1
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Adams R, Joyce C, Kuravskiy M, Harrison K, Ahdash Z, Balmforth M, Chia K, Marceddu C, Coates M, Snowden J, Goursaud E, Ménochet K, van den Elsen J, Payne RJ, Lawson ADG, Scott-Tucker A, Macpherson A. Serum albumin binding knob domains engineered within a V H framework III bispecific antibody format and as chimeric peptides. Front Immunol 2023; 14:1170357. [PMID: 37251411 PMCID: PMC10213618 DOI: 10.3389/fimmu.2023.1170357] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Background Serum albumin binding is an established mechanism to extend the serum half-life of antibody fragments and peptides. The cysteine rich knob domains, isolated from bovine antibody ultralong CDRH3, are the smallest single chain antibody fragments described to date and versatile tools for protein engineering. Methods Here, we used phage display of bovine immune material to derive knob domains against human and rodent serum albumins. These were used to engineer bispecific Fab fragments, by using the framework III loop as a site for knob domain insertion. Results By this route, neutralisation of the canonical antigen (TNFα) was retained but extended pharmacokinetics in-vivo were achieved through albumin binding. Structural characterisation revealed correct folding of the knob domain and identified broadly common but non-cross-reactive epitopes. Additionally, we show that these albumin binding knob domains can be chemically synthesised to achieve dual IL-17A neutralisation and albumin binding in a single chemical entity. Conclusions This study enables antibody and chemical engineering from bovine immune material, via an accessible discovery platform.
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Affiliation(s)
- Ralph Adams
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | - Callum Joyce
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | - Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Zainab Ahdash
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | - Kelda Chia
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | - Matthew Coates
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | - James Snowden
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | | | | | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
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2
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Macpherson A, Laabei M, Ahdash Z, Graewert MA, Birtley JR, Schulze MSE, Crennell S, Robinson SA, Holmes B, Oleinikovas V, Nilsson PH, Snowden J, Ellis V, Mollnes TE, Deane CM, Svergun D, Lawson AD, van den Elsen JM. The allosteric modulation of complement C5 by knob domain peptides. eLife 2021; 10:63586. [PMID: 33570492 PMCID: PMC7972453 DOI: 10.7554/elife.63586] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 09/29/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3–6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 Å from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential. Antibodies are proteins produced by the immune system that can selectively bind to other molecules and modify their behaviour. Cows are highly equipped at fighting-off disease-causing microbes due to the unique shape of some of their antibodies. Unlike other jawed vertebrates, cows’ antibodies contain an ultra-long loop region that contains a ‘knob domain’ which sticks out from the rest of the antibody. Recent research has shown that when detached, the knob domain behaves like an antibody fragment, and can independently bind to a range of different proteins. Antibody fragments are commonly developed in the laboratory to target proteins associated with certain diseases, such as arthritis and cancer. But it was unclear whether the knob domains from cows’ antibodies could also have therapeutic potential. To investigate this, Macpherson et al. studied how knob domains attach to complement C5, a protein in the inflammatory pathway which is a drug target for various diseases, including severe COVID-19. The experiments identified various knob domains that bind to complement C5 and inhibits its activity by altering its structure or movement. Further tests studying the structure of these interactions, led to the discovery of a common mechanism by which inhibitors can modify the behaviour of this inflammatory protein. Complement C5 is involved in numerous molecular pathways in the immune system, which means many of the drugs developed to inhibit its activity can also leave patients vulnerable to infection. However, one of the knob domains identified by Macpherson et al. was found to reduce the activity of complement C5 in some pathways, whilst leaving other pathways intact. This could potentially reduce the risk of bacterial infections which sometimes arise following treatment with these types of inhibitors. These findings highlight a new approach for developing drug inhibitors for complement C5. Furthermore, the ability of knob domains to bind to multiple sites of complement C5 suggests that this fragment could be used to target proteins associated with other diseases.
