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Abstract
With the development of accurate protein structure prediction algorithms, artificial intelligence (AI) has emerged as a powerful tool in the field of structural biology. AI-based algorithms have been used to analyze large amounts of protein sequence data including the human proteome, complementing experimental structure data found in resources such as the Protein Data Bank. The EBI AlphaFold Protein Structure Database (for example) contains over 230 million structures. In this study, these data have been analyzed to find all human proteins containing (or predicted to contain) the cytosolic glutathione transferase (cGST) fold. A total of 39 proteins were found, including the alpha-, mu-, pi-, sigma-, zeta- and omega-class GSTs, intracellular chloride channels, metaxins, multisynthetase complex components, elongation factor 1 complex components and others. Three broad themes emerge: cGST domains as enzymes, as chloride ion channels and as protein-protein interaction mediators. As the majority of cGSTs are dimers, the AI-based structure prediction algorithm AlphaFold-multimer was used to predict structures of all pairwise combinations of these cGST domains. Potential homo- and heterodimers are described. Experimental biochemical and structure data is used to highlight the strengths and limitations of AI-predicted structures.
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Affiliation(s)
- Aaron J Oakley
- School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
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2
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Paudel BP, Xu ZQ, Jergic S, Oakley AJ, Sharma N, Brown SHJ, Bouwer JC, Lewis PJ, Dixon NE, van Oijen AM, Ghodke H. Mechanism of transcription modulation by the transcription-repair coupling factor. Nucleic Acids Res 2022; 50:5688-5712. [PMID: 35641110 PMCID: PMC9177983 DOI: 10.1093/nar/gkac449] [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: 02/19/2022] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022] Open
Abstract
Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF.
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Affiliation(s)
- Bishnu P Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Simon H J Brown
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - James C Bouwer
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Peter J Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,ARC Industrial Transformation Training Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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3
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Shishmarev D, Rowland E, Aditya S, Sundararaj S, Oakley AJ, Dulhunty AF, Casarotto MG. Molecular interactions of
STAC
proteins with skeletal muscle dihydropyridine receptor and excitation‐contraction coupling. Protein Sci 2022; 31:e4311. [PMID: 35481653 PMCID: PMC9019556 DOI: 10.1002/pro.4311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/20/2022] [Accepted: 04/01/2022] [Indexed: 01/06/2023]
Abstract
Excitation‐contraction coupling (ECC) is the physiological process in which an electrical signal originating from the central nervous system is converted into muscle contraction. In skeletal muscle tissue, the key step in the molecular mechanism of ECC initiated by the muscle action potential is the cooperation between two Ca2+ channels, dihydropyridine receptor (DHPR; voltage‐dependent L‐type calcium channel) and ryanodine receptor 1 (RyR1). These two channels were originally postulated to communicate with each other via direct mechanical interactions; however, the molecular details of this cooperation have remained ambiguous. Recently, it has been proposed that one or more supporting proteins are in fact required for communication of DHPR with RyR1 during the ECC process. One such protein that is increasingly believed to play a role in this interaction is the SH3 and cysteine‐rich domain‐containing protein 3 (STAC3), which has been proposed to bind a cytosolic portion of the DHPR α1S subunit known as the II–III loop. In this work, we present direct evidence for an interaction between a small peptide sequence of the II–III loop and several residues within the SH3 domains of STAC3 as well as the neuronal isoform STAC2. Differences in this interaction between STAC3 and STAC2 suggest that STAC3 possesses distinct biophysical features that are potentially important for its physiological interactions with the II–III loop. Therefore, this work demonstrates an isoform‐specific interaction between STAC3 and the II–III loop of DHPR and provides novel insights into a putative molecular mechanism behind this association in the skeletal muscle ECC process.
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Affiliation(s)
- Dmitry Shishmarev
- John Curtin School of Medical Research Australian National University Canberra Australia
- Research School of Biology Australian National University Canberra Australia
| | - Emily Rowland
- John Curtin School of Medical Research Australian National University Canberra Australia
- Division of Structural Biology, Wellcome Centre for Human Genetics University of Oxford Oxford UK
| | - Shouvik Aditya
- John Curtin School of Medical Research Australian National University Canberra Australia
- Research School of Biology Australian National University Canberra Australia
| | - Srinivasan Sundararaj
- John Curtin School of Medical Research Australian National University Canberra Australia
| | - Aaron J. Oakley
- School of Chemistry & Molecular Bioscience and Molecular Horizons University of Wollongong Wollongong Australia
| | - Angela F. Dulhunty
- John Curtin School of Medical Research Australian National University Canberra Australia
| | - Marco G. Casarotto
- Research School of Biology Australian National University Canberra Australia
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4
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Oakley AJ. Proposed mechanism for monomethylarsonate reductase activity of human omega-class glutathione transferase GSTO1-1. Biochem Biophys Res Commun 2021; 590:7-13. [PMID: 34959192 DOI: 10.1016/j.bbrc.2021.12.072] [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: 11/23/2021] [Accepted: 12/20/2021] [Indexed: 11/02/2022]
Abstract
Contamination of drinking water with toxic inorganic arsenic is a major public health issue. The mechanisms of enzymes and transporters in arsenic elimination are therefore of interest. The human omega-class glutathione transferases have been previously shown to possess monomethylarsonate (V) reductase activity. To further understanding of this activity, molecular dynamics of human GSTO1-1 bound to glutathione with a monomethylarsonate isostere were simulated to reveal putative monomethylarsonate binding sites on the enzyme. The major binding site is in the active site, adjacent to the glutathione binding site. Based on this and previously reported biochemical data, a reaction mechanism for this enzyme is proposed. Further insights were gained from comparison of the human omega-class GSTs to homologs from a range of animals.
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Affiliation(s)
- Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.
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5
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Larsen JS, Miller M, Oakley AJ, Dixon NE, Lewis PJ. Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD. Microbiologyopen 2021; 10:e1251. [PMID: 34964291 PMCID: PMC8655204 DOI: 10.1002/mbo3.1251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
Efficient control of transcription is essential in all organisms. In bacteria, where DNA replication and transcription occur simultaneously, the replication machinery is at risk of colliding with highly abundant transcription complexes. This can be exacerbated by the fact that transcription complexes pause frequently. When pauses are long-lasting, the stalled complexes must be removed to prevent collisions with either another transcription complex or the replication machinery. HelD is a protein that represents a new class of ATP-dependent motor proteins distantly related to helicases. It was first identified in the model Gram-positive bacterium Bacillus subtilis and is involved in removing and recycling stalled transcription complexes. To date, two classes of HelD have been identified: one in the low G+C and the other in the high G+C Gram-positive bacteria. In this work, we have undertaken the first comprehensive investigation of the phylogenetic diversity of HelD proteins. We show that genes in certain bacterial classes have been inherited by horizontal gene transfer, many organisms contain multiple expressed isoforms of HelD, some of which are associated with antibiotic resistance, and that there is a third class of HelD protein found in Gram-negative bacteria. In summary, HelD proteins represent an important new class of transcription factors associated with genome maintenance and antibiotic resistance that are conserved across the Eubacterial kingdom.
