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Article ; Online: Integrating Hydrogen Deuterium Exchange-Mass Spectrometry with Molecular Simulations Enables Quantification of the Conformational Populations of the Sugar Transporter XylE.

Jia, Ruyu / Bradshaw, Richard T / Calvaresi, Valeria / Politis, Argyris

Journal of the American Chemical Society

2023 Volume 145, Issue 14, Page(s) 7768–7779

Abstract: A yet unresolved challenge in structural biology is to quantify the conformational states of proteins underpinning function. This challenge is particularly acute for membrane proteins owing to the difficulties in stabilizing them for in vitro studies. To ...

Abstract	A yet unresolved challenge in structural biology is to quantify the conformational states of proteins underpinning function. This challenge is particularly acute for membrane proteins owing to the difficulties in stabilizing them for in vitro studies. To address this challenge, we present an integrative strategy that combines hydrogen deuterium exchange-mass spectrometry (HDX-MS) with ensemble modeling. We benchmark our strategy on wild-type and mutant conformers of XylE, a prototypical member of the ubiquitous Major Facilitator Superfamily (MFS) of transporters. Next, we apply our strategy to quantify conformational ensembles of XylE embedded in different lipid environments. Further application of our integrative strategy to substrate-bound and inhibitor-bound ensembles allowed us to unravel protein-ligand interactions contributing to the alternating access mechanism of secondary transport in atomistic detail. Overall, our study highlights the potential of integrative HDX-MS modeling to capture, accurately quantify, and subsequently visualize co-populated states of membrane proteins in association with mutations and diverse substrates and inhibitors.
MeSH term(s)	Hydrogen Deuterium Exchange-Mass Spectrometry ; Deuterium Exchange Measurement/methods ; Membrane Proteins/chemistry ; Protein Conformation ; Sugars
Chemical Substances	Membrane Proteins ; Sugars
Language	English
Publishing date	2023-03-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c06148
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Article ; Online: Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Size-Exclusion Chromatography for Analysis of Complex Protein Samples.

Calvaresi, Valeria / Redsted, Andreas / Norais, Nathalie / Rand, Kasper D

Analytical chemistry

2021 Volume 93, Issue 33, Page(s) 11406–11414

Abstract: The growing use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ... ...

Abstract	The growing use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ligands, and/or highly ionizable reducing agents. Here, we describe how a short size-exclusion chromatography (SEC) column can be integrated with a conventional temperature-controlled HDX-MS setup to achieve fast and online removal of unwanted species from the HDX sample prior to chromatographic separation and MS analysis. Dual-mode valves permit labeled proteins eluting after SEC to be directed to the proteolytic and chromatographic columns, while unwanted sample components are led to waste. The SEC-coupled HDX-MS method allows analyses to be completed with lower or similar back-exchange compared to conventional experiments. We demonstrate the suitability of the method for the analysis of challenging protein samples, achieving efficient online removal of lipid components from protein-lipid systems, depletion of an antibody from an antigen during epitope mapping, and elimination of MS interfering compounds such as tris(2-carboxyethyl)phosphine (TCEP) during HDX-MS analysis of a disulfide-bonded protein. The implementation of the short SEC column to the conventional HDX-MS setup is straightforward and could be of significant general utility during the HDX-MS analysis of complex protein states.
MeSH term(s)	Chromatography, Gel ; Deuterium ; Deuterium Exchange Measurement ; Hydrogen Deuterium Exchange-Mass Spectrometry ; Mass Spectrometry
Chemical Substances	Deuterium (AR09D82C7G)
Language	English
Publishing date	2021-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c01171
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Article ; Online: Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies.

Hammerschmid, Dietmar / Calvaresi, Valeria / Bailey, Chloe / Russell Lewis, Benjamin / Politis, Argyris / Morris, Michael / Denbigh, Laetitia / Anderson, Malcolm / Reading, Eamonn

Analytical chemistry

2023 Volume 95, Issue 5, Page(s) 3002–3011

Abstract: Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid ... ...

