimer. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1168-73. [PMID: 17142890 PMCID: PMC2225380 DOI: 10.1107/s1744309106043685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 10/19/2006] [Indexed: 11/10/2022]
Abstract
The structure of a newly crystallized form of the copper-dependent amine oxidase from pea seedlings has been refined at a resolution of 2.2 A to a final R factor of 0.181. The structure (form II) was originally discovered during a study of xenon binding to copper-dependent amine oxidases as a probe for dioxygen-binding sites [Duff et al. (2004), J. Mol. Biol. 344, 599-607]. The form II crystals belong to space group P2(1), with two dimers in the asymmetric unit. The overall structure is very similar to the crystals of form I in space group P2(1)2(1)2(1) with a dimer in the asymmetric unit [Kumar et al. (1996), Structure, 4, 943-955]. In form I the last three residues (644-647) observable in the two subunits were apparently splayed apart. It was noted that the absence of a disulfide bond between the Cys647 residues of the two subunits was inconsistent with chemical evidence for the absence of free sulfhydryl groups. In both of the crystallographically independent dimers of form II the two subunits are clearly joined by a disulfide bridge between the C-terminal cysteine residues. This is only possible if the two polypeptide chains in the dimer adopt different conformations near the C-terminus so that the twofold symmetry is lost. A proline residue (645) two residues before the cysteine has a cis conformation in one chain and a trans conformation in the other. As a result, the disulfide bond lies more than 5 A from the twofold axis. The loss of local twofold symmetry in form II can be explained by intermolecular contacts, which provide an asymmetric environment.
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Affiliation(s)
- Anthony P Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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37
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Langley DB, Duff AP, Freeman HC, Guss JM. The copper-containing amine oxidase from Arthrobacter globiformis: refinement at 1.55 and 2.20 A resolution in two crystal forms. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1052-7. [PMID: 17077478 PMCID: PMC2225227 DOI: 10.1107/s1744309106038814] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 09/22/2006] [Indexed: 11/10/2022]
Abstract
Copper-containing amine oxidases are found in all the major kingdoms of life. They catalyse the oxidation of organic amines in the presence of molecular dioxygen to aldehydes and hydrogen peroxide. The catalytic centres contain a Cu atom and a topaquinone cofactor formed autocatalytically from a tyrosine residue in the presence of Cu and molecular oxygen. The structure of the Cu-containing amine oxidase from Arthrobacter globiformis, which was previously refined at 1.8 A resolution in space group C2 with unit-cell parameters a = 157.84, b = 63.24, c = 91.98 A, beta = 112.0 degrees [Wilce et al. (1997), Biochemistry, 36, 16116-16133], has been re-refined with newly recorded data at 1.55 A resolution. The structure has also been solved and refined at 2.2 A resolution in a new crystal form, space group C2, with unit-cell parameters a = 158.04, b = 64.06, c = 69.69 A, beta = 111.7 degrees.
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Affiliation(s)
- David B. Langley
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Hans C. Freeman
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - J. Mitchell Guss
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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38
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Duff AP, Cohen AE, Ellis PJ, Hilmer K, Langley DB, Dooley DM, Freeman HC, Guss JM. The 1.23 Å structure ofPichia pastorislysyl oxidase reveals a lysine–lysine cross-link. Acta Crystallogr D Biol Crystallogr 2006; 62:1073-84. [PMID: 16929109 DOI: 10.1107/s0907444906026333] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 07/06/2006] [Indexed: 11/10/2022]
Abstract
The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Angstrom resolution. PPLO, a copper amine oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor, differs from most other members of the CuAO enzyme family in having the ability to oxidize the side chain of lysine residues in a polypeptide. In the asymmetric unit of the crystals, the structure analysis has located residues 43-779 of the polypeptide chain, seven carbohydrate residues, the active-site Cu atom, an imidazole molecule bound at the active site, two buried Ca(2+) ions, five surface Mg(2+) ions, five surface Cl(-) ions and 1045 water molecules. The crystallographic residuals are R = 0.112 and R(free) = 0.146. The TPQ cofactor and several other active-site residues are poorly ordered, in contrast to the surrounding well ordered structure. A covalent cross-link is observed between two lysine residues, Lys778 and Lys66. The cross-link is likely to have been formed by the oxidation of Lys778 followed by a spontaneous reaction with Lys66. The link is modelled as dehydrolysinonorleucine.