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Affiliation(s)
- Joachim S Larsen
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Michael Miller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Aaron J Oakley
- School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Nicholas E Dixon
- School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
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6
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Abstract
The low G + C Gram-positive bacteria represent some of the most medically and industrially important microorganisms. They are relied on for the production of food and dietary supplements, enzymes and antibiotics, as well as being responsible for the majority of nosocomial infections and serving as a reservoir for antibiotic resistance. Control of gene expression in this group is more highly studied than in any bacteria other than the Gram-negative model Escherichia coli, yet until recently no structural information on RNA polymerase (RNAP) from this group was available. This review will summarize recent reports on the high-resolution structure of RNAP from the model low G + C representative Bacillus subtilis, including the role of auxiliary subunits δ and ε, and outline approaches for the development of antimicrobials to target RNAP from this group.
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Affiliation(s)
- Michael Miller
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Aaron J Oakley
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Peter J Lewis
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia.,School Of Chemistry And Molecular Bioscience, University Of Wollongong And Illawarra Health And Medical Research Institute, Wollongong, Nsw, Australia
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7
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Newing TP, Oakley AJ, Miller M, Dawson CJ, Brown SHJ, Bouwer JC, Tolun G, Lewis PJ. Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD. Nat Commun 2020; 11:6420. [PMID: 33339820 PMCID: PMC7749167 DOI: 10.1038/s41467-020-20157-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 07/06/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria.
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Affiliation(s)
- Timothy P Newing
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Michael Miller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Catherine J Dawson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Simon H J Brown
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - James C Bouwer
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Gökhan Tolun
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.
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8
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Xie Y, Tummala P, Oakley AJ, Deora GS, Nakano Y, Rooke M, Cuellar ME, Strasser JM, Dahlin JL, Walters MA, Casarotto MG, Board PG, Baell JB. Development of Benzenesulfonamide Derivatives as Potent Glutathione Transferase Omega-1 Inhibitors. J Med Chem 2020; 63:2894-2914. [PMID: 32105470 DOI: 10.1021/acs.jmedchem.9b01391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 12/13/2022]
Abstract
Glutathione transferase omega-1 (GSTO1-1) is an enzyme whose function supports the activation of interleukin (IL)-1β and IL-18 that are implicated in a variety of inflammatory disease states for which small-molecule inhibitors are sought. The potent reactivity of the active-site cysteine has resulted in reported inhibitors that act by covalent labeling. In this study, structure-activity relationship (SAR) elaboration of the reported GSTO1-1 inhibitor C1-27 was undertaken. Compounds were evaluated for inhibitory activity toward purified recombinant GSTO1-1 and for indicators of target engagement in cell-based assays. As covalent inhibitors, the kinact/KI values of selected compounds were determined, as well as in vivo pharmacokinetics analysis. Cocrystal structures of key novel compounds in complex with GSTO1-1 were also solved. This study represents the first application of a biochemical assay for GSTO1-1 to determine kinact/KI values for tested inhibitors and the most extensive set of cell-based data for a GSTO1-1 inhibitor SAR series reported to date. Our research culminated in the discovery of 25, which we propose as the preferred biochemical tool to interrogate cellular responses to GSTO1-1 inhibition.
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Affiliation(s)
- Yiyue Xie
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Padmaja Tummala
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Girdhar Singh Deora
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Yuji Nakano
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Melissa Rooke
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Matthew E Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Jessica M Strasser
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Jayme L Dahlin
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Marco G Casarotto
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Philip G Board
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Jonathan B Baell
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC 3052, Australia
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9
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Griffiths TM, Oakley AJ, Yu H. Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. J Comput Chem 2019; 41:587-603. [DOI: 10.1002/jcc.26125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas M. Griffiths
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2500 Australia
- Molecular Horizons University of Wollongong Wollongong New South Wales 2500 Australia
- Illawarra Health and Medical Research Institute, Northfields Ave Keiraville New South Wales 2500 Australia
| | - Aaron J. Oakley
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2500 Australia
- Molecular Horizons University of Wollongong Wollongong New South Wales 2500 Australia
- Illawarra Health and Medical Research Institute, Northfields Ave Keiraville New South Wales 2500 Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2500 Australia
- Molecular Horizons University of Wollongong Wollongong New South Wales 2500 Australia
- Illawarra Health and Medical Research Institute, Northfields Ave Keiraville New South Wales 2500 Australia
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10
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McGrath AE, Martyn AP, Whittell LR, Dawes FE, El Salamouni NS, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Corrigendum to "Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens" [J. Struct. Biol. 204 (3) (2018) 396-405]. J Struct Biol 2019; 207:234. [PMID: 31097372 DOI: 10.1016/j.jsb.2019.05.003] [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: 10/26/2022]
Affiliation(s)
- Amy E McGrath
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Alexander P Martyn
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Louise R Whittell
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Fay E Dawes
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Nehad S El Salamouni
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Jennifer L Beck
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Michael J Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia.
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11
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Abstract
DNA replication mechanisms are conserved across all organisms. The proteins required to initiate, coordinate, and complete the replication process are best characterized in model organisms such as Escherichia coli. These include nucleotide triphosphate-driven nanomachines such as the DNA-unwinding helicase DnaB and the clamp loader complex that loads DNA-clamps onto primer-template junctions. DNA-clamps are required for the processivity of the DNA polymerase III core, a heterotrimer of α, ε, and θ, required for leading- and lagging-strand synthesis. DnaB binds the DnaG primase that synthesizes RNA primers on both strands. Representative structures are available for most classes of DNA replication proteins, although there are gaps in our understanding of their interactions and the structural transitions that occur in nanomachines such as the helicase, clamp loader, and replicase core as they function. Reviewed here is the structural biology of these bacterial DNA replication proteins and prospects for future research.