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Affiliation(s)
- Alex Macpherson
- UCB, Slough, United Kingdom.,Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | | | | | | | - Susan Crennell
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sarah A Robinson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | | | - Per H Nilsson
- UCB, Slough, United Kingdom.,Department of Chemistry and Biomedicine, Linnaeus University, Kalmar, Sweden.,Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | | | - Tom Eirik Mollnes
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway.,Research Laboratory, Bodø Hospital, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway.,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | - Jean Mh van den Elsen
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
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3
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Lau AMC, Ahdash Z, Martens C, Politis A. Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry. Bioinformatics 2020; 35:3171-3173. [PMID: 30649183 PMCID: PMC6736138 DOI: 10.1093/bioinformatics/btz022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [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: 09/14/2018] [Revised: 12/03/2018] [Accepted: 01/09/2019] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Hydrogen deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful technique for interrogating the conformational dynamics of proteins and their complexes. Currently, analysis of HDX-MS data remains a laborious procedure, mainly due to the lack of streamlined software to process the large datasets. We present Deuteros which is a standalone software designed to be coupled with Waters DynamX HDX data analysis software, allowing the rapid analysis and visualization of data from differential HDX-MS. AVAILABILITY AND IMPLEMENTATION Deuteros is open-source and can be downloaded from https://github.com/andymlau/Deuteros, under the Apache 2.0 license. Written in MATLAB and supported on both Windows and MacOS. Requires the MATLAB runtime library. According to the Wellcome Trust and UK research councils' Common Principles on Data Policy on data, software and materials management and sharing, all data supporting this study will be openly available from the software repository.
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Affiliation(s)
- Andy M C Lau
- Department of Chemistry, King's College London, London, UK
| | - Zainab Ahdash
- Department of Chemistry, King's College London, London, UK
| | - Chloe Martens
- Department of Chemistry, King's College London, London, UK
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4
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Faull SV, Lau AMC, Martens C, Ahdash Z, Hansen K, Yebenes H, Schmidt C, Beuron F, Cronin NB, Morris EP, Politis A. Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome. Nat Commun 2019; 10:3814. [PMID: 31444342 PMCID: PMC6707232 DOI: 10.1038/s41467-019-11772-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members.
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Affiliation(s)
- Sarah V Faull
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Andy M C Lau
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Chloe Martens
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Zainab Ahdash
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Hugo Yebenes
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle/Saale, Germany
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Nora B Cronin
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK.
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5
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Ahdash Z, Pyle E, Allen WJ, Corey RA, Collinson I, Politis A. HDX-MS reveals nucleotide-dependent, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon. eLife 2019; 8:47402. [PMID: 31290743 PMCID: PMC6639072 DOI: 10.7554/elife.47402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/09/2019] [Indexed: 01/28/2023] Open
Abstract
The bacterial Sec translocon is a multi-protein complex responsible for translocating diverse proteins across the plasma membrane. For post-translational protein translocation, the Sec-channel – SecYEG – associates with the motor protein SecA to mediate the ATP-dependent transport of pre-proteins across the membrane. Previously, a diffusional-based Brownian ratchet mechanism for protein secretion has been proposed; the structural dynamics required to facilitate this mechanism remain unknown. Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal striking nucleotide-dependent conformational changes in the Sec protein-channel from Escherichia coli. In addition to the ATP-dependent opening of SecY, reported previously, we observe a counteracting, and ATP-dependent, constriction of SecA around the pre-protein. ATP binding causes SecY to open and SecA to close; while, ADP produced by hydrolysis, has the opposite effect. This alternating behaviour could help impose the directionality of the Brownian ratchet for protein transport through the Sec machinery.