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Affiliation(s)
- Anthony P Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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39
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Contakes SM, Juda GA, Langley DB, Halpern-Manners NW, Duff AP, Dunn AR, Gray HB, Dooley DM, Guss JM, Freeman HC. Reversible inhibition of copper amine oxidase activity by channel-blocking ruthenium(II) and rhenium(I) molecular wires. Proc Natl Acad Sci U S A 2005; 102:13451-6. [PMID: 16157884 PMCID: PMC1224652 DOI: 10.1073/pnas.0506336102] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular wires comprising a Ru(II)- or Re(I)-complex head group, an aromatic tail group, and an alkane linker reversibly inhibit the activity of the copper amine oxidase from Arthrobacter globiformis (AGAO), with K(i) values between 6 muM and 37 nM. In the crystal structure of a Ru(II)-wire:AGAO conjugate, the wire occupies the AGAO active-site substrate access channel, the trihydroxyphenylalanine quinone cofactor is ordered in the "off-Cu" position with its reactive carbonyl oriented toward the inhibitor, and the "gate" residue, Tyr-296, is in the "open" position. Head groups, tail-group substituents, and linker lengths all influence wire-binding interactions with the enzyme.
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Affiliation(s)
- Stephen M Contakes
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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40
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Sträter N, Jasper B, Scholte M, Krebs B, Duff AP, Langley DB, Han R, Averill BA, Freeman HC, Guss JM. Crystal Structures of Recombinant Human Purple Acid Phosphatase With and Without an Inhibitory Conformation of the Repression Loop. J Mol Biol 2005; 351:233-46. [PMID: 15993892 DOI: 10.1016/j.jmb.2005.04.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 04/01/2005] [Accepted: 04/07/2005] [Indexed: 01/02/2023]
Abstract
The crystal structure of human purple acid phosphatase recombinantly expressed in Escherichia coli (rHPAP(Ec)) and Pichia pastoris (rHPAP(Pp)) has been determined in two different crystal forms, both at 2.2A resolution. In both cases, the enzyme crystallized in its oxidized (inactive) state, in which both Fe atoms in the dinuclear active site are Fe(III). The main difference between the two structures is the conformation of the enzyme "repression loop". Proteolytic cleavage of this loop in vivo or in vitro results in significant activation of the mammalian PAPs. In the crystals obtained from rHPAP(Ec), the carboxylate side-chain of Asp145 of this loop acts as a bidentate ligand that bridges the two metal atoms, in a manner analogous to a possible binding mode for a phosphate ester substrate in the enzyme-substrate complex. The carboxylate side-chain of Asp145 and the neighboring Phe146 side-chain thus block the active site, thereby inactivating the enzyme. In the crystal structure of rHPAP(Pp), the enzyme "repression loop" has an open conformation similar to that observed in other mammalian PAP structures. The present structures demonstrate that the repression loop exhibits significant conformational flexibility, and the observed alternate binding mode suggests a possible inhibitory role for this loop.
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Affiliation(s)
- Norbert Sträter
- Biotechnologisch-Biomedizinisches Zentrum, Fakultät für Chemie und Mineralogie der Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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41
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Duff AP, Trambaiolo DM, Cohen AE, Ellis PJ, Juda GA, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM. Using Xenon as a Probe for Dioxygen-binding Sites in Copper Amine Oxidases. J Mol Biol 2004; 344:599-607. [PMID: 15533431 DOI: 10.1016/j.jmb.2004.09.075] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Revised: 09/21/2004] [Accepted: 09/24/2004] [Indexed: 11/28/2022]
Abstract
Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site.
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Affiliation(s)
- Anthony P Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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42
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O'Connell KM, Langley DB, Shepard EM, Duff AP, Jeon HB, Sun G, Freeman HC, Guss JM, Sayre LM, Dooley DM. Differential inhibition of six copper amine oxidases by a family of 4-(aryloxy)-2-butynamines: evidence for a new mode of inactivation. Biochemistry 2004; 43:10965-78. [PMID: 15323556 DOI: 10.1021/bi0492004] [Citation(s) in RCA: 20] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of compounds derived from a previously identified substrate analogue of copper amine oxidases (CuAOs) (Shepard et al. (2002) Eur. J. Biochem. 269, 3645-3658) has been screened against six different CuAOs with a view to designing potent and selective inhibitors. The substrate analogues investigated were 4-(1-naphthyloxy)-2-butyn-1-amine, 4-(2-methylphenoxy)-2-butyn-1-amine, 4-(3-methylphenoxy)-2-butyn-1-amine, 4-(4-methylphenoxy)-2-butyn-1-amine, and 4-phenoxy-2-butyn-1-amine. These compounds were screened against equine plasma amine oxidase (EPAO), Pisum sativum amine oxidase (PSAO), Pichia pastoris lysyl oxidase (PPLO), bovine plasma amine oxidase (BPAO), human kidney diamine oxidase (KDAO), and Arthrobacter globiformis amine oxidase (AGAO) to examine the effect of different substituent groups on potency. Despite the similar structures of the 4-aryloxy analogues evaluated, striking differences in potency were observed. In addition, crystal structures of AGAO derivitized with 4-(2-naphthyloxy)-2-butyn-1-amine and 4-(4-methylphenoxy)-2-butyn-1-amine were obtained at a resolution of 1.7 A. The structures reveal a novel and unprecedented reaction mechanism involving covalent attachment of the alpha,beta-unsaturated aldehyde turnover product to the amino group of the reduced 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor. Collectively, the structural and inhibition results support the feasibility of designing selective mechanism-based inhibitors of copper amine oxidases.