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Affiliation(s)
- Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
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12
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McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens. J Struct Biol 2018; 204:396-405. [DOI: 10.1016/j.jsb.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
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13
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Wegener KL, McGrath AE, Dixon NE, Oakley AJ, Scanlon DB, Abell AD, Bruning JB. Rational Design of a 3 10
-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp. Chemistry 2018. [DOI: 10.1002/chem.201803280] [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: 11/07/2022]
Affiliation(s)
- Kate L. Wegener
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences; The University of Adelaide; South Australia 5005 Australia
| | - Amy E. McGrath
- Molecular Horizons and School of Chemistry and Molecular Bioscience; University of Wollongong; NSW 2522 Australia
| | - Nicholas E. Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience; University of Wollongong; NSW 2522 Australia
| | - Aaron J. Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience; University of Wollongong; NSW 2522 Australia
| | - Denis B. Scanlon
- Department of Chemistry; The University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, and the Centre for Nanoscale BioPhotonics; The University of Adelaide; South Australia 5005 Australia
| | - John B. Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences; The University of Adelaide; South Australia 5005 Australia
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14
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Wegener KL, McGrath AE, Dixon NE, Oakley AJ, Scanlon DB, Abell AD, Bruning JB. Front Cover: Rational Design of a 3 10
-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp (Chem. Eur. J. 44/2018). Chemistry 2018. [DOI: 10.1002/chem.201803279] [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: 11/05/2022]
Affiliation(s)
- Kate L. Wegener
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences; The University of Adelaide; South Australia 5005 Australia
| | - Amy E. McGrath
- Molecular Horizons and School of Chemistry and Molecular Bioscience; University of Wollongong; NSW 2522 Australia
| | - Nicholas E. Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience; University of Wollongong; NSW 2522 Australia
| | - Aaron J. Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience; University of Wollongong; NSW 2522 Australia
| | - Denis B. Scanlon
- Department of Chemistry; The University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, and the Centre for Nanoscale BioPhotonics; The University of Adelaide; South Australia 5005 Australia
| | - John B. Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences; The University of Adelaide; South Australia 5005 Australia
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Wegener KL, McGrath AE, Dixon NE, Oakley AJ, Scanlon DB, Abell AD, Bruning JB. Rational Design of a 3 10 -Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp. Chemistry 2018; 24:11325-11331. [PMID: 29917264 DOI: 10.1002/chem.201801734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/17/2018] [Indexed: 12/29/2022]
Abstract
The human sliding clamp (PCNA) controls access to DNA for many proteins involved in DNA replication and repair. Proteins are recruited to the PCNA surface by means of a short, conserved peptide motif known as the PCNA-interacting protein box (PIP-box). Inhibitors of these essential protein-protein interactions may be useful as cancer therapeutics by disrupting DNA replication and repair in these highly proliferative cells. PIP-box peptide mimetics have been identified as a potentially rapid route to potent PCNA inhibitors. Here we describe the rational design and synthesis of the first PCNA peptidomimetic ligands, based on the high affinity PIP-box sequence from the natural PCNA inhibitor p21. These mimetics incorporate covalent i,i+4 side-chain/side-chain lactam linkages of different lengths, designed to constrain the peptides into the 310 -helical structure required for PCNA binding. NMR studies confirmed that while the unmodified p21 peptide had little defined structure in solution, mimetic ACR2 pre-organized into 310 -helical structure prior to interaction with PCNA. ACR2 displayed higher affinity binding than most known PIP-box peptides, and retains the native PCNA binding mode, as observed in the co-crystal structure of ACR2 bound to PCNA. This study offers a promising new strategy for PCNA inhibitor design for use as anti-cancer therapeutics.
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Affiliation(s)
- Kate L Wegener
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Amy E McGrath
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia
| | - Denis B Scanlon
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
| | - Andrew D Abell
- Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, and the Centre for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
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Kielkopf CS, Low JKK, Mok YF, Bhatia S, Palasovski T, Oakley AJ, Whitten AE, Garner B, Brown SHJ. Identification of a novel tetrameric structure for human apolipoprotein-D. J Struct Biol 2018; 203:205-218. [PMID: 29885491 DOI: 10.1016/j.jsb.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 03/07/2018] [Revised: 05/18/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Abstract
Apolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methionine-93. Therefore, apolipoprotein-D plays multiple roles throughout the body and is protective in Alzheimer's disease, where apolipoprotein-D overexpression reduces the amyloid-β burden in Alzheimer's disease mouse models. Oligomerisation is a common feature of lipocalins that can influence ligand binding. The native structure of apolipoprotein-D, however, has not been conclusively defined. Apolipoprotein-D is generally described as a monomeric protein, although it dimerises when reducing peroxidised lipids. Here, we investigated the native structure of apolipoprotein-D derived from plasma, breast cyst fluid (BCF) and cerebrospinal fluid. In plasma and cerebrospinal fluid, apolipoprotein-D was present in high-molecular weight complexes, potentially in association with lipoproteins. In contrast, apolipoprotein-D in BCF formed distinct oligomeric species. We assessed apolipoprotein-D oligomerisation using native apolipoprotein-D purified from BCF and a suite of complementary methods, including multi-angle laser light scattering, analytical ultracentrifugation and small-angle X-ray scattering. Our analyses showed that apolipoprotein-D predominantly forms a ∼95 to ∼100 kDa tetramer. Small-angle X-ray scattering analysis confirmed these findings and provided a structural model for apolipoprotein-D tetramer. These data indicate apolipoprotein-D rarely exists as a free monomer under physiological conditions and provide insights into novel native structures of apolipoprotein-D and into oligomerisation behaviour in the lipocalin family.
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Affiliation(s)
- Claudia S Kielkopf
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - Surabhi Bhatia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.
| | - Tony Palasovski
- Illawarra and Shoalhaven Local Health District (ISLHD), Wollongong, NSW, Australia; Specialist Breast Clinic Sutherland Shire and Wollongong, NSW, Australia; Integrated Specialist Health Care Sutherland Shire, NSW, Australia
| | - Aaron J Oakley
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia; School of Chemistry, University of Wollongong, Wollongong, NSW, Australia.
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia.
| | - Brett Garner
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
| | - Simon H J Brown
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
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17
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Xie Y, Dahlin JL, Oakley AJ, Casarotto MG, Board PG, Baell JB. Reviewing Hit Discovery Literature for Difficult Targets: Glutathione Transferase Omega-1 as an Example. J Med Chem 2018; 61:7448-7470. [PMID: 29652143 DOI: 10.1021/acs.jmedchem.8b00318] [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: 02/07/2023]
Abstract
Early stage drug discovery reporting on relatively new or difficult targets is often associated with insufficient hit triage. Literature reviews of such targets seldom delve into the detail required to critically analyze the associated screening hits reported. Here we take the enzyme glutathione transferase omega-1 (GSTO1-1) as an example of a relatively difficult target and review the associated literature involving small-molecule inhibitors. As part of this process we deliberately pay closer-than-usual attention to assay interference and hit quality aspects. We believe this Perspective will be a useful guide for future development of GSTO1-1 inhibitors, as well serving as a template for future review formats of new or difficult targets.
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Affiliation(s)
- Yiyue Xie
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , Victoria 3052 , Australia
| | - Jayme L Dahlin
- Department of Pathology , Brigham and Women's Hospital , Boston , Massachusetts 02135 , United States
| | - Aaron J Oakley
- School of Chemistry , University of Wollongong , Wollongong , NSW 2522 , Australia
| | - Marco G Casarotto
- John Curtin School of Medical Research , Australian National University , Canberra , ACT 2600 , Australia
| | - Philip G Board
- John Curtin School of Medical Research , Australian National University , Canberra , ACT 2600 , Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , Victoria 3052 , Australia.,School of Pharmaceutical Sciences , Nanjing Tech University , Nanjing , 211816 , People's Republic of China
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18
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Chilingaryan Z, Headey SJ, Lo ATY, Xu ZQ, Otting G, Dixon NE, Scanlon MJ, Oakley AJ. Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction. Antibiotics (Basel) 2018; 7:E14. [PMID: 29470422 PMCID: PMC5872125 DOI: 10.3390/antibiotics7010014] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 12/30/2022] Open
Abstract
In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. The C-terminal hexapeptide motif of SSB (DDDIPF; SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. Here, fragment-based screening by saturation-transfer difference nuclear magnetic resonance (STD-NMR) and surface plasmon resonance assays identified inhibitors of the primase/SSB-Ct interaction. Hits were shown to bind to the SSB-Ct-binding site using 15N-¹H HSQC spectra. STD-NMR was used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover new antibacterial compounds.
