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Bardelang P, Murray EJ, Blower I, Zandomeneghi S, Goode A, Hussain R, Kumari D, Siligardi G, Inoue K, Luckett J, Doutch J, Emsley J, Chan WC, Hill P, Williams P, Bonev BB. Conformational analysis and interaction of the Staphylococcus aureus transmembrane peptidase AgrB with its AgrD propeptide substrate. Front Chem 2023; 11:1113885. [PMID: 37214482 PMCID: PMC10196373 DOI: 10.3389/fchem.2023.1113885] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Virulence gene expression in the human pathogen, S. aureus is regulated by the agr (accessory gene regulator) quorum sensing (QS) system which is conserved in diverse Gram-positive bacteria. The agr QS signal molecule is an autoinducing peptide (AIP) generated via the initial processing of the AgrD pro-peptide by the transmembrane peptidase AgrB. Since structural information for AgrB and AgrBD interactions are lacking, we used homology modelling and molecular dynamics (MD) annealing to characterise the conformations of AgrB and AgrD in model membranes and in solution. These revealed a six helical transmembrane domain (6TMD) topology for AgrB. In solution, AgrD behaves as a disordered peptide, which binds N-terminally to membranes in the absence and in the presence of AgrB. In silico, membrane complexes of AgrD and dimeric AgrB show non-equivalent AgrB monomers responsible for initial binding and for processing, respectively. By exploiting split luciferase assays in Staphylococcus aureus, we provide experimental evidence that AgrB interacts directly with itself and with AgrD. We confirmed the in vitro formation of an AgrBD complex and AIP production after Western blotting using either membranes from Escherichia coli expressing AgrB or with purified AgrB and T7-tagged AgrD. AgrB and AgrD formed stable complexes in detergent micelles revealed using synchrotron radiation CD (SRCD) and Landau analysis consistent with the enhanced thermal stability of AgrB in the presence of AgrD. Conformational alteration of AgrB following provision of AgrD was observed by small angle X-ray scattering from proteodetergent micelles. An atomistic description of AgrB and AgrD has been obtained together with confirmation of the AgrB 6TMD membrane topology and existence of AgrBD molecular complexes in vitro and in vivo.
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Affiliation(s)
- Philip Bardelang
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ewan J. Murray
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Isobel Blower
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Sara Zandomeneghi
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alice Goode
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Divya Kumari
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Katsuaki Inoue
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Jeni Luckett
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - James Doutch
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Jonas Emsley
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Weng C. Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Philip Hill
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Boyan B. Bonev
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Micsonai A, Wien F, Bulyáki É, Kun J, Moussong É, Lee YH, Goto Y, Réfrégiers M, Kardos J. BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Res 2019; 46:W315-W322. [PMID: 29893907 PMCID: PMC6031044 DOI: 10.1093/nar/gky497] [Citation(s) in RCA: 657] [Impact Index Per Article: 131.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.
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Affiliation(s)
- András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Frank Wien
- Synchrotron SOLEIL, Gif-sur-Yvette 91192, France
| | - Éva Bulyáki
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Judit Kun
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Éva Moussong
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
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Isolated domains of recombinant human apo-metallothionein 1A are folded at neutral pH: a denaturant and heat-induced unfolding study using ESI-MS. Biosci Rep 2018; 38:BSR20180592. [PMID: 29858425 PMCID: PMC6050192 DOI: 10.1042/bsr20180592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 12/25/2022] Open
Abstract
Metallothioneins (MTs) are characterized by their high metal loading capacity, small molecular weight, and abundant cysteine residues. It has long been thought that metal-free, or apo-MT peptides were unstructured and only adopted as a distinct conformation upon forming the metal clusters, described as metal-induced folding. More recent studies have suggested that the presence of a globular, yet loosely defined structure actually exists that can be disrupted or unfolded. Residue modification and ion-mobility ESI (IM-ESI)-MS have been used to examine this unusual unfolding process. The structure of apo-MT plays a critical role as the starting point in the flexible metalation pathways that can accommodate numerous soft metals. ESI-MS measurements of the product species formed following the cysteine alkylation of the isolated domain fragments of recombinant human apo-MT 1A with n-ethylmaleimide (NEM) were used in the present study to monitor the denaturant- and heat-induced unfolding at physiological pH. The results indicate that these apo-MT fragments adopt distinct structures at neutral pH that react co-operatively with NEM when folded and non-cooperatively when heated or exposed to high concentrations of the denaturant guanidinium chloride (GdmCl). From these studies, we can conclude that at neutral pH, the domain fragments are folded into globular structures where some of the free cysteine residues are buried within the core and are stabilized by hydrogen bonds. Metalation therefore, must take place from the folded conformation.
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