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Britt HM, Cragnolini T, Khatun S, Hatimy A, James J, Page N, Williams JP, Hughes C, Denny R, Thalassinos K, Vissers JPC. Evaluation of acquisition modes for semi-quantitative analysis by targeted and untargeted mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9308. [PMID: 35353398 PMCID: PMC9287043 DOI: 10.1002/rcm.9308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Analyte quantitation by mass spectrometry underpins a diverse range of scientific endeavors. The fast-growing field of mass spectrometer development has resulted in several targeted and untargeted acquisition modes suitable for these applications. By characterizing the acquisition methods available on an ion mobility (IM)-enabled orthogonal acceleration time-of-flight (oa-ToF) instrument, the optimum modes for analyte semi-quantitation can be deduced. METHODS Serial dilutions of commercial metabolite, peptide, or cross-linked peptide analytes were prepared in matrices of human urine or Escherichia coli digest. Each analyte dilution was introduced into an IM separation-enabled oa-ToF mass spectrometer by reversed-phase liquid chromatography and electrospray ionization. Data were acquired for each sample in duplicate using nine different acquisition modes, including four IM-enabled acquisitions modes, available on the mass spectrometer. RESULTS Five (metabolite) or seven (peptide/cross-linked peptide) point calibration curves were prepared for analytes across each of the acquisition modes. A nonlinear response was observed at high concentrations for some modes, attributed to saturation effects. Two correction methods, one MS1 isotope-correction and one MS2 ion intensity-correction, were applied to address this observation, resulting in an up to twofold increase in dynamic range. By averaging the semi-quantitative results across analyte classes, two parameters, linear dynamic range (LDR) and lower limit of quantification (LLOQ), were determined to evaluate each mode. CONCLUSION A comparison of the acquisition modes revealed that data-independent acquisition and parallel reaction monitoring methods are most robust for semi-quantitation when considering achievable LDR and LLOQ. IM-enabled modes exhibited sensitivity increases, but a simultaneous reduction in dynamic range required correction methods to recover. These findings will assist users in identifying the optimum acquisition mode for their analyte quantitation needs, supporting a diverse range of applications and providing guidance for future acquisition mode developments.
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Affiliation(s)
- Hannah M. Britt
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUK
| | - Suniya Khatun
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Abubakar Hatimy
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Juliette James
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Nathanael Page
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- LGC GroupTeddingtonUK
| | | | | | | | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUK
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Soloviev Z, Bullock JMA, James JMB, Sauerwein AC, Nettleship JE, Owens RJ, Hansen DF, Topf M, Thalassinos K. Structural mass spectrometry decodes domain interaction and dynamics of the full-length Human Histone Deacetylase 2. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140759. [PMID: 35051665 PMCID: PMC8825994 DOI: 10.1016/j.bbapap.2022.140759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/11/2022] [Indexed: 11/30/2022]
Abstract
Human Histone Deacetylase 2 (HDAC2) belongs to a conserved enzyme superfamily that regulates deacetylation inside cells. HDAC2 is a drug target as it is known to be upregulated in cancers and neurodegenerative disorders. It consists of globular deacetylase and C-terminus intrinsically-disordered domains [1-3]. To date, there is no full-length structure of HDAC2 available due to the high intrinsic flexibility of its C-terminal domain. The intrinsically-disordered domain, however, is known to be important for the enzymatic function of HDAC2 [1, 4]. Here we combine several structural Mass Spectrometry (MS) methodologies such as denaturing, native, ion mobility and chemical crosslinking, alongside biochemical assays and molecular modelling to study the structure and dynamics of the full-length HDAC2 for the first time. We show that MS can easily dissect heterogeneity inherent within the protein sample and at the same time probe the structural arrangement of the different conformers present. Activity assays combined with data from MS and molecular modelling suggest how the structural dynamics of the C-terminal domain, and its interactions with the catalytic domain, regulate the activity of this enzyme.