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Affiliation(s)
- Zorik Chilingaryan
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Stephen J Headey
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Martin J Scanlon
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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19
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Menon D, Innes A, Oakley AJ, Dahlstrom JE, Jensen LM, Brüstle A, Tummala P, Rooke M, Casarotto MG, Baell JB, Nguyen N, Xie Y, Cuellar M, Strasser J, Dahlin JL, Walters MA, Burgio G, O’Neill LAJ, Board PG. GSTO1-1 plays a pro-inflammatory role in models of inflammation, colitis and obesity. Sci Rep 2017; 7:17832. [PMID: 29259211 PMCID: PMC5736720 DOI: 10.1038/s41598-017-17861-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/01/2017] [Indexed: 01/07/2023] Open
Abstract
Glutathione transferase Omega 1 (GSTO1-1) is an atypical GST reported to play a pro-inflammatory role in response to LPS. Here we show that genetic knockout of Gsto1 alters the response of mice to three distinct inflammatory disease models. GSTO1-1 deficiency ameliorates the inflammatory response stimulated by LPS and attenuates the inflammatory impact of a high fat diet on glucose tolerance and insulin resistance. In contrast, GSTO1-1 deficient mice show a more severe inflammatory response and increased escape of bacteria from the colon into the lymphatic system in a dextran sodium sulfate mediated model of inflammatory bowel disease. These responses are similar to those of TLR4 and MyD88 deficient mice in these models and confirm that GSTO1-1 is critical for a TLR4-like pro-inflammatory response in vivo. In wild-type mice, we show that a small molecule inhibitor that covalently binds in the active site of GSTO1-1 can be used to ameliorate the inflammatory response to LPS. Our findings demonstrate the potential therapeutic utility of GSTO1-1 inhibitors in the modulation of inflammation and suggest their possible application in the treatment of a range of inflammatory conditions.
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Affiliation(s)
- Deepthi Menon
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia ,0000 0004 1936 9705grid.8217.cSchool of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Ashlee Innes
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Aaron J. Oakley
- 0000 0004 0486 528Xgrid.1007.6School of Chemistry, University of Wollongong, Wollongong, NSW 2522 Australia
| | - Jane E. Dahlstrom
- 0000 0000 9984 5644grid.413314.0ACT Pathology and ANU Medical School, The Canberra Hospital, Garran, ACT 2605 Australia
| | - Lora M. Jensen
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Anne Brüstle
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Padmaja Tummala
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Melissa Rooke
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Marco G. Casarotto
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Jonathan B. Baell
- 0000 0004 1936 7857grid.1002.3Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052 Australia ,0000 0000 9389 5210grid.412022.7School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Nghi Nguyen
- 0000 0004 1936 7857grid.1002.3Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052 Australia
| | - Yiyue Xie
- 0000 0004 1936 7857grid.1002.3Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052 Australia
| | - Matthew Cuellar
- 0000000419368657grid.17635.36Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN USA
| | - Jessica Strasser
- 0000000419368657grid.17635.36Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN USA
| | - Jayme L. Dahlin
- 0000 0004 0378 8294grid.62560.37Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA
| | - Michael A. Walters
- 0000000419368657grid.17635.36Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN USA
| | - Gaetan Burgio
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - Luke A. J. O’Neill
- 0000 0004 1936 9705grid.8217.cSchool of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Philip G. Board
- 0000 0001 2180 7477grid.1001.0John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
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20
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Norris NC, Joseph S, Aditya S, Karunasekara Y, Board PG, Dulhunty AF, Oakley AJ, Casarotto MG. Structural and biophysical analyses of the skeletal dihydropyridine receptor β subunit β 1a reveal critical roles of domain interactions for stability. J Biol Chem 2017; 292:8401-8411. [PMID: 28351836 DOI: 10.1074/jbc.m116.763896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 10/19/2016] [Revised: 03/16/2017] [Indexed: 01/02/2023] Open
Abstract
Excitation-contraction (EC) coupling in skeletal muscle requires a physical interaction between the voltage-gated calcium channel dihydropyridine receptor (DHPR) and the ryanodine receptor Ca2+ release channel. Although the exact molecular mechanism that initiates skeletal EC coupling is unresolved, it is clear that both the α1 and β subunits of DHPR are essential for this process. Here, we employed a series of techniques, including size-exclusion chromatography-multi-angle light scattering, differential scanning fluorimetry, and isothermal calorimetry, to characterize various biophysical properties of the skeletal DHPR β subunit β1a Removal of the intrinsically disordered N and C termini and the hook region of β1a prevented oligomerization, allowing for its structural determination by X-ray crystallography. The structure had a topology similar to that of previously determined β isoforms, which consist of SH3 and guanylate kinase domains. However, transition melting temperatures derived from the differential scanning fluorimetry experiments indicated a significant difference in stability of ∼2-3 °C between the β1a and β2a constructs, and the addition of the DHPR α1s I-II loop (α-interaction domain) peptide stabilized both β isoforms by ∼6-8 °C. Similar to other β isoforms, β1a bound with nanomolar affinity to the α-interaction domain, but binding affinities were influenced by amino acid substitutions in the adjacent SH3 domain. These results suggest that intramolecular interactions between the SH3 and guanylate kinase domains play a role in the stability of β1a while also providing a conduit for allosteric signaling events.
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Affiliation(s)
- Nicole C Norris
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Soumya Joseph
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Shouvik Aditya
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Yamuna Karunasekara
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Philip G Board
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Angela F Dulhunty
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Aaron J Oakley
- Department of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Marco G Casarotto
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia.
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21
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Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM. Replisome speed determines the efficiency of the Tus−Ter replication termination barrier. Nature 2015; 525:394-8. [DOI: 10.1038/nature14866] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/26/2015] [Indexed: 11/09/2022]
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Yin Z, Whittell LR, Wang Y, Jergic S, Ma C, Lewis PJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. J Med Chem 2015; 58:4693-702. [PMID: 25970224 DOI: 10.1021/acs.jmedchem.5b00232] [Citation(s) in RCA: 24] [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] [Indexed: 01/05/2023]
Abstract
The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.
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Affiliation(s)
- Zhou Yin
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Louise R Whittell
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Yao Wang
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Cong Ma
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J Lewis
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas E Dixon
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Jennifer L Beck
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Michael J Kelso
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Aaron J Oakley
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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Yin Z, Whittell LR, Wang Y, Jergic S, Liu M, Harry EJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. J Med Chem 2014; 57:2799-806. [PMID: 24592885 DOI: 10.1021/jm500122r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins. Here, fragment-based screening using X-ray crystallography produced four hits bound in the linear-motif-binding pocket of the Escherichia coli SC. Compounds structurally related to the hits were identified that inhibited the E. coli SC and SC-mediated DNA replication in vitro. A tetrahydrocarbazole derivative emerged as a promising lead whose methyl and ethyl ester prodrug forms showed minimum inhibitory concentrations in the range of 21-43 μg/mL against representative Gram-negative and Gram-positive bacteria species. The work demonstrates the utility of a fragment-based approach for identifying bacterial sliding clamp inhibitors as lead compounds with broad-spectrum antibacterial activity.