Abstract	Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins due to their presence of impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Herein, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium-labeled protein-lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein-lipid nanodisc─both empty and loaded with the ∼115 kDa transmembrane protein AcrB─proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO
MeSH term(s)	Phospholipids ; Deuterium ; Membrane Lipids ; Mass Spectrometry/methods ; Deuterium Exchange Measurement/methods ; Membrane Proteins ; Peptide Hydrolases
Chemical Substances	Phospholipids ; Deuterium (AR09D82C7G) ; Membrane Lipids ; Membrane Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2023-01-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04876
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Article: Hydrogen–Deuterium Exchange Mass Spectrometry with Integrated Size-Exclusion Chromatography for Analysis of Complex Protein Samples

Calvaresi, Valeria / Redsted, Andreas / Norais, Nathalie / Rand, Kasper D.

Analytical chemistry. 2021 Aug. 13, v. 93, no. 33

2021

Abstract: The growing use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ... ...

Abstract	The growing use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ligands, and/or highly ionizable reducing agents. Here, we describe how a short size-exclusion chromatography (SEC) column can be integrated with a conventional temperature-controlled HDX-MS setup to achieve fast and online removal of unwanted species from the HDX sample prior to chromatographic separation and MS analysis. Dual-mode valves permit labeled proteins eluting after SEC to be directed to the proteolytic and chromatographic columns, while unwanted sample components are led to waste. The SEC-coupled HDX-MS method allows analyses to be completed with lower or similar back-exchange compared to conventional experiments. We demonstrate the suitability of the method for the analysis of challenging protein samples, achieving efficient online removal of lipid components from protein–lipid systems, depletion of an antibody from an antigen during epitope mapping, and elimination of MS interfering compounds such as tris(2-carboxyethyl)phosphine (TCEP) during HDX-MS analysis of a disulfide-bonded protein. The implementation of the short SEC column to the conventional HDX-MS setup is straightforward and could be of significant general utility during the HDX-MS analysis of complex protein states.
Keywords	analytical chemistry ; antibodies ; epitopes ; gel chromatography ; ligands ; lipids ; mass spectrometry ; phosphine ; proteolysis
Language	English
Dates of publication	2021-0813
Size	p. 11406-11414.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c01171
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein–Lipid Assemblies

Hammerschmid, Dietmar / Calvaresi, Valeria / Bailey, Chloe / Russell Lewis, Benjamin / Politis, Argyris / Morris, Michael / Denbigh, Laetitia / Anderson, Malcolm / Reading, Eamonn

Analytical Chemistry. 2023 Jan. 27, v. 95, no. 5 p.3002-3011

2023

Abstract	Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins due to their presence of impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Herein, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium-labeled protein–lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein–lipid nanodisc—both empty and loaded with the ∼115 kDa transmembrane protein AcrB—proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO₂-coated and TiO₂ beads and describe how solution conditions can be optimized to maximize not only the performance of our online but also the existing offline, delipidation workflows for HDX-MS. We envision that this HDX-MS method will significantly ease membrane protein analysis, allowing to better interrogate their dynamics in artificial lipid bilayers or even native cell membranes.
Keywords	analytical chemistry ; automation ; deuterium ; digestion ; lipid bilayers ; liquid chromatography ; mass spectrometry ; peptides ; phospholipids ; protein depletion ; proteinases ; proteolysis ; transmembrane proteins
Language	English
Dates of publication	2023-0127
Size	p. 3002-3011.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04876
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Epitope and Paratope Mapping by HDX-MS Combined with SPR Elucidates the Difference in Bactericidal Activity of Two Anti-NadA Monoclonal Antibodies.

Grauslund, Laura R / Calvaresi, Valeria / Pansegrau, Werner / Norais, Nathalie / Rand, Kasper D

Journal of the American Society for Mass Spectrometry

2021 Volume 32, Issue 7, Page(s) 1575–1582

Abstract: Characterization of antigen-antibody interactions is crucial for understanding antibody-mediated protection against pathogens, biopharmaceutical development, as well as evaluation of the immune response post vaccination. Bexsero is a multicomponent ... ...

Abstract	Characterization of antigen-antibody interactions is crucial for understanding antibody-mediated protection against pathogens, biopharmaceutical development, as well as evaluation of the immune response post vaccination. Bexsero is a multicomponent vaccine against
MeSH term(s)	Adhesins, Bacterial/chemistry ; Adhesins, Bacterial/metabolism ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/metabolism ; Binding Sites, Antibody ; Epitope Mapping/methods ; Hydrogen Deuterium Exchange-Mass Spectrometry/methods ; Protein Binding ; Surface Plasmon Resonance/methods
Chemical Substances	Adhesins, Bacterial ; Anti-Bacterial Agents ; Antibodies, Monoclonal ; NadA protein, Neisseria meningitidis
Language	English
Publishing date	2021-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.0c00431
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Article ; Online: Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein.