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Affiliation(s)
- Kimberly M O'Connell
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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43
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Duff AP, Cohen AE, Ellis PJ, Kuchar JA, Langley DB, Shepard EM, Dooley DM, Freeman HC, Guss JM. The crystal structure of Pichia pastoris lysyl oxidase. Biochemistry 2003; 42:15148-57. [PMID: 14690425 DOI: 10.1021/bi035338v] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pichia pastoris lysyl oxidase (PPLO) is unique among the structurally characterized copper amine oxidases in being able to oxidize the side chain of lysine residues in polypeptides. Remarkably, the yeast PPLO is nearly as effective in oxidizing a mammalian tropoelastin substrate as is a true mammalian lysyl oxidase isolated from bovine aorta. Thus, PPLO is functionally related to the copper-containing lysyl oxidases despite the lack of any significant sequence similarity with these enzymes. The structure of PPLO has been determined at 1.65 A resolution. PPLO is a homodimer in which each subunit contains a Type II copper atom and a topaquinone cofactor (TPQ) formed by the posttranslational modification of a tyrosine residue. While PPLO has tertiary and quaternary topologies similar to those found in other quinone-containing copper amine oxidases, its active site is substantially more exposed and accessible. The structural elements that are responsible for the accessibility of the active site are identified and discussed.
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Affiliation(s)
- Anthony P Duff
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia
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44
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Freeman HC, Cohen A, Dooley DM, Duff AP, Ellis PJ, Guss J, Langley DB, Trambaiolo DM. New crystallographic studies of copper amine oxidases. J Inorg Biochem 2003. [DOI: 10.1016/s0162-0134(03)80615-3] [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: 10/26/2022]
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45
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Duff AP, Andrews TJ, Curmi PM. The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate. J Mol Biol 2000; 298:903-16. [PMID: 10801357 DOI: 10.1006/jmbi.2000.3724] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
d-Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the central CO(2)-fixing reaction of photosynthesis in a complex, multiple-step process. Several structures of rubisco complexed with substrate analogues, inhibitors and products have been determined by X-ray crystallography. The structures fall into two well-defined and distinct states. The active site is either "open" or "closed". The timing and mechanism of the transition between these two states have been uncertain. We solved the crystal structure of unactivated (metal-free) rubisco from tobacco with only inorganic phosphate bound and conclude that phosphate binding per se does not trigger closure, as it does in the similarly structured enzyme, triosephosphate isomerase. Comparison of all available rubisco structures suggests that, instead, the distance between the terminal phosphates (P1 and P2) of the bisphosphate ligand is the trigger: if that distance is less than 9.1 A, then the active site closes; if it is greater than 9.4 A then the enzyme remains open. Shortening of the inter-phosphate distance results from the ligand binding in a more curved conformation when O atoms of the ligand's sugar backbone interact either with the metal, if it is present, or with charged groups in the metal-binding site, if the metal is absent. This shortening brings the P1 phosphate into hydrogen bonding contact with Thr65. Thr65 exists in two discrete states related by a rotation of the backbone psi torsion angle. This rotation is coupled to domain rotation and hence to active site closure. Rotation of the side-chain of Thr65 also affects the C-terminal strand of large subunit which packs against Loop 6 after closure. The position of the C-terminal strand in the closed state is stabilised by multiple polar interactions with a distinctive highly-charged latch site involving the side-chain of Asp473. In the open state, this latch site may be occupied instead by phosphorylated anions.
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Affiliation(s)
- A P Duff
- Initiative in Biomolecular Structure, School of Physics University of New South Wales, Sydney, NSW 2052, Australia
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