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Affiliation(s)
- Zhou Yin
- School of Chemistry and Centre for Medical and Molecular Bioscience, University of Wollongong , Wollongong, New South Wales 2522, Australia
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Casarotto MG, Karunasekara Y, Aditya S, Cappello J, Dulhunty AF, Board PG, Oakley AJ, Norris NC. Structural and Binding Studies of the Cav1.1 β1A Subunit. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2531] [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: 11/25/2022] Open
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Shishmarev D, Wang Y, Mason CE, Su XC, Oakley AJ, Graham B, Huber T, Dixon NE, Otting G. Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy. Nucleic Acids Res 2013; 42:2750-7. [PMID: 24288378 PMCID: PMC3936761 DOI: 10.1093/nar/gkt1238] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of ∼64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron density of the C-peptide. Here we show that SSB forms a monomer at pH 3.4, which is suitable for studies by high-resolution nuclear magnetic resonance (NMR) spectroscopy. The OB-domain retains its 3D structure in the monomer, and the C-peptide is shown by nuclear Overhauser effects and lanthanide-induced pseudocontact shifts to bind to the OB-domain at a site that harbors ssDNA in the crystal structure of the SSB–ssDNA complex. 15N relaxation data demonstrate high flexibility of the polypeptide segment linking the C-peptide to the OB-domain and somewhat increased flexibility of the C-peptide compared with the OB-domain, suggesting that the C-peptide either retains high mobility in the bound state or is in a fast equilibrium with an unbound state.
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Affiliation(s)
- Dmitry Shishmarev
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia, Centre for Medical and Molecular Bioscience and School of Chemistry, University of Wollongong, New South Wales 2522, Australia and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville Victoria 3052, Australia
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Yin Z, Kelso MJ, Beck JL, Oakley AJ. Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp. J Med Chem 2013; 56:8665-73. [DOI: 10.1021/jm401118f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhou Yin
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Michael J. Kelso
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Jennifer L. Beck
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Aaron J. Oakley
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
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28
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Ozawa K, Horan NP, Robinson A, Yagi H, Hill FR, Jergic S, Xu ZQ, Loscha KV, Li N, Tehei M, Oakley AJ, Otting G, Huber T, Dixon NE. Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, epsilon, θ and β reveals a highly flexible arrangement of the proofreading domain. Nucleic Acids Res 2013; 41:5354-67. [PMID: 23580545 PMCID: PMC3664792 DOI: 10.1093/nar/gkt162] [Citation(s) in RCA: 34] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 11/24/2022] Open
Abstract
A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β2 replicase complex with primer-template DNA combine all available structural data.
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Affiliation(s)
- Kiyoshi Ozawa
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas P. Horan
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Andrew Robinson
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Hiromasa Yagi
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Flynn R. Hill
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Slobodan Jergic
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Zhi-Qiang Xu
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Karin V. Loscha
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nan Li
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Moeava Tehei
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Aaron J. Oakley
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Gottfried Otting
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Thomas Huber
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Nicholas E. Dixon
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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Abstract
Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.
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Affiliation(s)
- Zorik Chilingaryan
- School of Chemistry, University of Wollongong, Northfields Ave, Wollongong 2522, NSW, Australia.
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30
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Brown SHJ, Mitchell TW, Oakley AJ, Pham HT, Blanksby SJ. Time to face the fats: what can mass spectrometry reveal about the structure of lipids and their interactions with proteins? J Am Soc Mass Spectrom 2012; 23:1441-1449. [PMID: 22669763 DOI: 10.1007/s13361-012-0410-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 06/01/2023]
Abstract
Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.
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Affiliation(s)
- Simon H J Brown
- School of Chemistry, University of Wollongong, Wollongong, NSW, Australia.
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31
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Zhou H, Brock J, Liu D, Board PG, Oakley AJ. Structural Insights into the Dehydroascorbate Reductase Activity of Human Omega-Class Glutathione Transferases. J Mol Biol 2012; 420:190-203. [DOI: 10.1016/j.jmb.2012.04.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 04/09/2012] [Accepted: 04/11/2012] [Indexed: 11/30/2022]
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Oakley AJ, Bhatia S, Ecroyd H, Garner B. Molecular dynamics analysis of apolipoprotein-D-lipid hydroperoxide interactions: mechanism for selective oxidation of Met-93. PLoS One 2012; 7:e34057. [PMID: 22479522 PMCID: PMC3316614 DOI: 10.1371/journal.pone.0034057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [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: 01/19/2012] [Accepted: 02/23/2012] [Indexed: 01/01/2023] Open
Abstract
Background Recent studies suggest reduction of radical-propagating fatty acid hydroperoxides to inert hydroxides by interaction with apolipoprotein-D (apoD) Met93 may represent an antioxidant function for apoD. The nature and structural consequences of this selective interaction are unknown. Methodology/Principal Findings Herein we used molecular dynamics (MD) analysis to address these issues. Long-timescale simulations of apoD suggest lipid molecules are bound flexibly, with the molecules free to explore multiple conformations in a binding site at the entrance to the classical lipocalin ligand-binding pocket. Models of 5s- 12s- and 15s-hydroperoxyeicosatetraenoic acids were created and the lipids found to wrap around Met93 thus providing a plausible mechanism by which eicosatetraenoic acids bearing hydroperoxides on different carbon atoms can interact with Met93 to yield Met93 sulfoxide (Met93SO). Simulations of glycosylated apoD indicated that a second solvent exposed Met at position 49 was shielded by a triantennerary N-glycan attached to Asn45 thereby precluding lipid interactions. MD simulations of apoD showed B-factors of the loop containing Met93SO were higher in the oxidized protein, indicating increased flexibility that is predicted to destabilize the protein and promote self-association. Conclusions/Significance These studies provide novel insights into the mechanisms that may contribute to the antioxidant function of apoD and the structural consequences that result if Met93SO is not redox-cycled back to its native state.