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Affiliation(s)
- Zoja Soloviev
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK.
| | - Joshua M A Bullock
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Juliette M B James
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK
| | - Andrea C Sauerwein
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Joanne E Nettleship
- PPUK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK; Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Raymond J Owens
- PPUK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK; Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK; Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6AR, UK.
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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Goold R, Hamilton J, Menneteau T, Flower M, Bunting EL, Aldous SG, Porro A, Vicente JR, Allen ND, Wilkinson H, Bates GP, Sartori AA, Thalassinos K, Balmus G, Tabrizi SJ. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease. Cell Rep 2021; 36:109649. [PMID: 34469738 PMCID: PMC8424649 DOI: 10.1016/j.celrep.2021.109649] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/30/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
CAG repeat expansion in the HTT gene drives Huntington's disease (HD) pathogenesis and is modulated by DNA damage repair pathways. In this context, the interaction between FAN1, a DNA-structure-specific nuclease, and MLH1, member of the DNA mismatch repair pathway (MMR), is not defined. Here, we identify a highly conserved SPYF motif at the N terminus of FAN1 that binds to MLH1. Our data support a model where FAN1 has two distinct functions to stabilize CAG repeats. On one hand, it binds MLH1 to restrict its recruitment by MSH3, thus inhibiting the assembly of a functional MMR complex that would otherwise promote CAG repeat expansion. On the other hand, it promotes accurate repair via its nuclease activity. These data highlight a potential avenue for HD therapeutics in attenuating somatic expansion.
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Affiliation(s)
- Robert Goold
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK
| | - Joseph Hamilton
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK
| | - Thomas Menneteau
- UK Dementia Research Institute, University College London, London WC1N 3BG, UK; Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Michael Flower
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK
| | - Emma L Bunting
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Sarah G Aldous
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - José R Vicente
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | | | | | - Gillian P Bates
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Gabriel Balmus
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK.
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK.
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Sinnott M, Malhotra S, Madhusudhan MS, Thalassinos K, Topf M. Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures. Structure 2020; 28:1061-1070.e3. [DOI: 10.1016/j.str.2020.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022]
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Rodríguez-Alonso R, Létoquart J, Nguyen VS, Louis G, Calabrese AN, Iorga BI, Radford SE, Cho SH, Remaut H, Collet JF. Structural insight into the formation of lipoprotein-β-barrel complexes. Nat Chem Biol 2020; 16:1019-1025. [PMID: 32572278 PMCID: PMC7610366 DOI: 10.1038/s41589-020-0575-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
The β-barrel assembly machinery (BAM) inserts outer membrane β-barrel proteins (OMPs) in the outer membrane of Gram-negative bacteria. In Enterobacteriacea, BAM also mediates export of the stress sensor lipoprotein RcsF to the cell surface by assembling RcsF-OMP complexes. Here, we report the crystal structure of the key BAM component BamA in complex with RcsF. BamA adopts an inward-open conformation, with the lateral gate to the membrane closed. RcsF is lodged deep inside the lumen of the BamA barrel, binding regions proposed to undergo an outward and lateral opening during OMP insertion. On the basis of our structural and biochemical data, we propose a push-and-pull model for RcsF export upon conformational cycling of BamA and provide a mechanistic explanation for how RcsF uses its interaction with BamA to detect envelope stress. Our data also suggest that the flux of incoming OMP substrates is involved in the control of BAM activity.
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Affiliation(s)
- Raquel Rodríguez-Alonso
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Juliette Létoquart
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Van Son Nguyen
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium
| | - Gwennaelle Louis
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Bogdan I Iorga
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium.,Université Paris-Saclay, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Seung-Hyun Cho
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium. .,de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium. .,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium.
| | - Jean-François Collet
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium. .,de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
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Vissers JPC, McCullagh M. An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry. Methods Mol Biol 2020; 2084:161-178. [PMID: 31729660 DOI: 10.1007/978-1-0716-0030-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.
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