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Affiliation(s)
- Zainab Ahdash
- Department of Chemistry, King's College London, London, United Kingdom
| | - Euan Pyle
- Department of Chemistry, King's College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom
| | | | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, London, United Kingdom
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6
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Cruz-Gallardo I, Martino L, Kelly G, Atkinson R, Trotta R, De Tito S, Coleman P, Ahdash Z, Gu Y, Bui TTT, Conte MR. LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Res 2019; 47:4272-4291. [PMID: 30820564 PMCID: PMC6486636 DOI: 10.1093/nar/gkz144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/22/2022] Open
Abstract
LARP4A belongs to the ancient RNA-binding protein superfamily of La-related proteins (LARPs). In humans, it acts mainly by stabilizing mRNAs, enhancing translation and controlling polyA lengths of heterologous mRNAs. These activities are known to implicate its association with mRNA, protein partners and translating ribosomes, albeit molecular details are missing. Here, we characterize the direct interaction between LARP4A, oligoA RNA and the MLLE domain of the PolyA-binding protein (PABP). Our study shows that LARP4A-oligoA association entails novel RNA recognition features involving the N-terminal region of the protein that exists in a semi-disordered state and lacks any recognizable RNA-binding motif. Against expectations, we show that the La module, the conserved RNA-binding unit across LARPs, is not the principal determinant for oligoA interaction, only contributing to binding to a limited degree. Furthermore, the variant PABP-interacting motif 2 (PAM2w) featured in the N-terminal region of LARP4A was found to be important for both RNA and PABP recognition, revealing a new role for this protein-protein binding motif. Our analysis demonstrates the mutual exclusive nature of the PAM2w-mediated interactions, thereby unveiling a tantalizing interplay between LARP4A, polyA and PABP.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Luigi Martino
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| | - Roberta Trotta
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Stefano De Tito
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Pierre Coleman
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Zainab Ahdash
- Department of Chemistry, King’s College London, London SE1 1DB, UK
| | - Yifei Gu
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Tam T T Bui
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
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7
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Corey RA, Ahdash Z, Shah A, Pyle E, Allen WJ, Fessl T, Lovett JE, Politis A, Collinson I. ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery. eLife 2019; 8:41803. [PMID: 30601115 PMCID: PMC6335059 DOI: 10.7554/elife.41803] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/01/2019] [Indexed: 11/13/2022] Open
Abstract
Transport of proteins across membranes is a fundamental process, achieved in every cell by the 'Sec' translocon. In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. Previously, we proposed a Brownian ratchet model for transport, whereby the free energy of ATP-turnover favours the directional diffusion of the polypeptide (Allen et al., 2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. A combination of molecular simulation with hydrogendeuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP-induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria.
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Affiliation(s)
- Robin A Corey
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Zainab Ahdash
- Department of Chemistry, King's College London, London, United Kingdom
| | - Anokhi Shah
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, Scotland, United Kingdom
| | - Euan Pyle
- Department of Chemistry, King's College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Tomas Fessl
- University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, Scotland, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, London, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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8
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Hellwig N, Peetz O, Ahdash Z, Tascón I, Booth PJ, Mikusevic V, Diskowski M, Politis A, Hellmich Y, Hänelt I, Reading E, Morgner N. Native mass spectrometry goes more native: investigation of membrane protein complexes directly from SMALPs. Chem Commun (Camb) 2018; 54:13702-13705. [PMID: 30452022 PMCID: PMC6289172 DOI: 10.1039/c8cc06284f] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/06/2018] [Indexed: 01/07/2023]
Abstract
Other than more widely used methods, the use of styrene maleic acid allows the direct extraction of membrane proteins from the lipid bilayer into SMALPs keeping it in its native lipid surrounding. Here we present the combined use of SMALPs and LILBID-MS, allowing determination of oligomeric states of membrane proteins of different functionality directly from the native nanodiscs.
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Affiliation(s)
- Nils Hellwig
- Institute of Physical and Theoretical Chemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 7
, 60438 Frankfurt
, Germany
.
| | - Oliver Peetz
- Institute of Physical and Theoretical Chemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 7
, 60438 Frankfurt
, Germany
.
| | - Zainab Ahdash
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Igor Tascón
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Paula J. Booth
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Vedrana Mikusevic
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Marina Diskowski
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Argyris Politis
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Yvonne Hellmich
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Inga Hänelt
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Eamonn Reading
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 7
, 60438 Frankfurt
, Germany
.
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9
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Abstract
Proteins are an important class of biological macromolecules that play many key roles in cellular functions including gene expression, catalyzing metabolic reactions, DNA repair and replication. Therefore, a detailed understanding of these processes provides critical information on how cells function. Integrative structural MS methods offer structural and dynamical information on protein complex assembly, complex connectivity, subunit stoichiometry, protein oligomerization and ligand binding. Recent advances in integrative structural MS have allowed for the characterization of challenging biological systems including large DNA binding proteins and membrane proteins. This protocol describes how to integrate diverse MS data such as native MS and ion mobility-mass spectrometry (IM-MS) with molecular dynamics simulations to gain insights into a helicase-nuclease DNA repair protein complex. The resulting approach provides a framework for detailed studies of ligand binding to other protein complexes involved in important biological processes.