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Affiliation(s)
- Aaron J. Oakley
- Illawarra Health and Medical Research Institute, University of Wollongong, New South Wales, Australia
- School of Chemistry, University of Wollongong, New South Wales, Australia
- * E-mail: (AJO); (BG)
| | - Surabhi Bhatia
- Neuroscience Research Australia, Sydney, New South Wales, Australia
| | - Heath Ecroyd
- Illawarra Health and Medical Research Institute, University of Wollongong, New South Wales, Australia
- School of Biological Sciences, University of Wollongong, New South Wales, Australia
| | - Brett Garner
- Illawarra Health and Medical Research Institute, University of Wollongong, New South Wales, Australia
- School of Biological Sciences, University of Wollongong, New South Wales, Australia
- * E-mail: (AJO); (BG)
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33
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Wijffels G, Johnson WM, Oakley AJ, Turner K, Epa VC, Briscoe SJ, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple BP, Alewood PF, Jennings PA, Dixon NE, Winkler DA. Binding Inhibitors of the Bacterial Sliding Clamp by Design. J Med Chem 2011; 54:4831-8. [DOI: 10.1021/jm2004333] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gene Wijffels
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Wynona M. Johnson
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Aaron J. Oakley
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - Kathleen Turner
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - V. Chandana Epa
- CSIRO Material Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Susan J. Briscoe
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Mitchell Polley
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Andris J. Liepa
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Albert Hofmann
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
| | - Jens Buchardt
- Institute of Molecular Bioscience, 306 Carmody Road, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Caspar Christensen
- Institute of Molecular Bioscience, 306 Carmody Road, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Pavel Prosselkov
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Brian P. Dalrymple
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Paul F. Alewood
- Institute of Molecular Bioscience, 306 Carmody Road, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Philip A. Jennings
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Nicholas E. Dixon
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
- School of Chemistry, University of Wollongong, New South Wales 2522, Australia
| | - David A. Winkler
- CSIRO Material Science and Engineering, Bayview Avenue, Clayton, Victoria 3168, Australia
- Monash Institute for Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria 3052, Australia
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34
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Zhou H, Brock J, Casarotto MG, Oakley AJ, Board PG. Novel folding and stability defects cause a deficiency of human glutathione transferase omega 1. J Biol Chem 2010; 286:4271-9. [PMID: 21106529 DOI: 10.1074/jbc.m110.197822] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The polymorphic deletion of Glu-155 from human glutathione transferase omega1 (GSTO1-1) occurs in most populations. Although the recombinant ΔGlu-155 enzyme expressed in Escherichia coli is active, the deletion causes a deficiency of the active enzyme in vivo. The crystal structure and the folding/unfolding kinetics of the ΔGlu-155 variant were determined in order to investigate the cause of the rapid loss of the enzyme in human cells. The crystal structure revealed altered packing around the Glu-155 deletion, an increase in the predicted solvent-accessible area and a corresponding reduction in the buried surface area. This increase in solvent accessibility was consistent with an elevated Stern-Volmer constant. The unfolding of both the wild type and ΔGlu-155 enzyme in urea is best described by a three-state model, and there is evidence for the more pronounced population of an intermediate state by the ΔGlu-155 enzymes. Studies using intrinsic fluorescence revealed a free energy change around 14.4 kcal/mol for the wild type compared with around 8.6 kcal/mol for the ΔGlu-155 variant, which indicates a decrease in stability associated with the Glu-155 deletion. Urea induced unfolding of the wild type GSTO1-1 was reversible through an initial fast phase followed by a second slow phase. In contrast, the ΔGlu-155 variant lacks the slow phase, indicating a refolding defect. It is possible that in some conditions in vivo, the increased solvent-accessible area and the low stability of the ΔGlu-155 variant may promote its unfolding, whereas the refolding defect limits its refolding, resulting in GSTO1-1 deficiency.
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Affiliation(s)
- Huina Zhou
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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35
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Oakley AJ, Barrett S, Peat TS, Newman J, Streltsov VA, Waddington L, Saito T, Tashiro M, McKimm-Breschkin JL. Structural and functional basis of resistance to neuraminidase inhibitors of influenza B viruses. J Med Chem 2010; 53:6421-31. [PMID: 20695427 PMCID: PMC2932999 DOI: 10.1021/jm100621s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase (NA), which confers cross-resistance to all NA inhibitors. We analyzed enzyme properties of the D197 and E197 NAs and compared these to a D197N NA, known to arise after oseltamivir treatment. Zanamivir and peramivir bound slowly to the wild type NA, but binding of oseltamivir was more rapid. The D197E/N mutations resulted in faster binding of all three inhibitors. Analysis of the crystal structures of D197 and E197 NAs with and without inhibitors showed that the D197E mutation compromised the interaction of neighboring R150 with the N-acetyl group, common to the substrate sialic acid and all NA inhibitors. Although rotation of the E275 in the NA active site occurs upon binding peramivir in both the D197 and E197 NAs, this does not occur upon binding oseltamivir in the E197 NA. Lack of the E275 rotation would also account for the loss of slow binding and the partial resistance of influenza B wild type NAs to oseltamivir.
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Affiliation(s)
- Aaron J Oakley
- CSIRO Materials Science and Engineering, Parkville, 343 Royal Parade, Parkville, Victoria, 3052, Australia
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36
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Oakley AJ. The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic. Biochem Biophys Res Commun 2010; 397:745-9. [DOI: 10.1016/j.bbrc.2010.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 06/06/2010] [Indexed: 10/19/2022]
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37
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Oakley AJ, Coggan M, Board PG. Identification and characterization of gamma-glutamylamine cyclotransferase, an enzyme responsible for gamma-glutamyl-epsilon-lysine catabolism. J Biol Chem 2010; 285:9642-9648. [PMID: 20110353 DOI: 10.1074/jbc.m109.082099] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gamma-glutamylamine cyclotransferase (GGACT) is an enzyme that converts gamma-glutamylamines to free amines and 5-oxoproline. GGACT shows high activity toward gamma-glutamyl-epsilon-lysine, derived from the breakdown of fibrin and other proteins cross-linked by transglutaminases. The enzyme adopts the newly identified cyclotransferase fold, observed in gamma-glutamylcyclotransferase (GGCT), an enzyme with activity toward gamma-glutamyl-alpha-amino acids (Oakley, A. J., Yamada, T., Liu, D., Coggan, M., Clark, A. G., and Board, P. G. (2008) J. Biol. Chem. 283, 22031-22042). Despite the absence of significant sequence identity, several residues are conserved in the active sites of GGCT and GGACT, including a putative catalytic acid/base residue (GGACT Glu(82)). The structure of GGACT in complex with the reaction product 5-oxoproline provides evidence for a common catalytic mechanism in both enzymes. The proposed mechanism, combined with the three-dimensional structures, also explains the different substrate specificities of these enzymes. Despite significant sequence divergence, there are at least three subfamilies in prokaryotes and eukaryotes that have conserved the GGCT fold and GGCT enzymatic activity.
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Affiliation(s)
- Aaron J Oakley
- Division of Molecular and Health Technologies, Commonwealth Scientific and Industrial Research Organization, Parkville, Victoria 3052
| | - Marjorie Coggan
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Philip G Board
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia.
