HDX-MS analysis of the full human proteasome in complex with regulators
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Julien Marcoux
LAB HEAD: Julien Marcoux
PROVIDER: PXD018921 | Pride | 2020-09-11
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20Smature-PA28.fasta | Fasta | |||
| PA28ab_raw_files.zip | Other | |||
| PA28g_raw_files.zip | Other | |||
| PLGS_IA_final_peptide.zip | Other | |||
| csv_files.zip | Other |
Items per page: 5 1 - 5 of 15 |
Similar Datasets
Project description:The conserved Tweety homolog (TTYH) family consists of three paralogs in vertebrates, displaying a ubiquitous expression pattern. Although considered as ion channels for almost two decades, recent structural and functional analyses refuted this role. Intriguingly, while all paralogs shared a dimeric stoichiometry following detergent solubilization, their structures revealed divergence in their relative subunit orientation. Here, we determined the stoichiometry of intact mouse TTYH (mTTYH) complexes in cells. Using cross-linking and single-molecule fluorescence microscopy, we demonstrate that mTTYH1 and mTTYH3 form tetramers at the plasma membrane, stabilized by interactions between their extracellular domains. Using blue-native PAGE, fluorescence-detection size-exclusion chromatography and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we reveal that detergent solubilization results in tetramers destabilization, leading to their dissolution into dimers. Moreover, HDX-MS demonstrates that the extracellular domains are stabilized in the context of the tetrameric mTTYH complex. Together, our results expose the innate tetrameric organization of TTYH complexes at the cell membrane. Future structural analyses of these assemblies in native membranes are required to illuminate their long-sought cellular function.
2022-08-31 | PXD031833 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053843 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053847 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053875 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053871 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD066006 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053877 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053845 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053851 | Pride
Project description:Characterization of protein-ligand interactions is essential for the pre-clinical development of drug candidates and Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a valuable tool in this process. HDX-MS has predominantly been employed with high affinity compounds with only a few examples of its application for weaker binders such as fragments. Nevertheless, HDX-MS usage could be instrumental in Fragment-Based Drug Discovery (FBDD) programs, especially when dealing with challenging targets that cannot be studied by other higher resolution structural techniques, such as X-Ray crystallography, Cryogenic Electron Microscopy (Cryo-EM) or Nuclear Magnetic Resonance (NMR). In this work we used the drug-target protein Cyclophilin D (CypD) as model to explore how far fragments binding characterization by HDX-MS (fHDX-MS) can be pushed. We performed a systematic study on the best conditions for fHDX-MS execution and found that fragments with binding affinities in the double-digit mM range are still amenable to HDX-MS. We observed how, despite the intrinsic low resolution of HDX-MS, partially overlapping fragments binding sites can still be distinguished. This study contributes to asserting fHDX-MS as an instrumental method for FBDD and offers a methodological framework to investigate such interactions using HDX-MS.
2025-12-23 | PXD053849 | Pride