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Affiliation(s)
| | - Andy M Lau
- Department of Chemistry, King's College London
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10
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Ahdash Z, Lau AM, Thomas Byrne R, Lammens K, Booth PJ, Reading E, Hopfner KP, Politis A. Mechanistic Insight into the Assembly of the HerA-NurA Helicase-Nuclease DNA End Resection Complex using Native Mass Spectrometry. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2433] [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: 11/29/2022] Open
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11
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Ahdash Z, Lau AM, Byrne RT, Lammens K, Stüetzer A, Urlaub H, Booth PJ, Reading E, Hopfner KP, Politis A. Mechanistic insight into the assembly of the HerA-NurA helicase-nuclease DNA end resection complex. Nucleic Acids Res 2017; 45:12025-12038. [PMID: 29149348 PMCID: PMC5715905 DOI: 10.1093/nar/gkx890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
The HerA–NurA helicase–nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA–NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA–NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate. The binding of either NurA or ATP stabilizes the hexameric HerA, indicating that HerA–NurA is activated by substrates and complex assembly. To examine the role of ATP in DNA translocation and processing, we investigated how nucleotides interact with the HerA–NurA. We show that while the hexameric HerA binds six nucleotides in an ‘all-or-none’ fashion, HerA–NurA harbors a highly coordinated pairwise binding mechanism and enables the translocation and processing of double-stranded DNA. Using molecular dynamics simulations, we reveal novel inter-residue interactions between the external ATP and the internal DNA binding sites. Overall, here we propose a stepwise assembly mechanism detailing the synergistic activation of HerA–NurA by ATP, which allows efficient processing of double-stranded DNA.
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Affiliation(s)
- Zainab Ahdash
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Andy M Lau
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Robert Thomas Byrne
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Katja Lammens
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Alexandra Stüetzer
- Bioanalytical Mass Spectrometry Group, MPI for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, MPI for Biophysical Chemistry, D-37077 Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Paula J Booth
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Eamonn Reading
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
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12
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Reading E, Hall Z, Martens C, Haghighi T, Findlay H, Ahdash Z, Politis A, Booth PJ. Interrogating Membrane Protein Conformational Dynamics within Native Lipid Compositions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Eamonn Reading
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Zoe Hall
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road Cambridge CB2 1GA UK
| | - Chloe Martens
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Tabasom Haghighi
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Heather Findlay
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Zainab Ahdash
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Argyris Politis
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
| | - Paula J. Booth
- Department of Chemistry; King's College London; Britannia House, 7 Trinity Street London SE1 1DB UK
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Reading E, Hall Z, Martens C, Haghighi T, Findlay H, Ahdash Z, Politis A, Booth PJ. Interrogating Membrane Protein Conformational Dynamics within Native Lipid Compositions. Angew Chem Int Ed Engl 2017; 56:15654-15657. [PMID: 29049865 DOI: 10.1002/anie.201709657] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/18/2017] [Indexed: 12/14/2022]
Abstract
The interplay between membrane proteins and the lipids of the membrane is important for cellular function, however, tools enabling the interrogation of protein dynamics within native lipid environments are scarce and often invasive. We show that the styrene-maleic acid lipid particle (SMALP) technology can be coupled with hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate membrane protein conformational dynamics within native lipid bilayers. We demonstrate changes in accessibility and dynamics of the rhomboid protease GlpG, captured within three different native lipid compositions, and identify protein regions sensitive to changes in the native lipid environment. Our results illuminate the value of this approach for distinguishing the putative role(s) of the native lipid composition in modulating membrane protein conformational dynamics.
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Affiliation(s)
- Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Zoe Hall
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Chloe Martens
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Tabasom Haghighi
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Heather Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Zainab Ahdash
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
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Ahdash Z, Byrne R, Hopfner KP, Politis A. Dissecting the Mechanism of the HerA NurA DNA Break Resection Complex using Native Mass Spectrometry. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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