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38
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Weber JE, Oakley AJ, Christ AN, Clark AG, Hayes JD, Hall R, Hume DA, Board PG, Smythe ML, Flanagan JU. Identification and characterisation of new inhibitors for the human hematopoietic prostaglandin D2 synthase. Eur J Med Chem 2009; 45:447-54. [PMID: 19939518 DOI: 10.1016/j.ejmech.2009.10.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 07/18/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
Abstract
Prostaglandin D(2) synthesised by the hematopoietic prostaglandin D(2) synthase has a pro-inflammatory effect in allergic asthma, regulating many hallmark characteristics of the disease. Here we describe identification of hematopoietic prostaglandin D(2) synthase inhibitors including cibacron blue, bromosulfophthalein and ethacrynic acid. Expansion around the drug-like ethacrynic acid identified a novel inhibitor, nocodazole, and a fragment representing its aromatic core. Nocodazole binding was further characterised by docking calculations in combination with conformational strain analysis. The benzyl thiophene core was predicted to be buried in the active site, binding in the putative prostaglandin binding site, and a likely hydrogen bond donor site identified. X-ray crystallographic studies supported the predicted binding mode.
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Affiliation(s)
- Jane E Weber
- The University of Queensland, Institute for Molecular Bioscience, Building 80, St Lucia, Queensland 4072, Australia
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39
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Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL. Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:681-5. [PMID: 18678932 DOI: 10.1107/s1744309108017600] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 06/11/2008] [Indexed: 11/10/2022]
Abstract
The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 A to a final R factor of 17.1%. The structure was originally solved to 2.9 A resolution using SAD phases from Zn2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 A resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activity in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe2+ metal-ion preference are discussed.
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Affiliation(s)
- Colin J Jackson
- Research School of Chemistry, Australian National University, Australia
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40
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Oakley AJ, Yamada T, Liu D, Coggan M, Clark AG, Board PG. The identification and structural characterization of C7orf24 as gamma-glutamyl cyclotransferase. An essential enzyme in the gamma-glutamyl cycle. J Biol Chem 2008; 283:22031-42. [PMID: 18515354 DOI: 10.1074/jbc.m803623200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hypothetical protein C7orf24 has been implicated as a cancer marker with a potential role in cell proliferation. We have identified C7orf24 as gamma-glutamyl cyclotransferase (GGCT) that catalyzes the formation of 5-oxoproline (pyroglutamic acid) from gamma-glutamyl dipeptides and potentially plays a significant role in glutathione homeostasis. In the present study we have identified the first cDNA clones encoding a gamma-glutamyl cyclotransferase. The GGCT gene is located on chromosome 7p14-15 and consists of four exons that span 8 kb. The primary sequence is 188 amino acids in length and is unlike any protein of known function. We crystallized functional recombinant gamma-glutamyl cyclotransferase and determined its structure at 1.7 A resolution. The enzyme is a dimer of 20,994-Da subunits. The topology of GGCT is unrelated to other enzymes associated with cyclotransferase-like activity. The fold was originally classified as "BtrG-like," a small family that only includes structures of hypothetical proteins from Mus musculus, Escherichia coli, Pyrococcus horikoshii, and Arabidopsis thaliana. Since this is the first member of this family with a defined function, we propose to refer to this structure as the gamma-glutamyl cyclotransferase fold. We have identified a potential active site pocket that contains a highly conserved glutamic acid (Glu(98)) and propose that it acts as a general acid/base in the reaction mechanism. Mutation of Glu(98) to Ala or Gln completely inactivates the enzyme without altering the overall fold.
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Affiliation(s)
- Aaron J Oakley
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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41
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Board PG, Coggan M, Cappello J, Zhou H, Oakley AJ, Anders M. S-(4-Nitrophenacyl)glutathione is a specific substrate for glutathione transferase omega 1-1. Anal Biochem 2008; 374:25-30. [DOI: 10.1016/j.ab.2007.09.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 09/26/2007] [Accepted: 09/26/2007] [Indexed: 11/15/2022]
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42
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Abstract
Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.
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Affiliation(s)
- Conrad J Burden
- Centre for Bioinformation Science, Mathematical Sciences Institute, Australian National University, Canberra, ACT, Australia.
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43
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Qi R, Fetzner S, Oakley AJ. Crystallization and diffraction data of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase: a cofactor-free oxygenase of the alpha/beta-hydrolase family. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:378-81. [PMID: 17565175 PMCID: PMC2335004 DOI: 10.1107/s1744309107013760] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 01/09/2007] [Accepted: 03/21/2007] [Indexed: 11/11/2022]
Abstract
1H-3-Hydroxy-4-oxoquinoline 2,4-dioxygenase (QDO) from Pseudomonas putida 33/1 catalyses the oxygenolysis of 1H-3-hydroxy-4-oxoquinoline to form N-formylanthranilic acid and carbon monoxide without the aid of cofactors. Both N-terminally His6-tagged and native QDO were overexpressed in Escherichia coli and purified by conventional chromatographic procedures. Untagged QDO, but not His6-tagged QDO, was crystallized by the vapour-diffusion method, giving hexagonal bipyramid crystals belonging to space group P6(1)22. Selenomethionine-containing native QDO was prepared and crystallized under identical conditions. The unit-cell parameters were a = b = 90.1, c = 168.6 A, alpha = beta = 90, gamma = 120 degrees. Using synchrotron radiation, these crystals diffract to 2.5 A. The expression, purification and crystallization of QDO are reported here.
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Affiliation(s)
- Ruhu Qi
- Research School of Chemistry, Australian National University, Acton, ACT 0200, Australia
| | - Susanne Fetzner
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | - Aaron J. Oakley
- Research School of Chemistry, Australian National University, Acton, ACT 0200, Australia
- Correspondence e-mail:
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Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon C, Hill TM, Dixon NE. A molecular mousetrap determines polarity of termination of DNA replication in E. coli. Cell 2006; 125:1309-19. [PMID: 16814717 DOI: 10.1016/j.cell.2006.04.040] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [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: 12/19/2005] [Revised: 03/16/2006] [Accepted: 04/26/2006] [Indexed: 11/24/2022]
Abstract
During chromosome synthesis in Escherichia coli, replication forks are blocked by Tus bound Ter sites on approach from one direction but not the other. To study the basis of this polarity, we measured the rates of dissociation of Tus from forked TerB oligonucleotides, such as would be produced by the replicative DnaB helicase at both the fork-blocking (nonpermissive) and permissive ends of the Ter site. Strand separation of a few nucleotides at the permissive end was sufficient to force rapid dissociation of Tus to allow fork progression. In contrast, strand separation extending to and including the strictly conserved G-C(6) base pair at the nonpermissive end led to formation of a stable locked complex. Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 A from its normal position to bind in a cytosine-specific pocket on the surface of Tus.
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Affiliation(s)
- Mark D Mulcair
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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Abstract
Well known as detoxification enzymes, the glutathione transferases also function in prostaglandin and steroid hormone synthesis. New uses for the canonical glutathione transferase fold are becoming apparent; the bacterial stringent starvation protein SspA and the yeast prion protein Ure2p (both transcription factors) were found to adopt this fold, but their roles remain unclear. The intracellular chloride ion channel CLIC1 adopts the canonical glutathione transferase fold in its soluble form and appears to undergo radical structural modification as part of its membrane insertion process. The structures of rat and human mitochondrial glutathione transferases have been solved: they adopt a topology similar to that of bacterial disulfide bond isomerases, leading to the suggestion that they have evolved independently of the canonical enzymes. Recent structural studies of integral membrane glutathione S-transferases from microsomes have revealed common patterns of tertiary and quaternary structure.