Calvaresi, Valeria / Wrobel, Antoni G / Toporowska, Joanna / Hammerschmid, Dietmar / Doores, Katie J / Bradshaw, Richard T / Parsons, Ricardo B / Benton, Donald J / Roustan, Chloë / Reading, Eamonn / Malim, Michael H / Gamblin, Steve J / Politis, Argyris

Nature communications

2023 Volume 14, Issue 1, Page(s) 1421

Abstract: SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic ... ...

Abstract	SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
MeSH term(s)	Humans ; Spike Glycoprotein, Coronavirus/genetics ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; SARS-CoV-2/genetics ; Mutation
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2023-03-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36745-0
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Article ; Online: Unravelling the interaction of Bat Influenza viruses with their proteinaceous receptor MHC-II

Robert, Jonathan* / Kaukab Osman, Maria / Halw, Nico Joel / Franchini, Selene / Calvaresi, Valeria / Reading, Eamonn / Martin, Stephen / Gamblin, Steve / Skehel, John / Beer, Martin / Schwemmle, Martin / Wrobel, Antoni / Reuther, Peter

[Vortrag]

2024

Keywords	Text ; abstract_or_summary ; ddc:570
Language	English
Publishing date	2024-03-25
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Conformational dynamics of free and membrane-bound human Hsp70 in model cytosolic and endo-lysosomal environments.

Calvaresi, Valeria / Truelsen, Line T / Larsen, Sidsel B / Petersen, Nikolaj H T / Kirkegaard, Thomas / Rand, Kasper D

Communications biology

2021 Volume 4, Issue 1, Page(s) 1369

Abstract: The binding of the major stress-inducible human 70-kDa heat shock protein (Hsp70) to the anionic phospholipid bis-(monoacylglycero)-phosphate (BMP) in the lysosomal membrane is crucial for its impact on cellular pathology in lysosomal storage disorders. ... ...

Abstract	The binding of the major stress-inducible human 70-kDa heat shock protein (Hsp70) to the anionic phospholipid bis-(monoacylglycero)-phosphate (BMP) in the lysosomal membrane is crucial for its impact on cellular pathology in lysosomal storage disorders. However, the conformational features of this protein-lipid complex remain unclear. Here, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the dynamics of the full-length Hsp70 in the cytosol and its conformational changes upon translocation into lysosomes. Using wild-type and W90F mutant proteins, we also map and discriminate the interaction of Hsp70 with BMP and other lipid components of the lysosomal membrane. We identify the N-terminal of the nucleotide binding domain (residues 87-118) as the primary orchestrator of BMP interaction. We show that the conformation of this domain is significantly reorganized in the W90F mutant, explaining its inability to stabilize lysosomal membranes. Overall, our results reveal important new molecular details of the protective effect of Hsp70 in lysosomal storage diseases, which, in turn, could guide future drug development.
MeSH term(s)	Cytosol/chemistry ; HSP70 Heat-Shock Proteins/chemistry ; Humans ; Lysophospholipids/metabolism ; Lysosomes/chemistry ; Molecular Conformation ; Monoglycerides/metabolism
Chemical Substances	HSP70 Heat-Shock Proteins ; Lysophospholipids ; Monoglycerides ; bis(monoacylglyceryl)phosphate
Language	English
Publishing date	2021-12-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-021-02892-7
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Article ; Online: A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination.

Seow, Jeffrey / Khan, Hataf / Rosa, Annachiara / Calvaresi, Valeria / Graham, Carl / Pickering, Suzanne / Pye, Valerie E / Cronin, Nora B / Huettner, Isabella / Malim, Michael H / Politis, Argyris / Cherepanov, Peter / Doores, Katie J

Cell reports

2022 Volume 40, Issue 8, Page(s) 111276

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 ; Cryoelectron Microscopy ; Epitopes ; Humans ; Neutralization Tests ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Syndactyly ; Vaccination
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-08-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111276
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