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Affiliation(s)
- Aaron J Oakley
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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46
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Bourgault R, Oakley AJ, Bewley JD, Wilce MCJ. Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit. Protein Sci 2005; 14:1233-41. [PMID: 15840830 PMCID: PMC2253274 DOI: 10.1110/ps.041260905] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [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: 12/17/2004] [Revised: 01/16/2005] [Accepted: 01/19/2005] [Indexed: 10/25/2022]
Abstract
The three-dimensional crystal structure of tomato (Lycopersicon esculentum) beta-mannanase 4a (LeMAN4a) has been determined to 1.5 A resolution. The enzyme adopts the (beta/alpha)(8) fold common to the members of glycohydrolase family GH5. The structure is comparable with those of the homologous Trichoderma reesei and Thermomonospora fusca beta-mannanases: There is a conserved three-stranded beta-sheet located near the N terminus that stacks against the central beta-barrel at the end opposite the active site. Three noncanonical beta-helices surround the active site. Similar helices are found in T. reesei but not T. fusca beta-mannanase. By analogy with other beta-mannanases, the catalytic acid/base residue is E204 and the nucleophile residue is E318. The active site cleft of L. esculentum beta-mannanase most closely resembles that of the T. reesei isozyme. A model of substrate binding in LeMAN4a is proposed in which the mannosyl residue occupying the -1 subsite of the enzyme adopts the (1)S(5) skew-boat conformation.
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47
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Oakley AJ, Loscha KV, Schaeffer PM, Liepinsh E, Pintacuda G, Wilce MCJ, Otting G, Dixon NE. Crystal and Solution Structures of the Helicase-binding Domain of Escherichia coli Primase. J Biol Chem 2005; 280:11495-504. [PMID: 15649896 DOI: 10.1074/jbc.m412645200] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During bacterial DNA replication, the DnaG primase interacts with the hexameric DnaB helicase to synthesize RNA primers for extension by DNA polymerase. In Escherichia coli, this occurs by transient interaction of primase with the helicase. Here we demonstrate directly by surface plasmon resonance that the C-terminal domain of primase is responsible for interaction with DnaB6. Determination of the 2.8-angstroms crystal structure of the C-terminal domain of primase revealed an asymmetric dimer. The monomers have an N-terminal helix bundle similar to the N-terminal domain of DnaB, followed by a long helix that connects to a C-terminal helix hairpin. The connecting helix is interrupted differently in the two monomers. Solution studies using NMR showed that an equilibrium exists between a monomeric species with an intact, extended but naked, connecting helix and a dimer in which this helix is interrupted in the same way as in one of the crystal conformers. The other conformer is not significantly populated in solution, and its presence in the crystal is due largely to crystal packing forces. It is proposed that the connecting helix contributes necessary structural flexibility in the primase-helicase complex at replication forks.
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Affiliation(s)
- Aaron J Oakley
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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Schmidberger JW, Oakley AJ, Tsang JSH, Wilce MCJ. Purification, crystallization and preliminary crystallographic analysis of DehIVa, a dehalogenase from Burkholderia cepacia MBA4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:271-3. [PMID: 16511015 PMCID: PMC1952274 DOI: 10.1107/s1744309105002472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 10/13/2004] [Accepted: 01/23/2005] [Indexed: 11/10/2022]
Abstract
DehIVa is one of two dehalogenases produced by the soil- and water-borne bacterium Burkholderia cepacia MBA4. It acts to break down short-chain halogenated aliphatic acids through a nucleophilic attack and subsequent hydrolysis of an enzyme-substrate intermediate to remove the halide ions from L-enantiomers substituted at the C2 position (e.g L-2-monochloropropionic acid). Dehalogenases are an important group of enzymes that are responsible for breaking down a diverse range of halogenated environmental pollutants. The dhlIVa gene coding for DehIVa was expressed in Escherichia coli and the protein was purified and crystallized using the hanging-drop method. Crystals grown in PEG 4000 and ammonium sulfate diffracted to 3.1 A. The crystals had a primitive hexagonal unit cell, with unit-cell parameters a = b = 104.2, c = 135.8 A, alpha = beta = 90, gamma = 120 degrees. Determining this structure will provide valuable insights into the characterization of the catalytic mechanisms of this group of enzymes.
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Affiliation(s)
- Jason W Schmidberger
- Structural Biology and Bioinformatics Group, School of Pharmacology and Medicine, University Of Western Australia, Crawley, Western Australia, Australia.
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Loscha K, Oakley AJ, Bancia B, Schaeffer PM, Prosselkov P, Otting G, Wilce MCJ, Dixon NE. Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase. Protein Expr Purif 2004; 33:304-10. [PMID: 14711519 DOI: 10.1016/j.pep.2003.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 10/26/2022]
Abstract
In Escherichia coli, the DnaG primase is the RNA polymerase that synthesizes RNA primers at replication forks. It is composed of three domains, a small N-terminal zinc-binding domain, a larger central domain responsible for RNA synthesis, and a C-terminal domain comprising residues 434-581 [DnaG(434-581)] that interact with the hexameric DnaB helicase. Presumably because of this interaction, it had not been possible previously to express the C-terminal domain in a stably transformed E. coli strain. This problem was overcome by expression of DnaG(434-581) under control of tandem bacteriophage lambda-promoters, and the protein was purified in yields of 4-6 mg/L of culture and studied by NMR. A TOCSY spectrum of a 2mM solution of the protein at pH 7.0, indicated that its structured core comprises residues 444-579. This was consistent with sequence conservation among most-closely related primases. Linewidths in a NOESY spectrum of a 0.5mM sample in 10mM phosphate, pH 6.05, 0.1M NaCl, recorded at 36 degrees C, indicated the protein to be monomeric. Crystals of selenomethionine-substituted DnaG(434-581) obtained by the hanging-drop vapor-diffusion method were body-centered tetragonal, space group I4(1)22, with unit cell parameters a=b=142.2A, c=192.1A, and diffracted beyond 2.7A resolution with synchrotron radiation.
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Affiliation(s)
- Karin Loscha
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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Oakley AJ, Klvana M, Otyepka M, Nagata Y, Wilce MCJ, Damborský J. Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry 2004; 43:870-8. [PMID: 14744129 DOI: 10.1021/bi034748g] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [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
We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in conformation B was mainly in the C(alpha)-C(beta)-C(gamma) angle (126 degrees ) that deviated by 13.4 degrees from the "ideal" bond angle of 112.6 degrees. On the basis of these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that protonation of the His272 side-chain nitrogen atoms does indeed reduce the distance between the side-chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in the Asp108 C(alpha)-C(beta)-C(gamma) angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at N(delta)(1) and Asp108 in conformation A gave the most exothermic reaction (DeltaH = -22 kcal/mol). With His272 doubly protonated at N(delta)(1) and N(epsilon)(2), the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in conformation B, the Asp108 C(alpha)-C(beta)-C(gamma) angle changed during the reaction and the Asp108 moved to conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.
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Affiliation(s)
- Aaron J Oakley
- Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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