PXD070481 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | An integrative structural biology approach to identify the binding mode of a nanobody towards the pea Ascorbate Peroxidase |
| Description | The optimization of diagnostic devices such as biosensors often requires understanding the molecular details of the interaction between capture and target biomolecules. This can be experimentally obtained by cryo-electron microscopy, the preferred method for the analysis of large protein complexes, while NMR and x-ray crystallography are effective for determining the structure of complexes formed by relatively small molecules. Nevertheless, all these approaches are demanding in terms of time and resources and, therefore, we explored the possibility to reduce the experimental load by compensating with in silico modelling. Here we demonstrate that an accurate prediction of the binding mode between a nanobody and its target pea ascorbate peroxidase, an oxidative stress biomarker in plants, can be obtained by combining cross-linking mass spectrometry, hydrogen-deuterium exchange coupled to mass spectrometry and in silico modelling. Such model allowed to precisely design negative mutants that confirmed its accuracy. In conclusion, this study shows that an unconstrained prediction based on deep learning models is still not sufficiently reliable for new targets and difficult-to-model biomolecule classes such as nanobodies, while an experimental-guided approach can provide valuable structural information for lead optimization campaigns of such reagents. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-03-10 |
| AnnouncementXML | Submission_2026-03-09_18:26:06.409.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Pavla Vankova |
| SpeciesList | scientific name: Populus nigra x Populus x canadensis; NCBI TaxID: NEWT:1001135; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF SCP |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-11-07 17:46:30 | ID requested | |
| ⏵ 1 | 2026-03-09 18:26:06 | announced | |
Publication List
Keyword List
| submitter keyword: nanobodies |
| ascorbate peroxidase |
| hydrogen-deuterium exchange coupled to mass spectrometry |
| integrative structural biology |
| protein cross-linking |
Contact List
| Claudia D’Ercole |
|---|
| contact affiliation | Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000, Nova Gorica, Slovenia |
| contact email | claudia.dercole@ung.si |
| lab head | |
| Pavla Vankova |
|---|
| contact affiliation | Institute of Biotechnology of the Czech Academy of Sciences, BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic |
| contact email | pavla.vankova@ibt.cas.cz |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD070481 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD070481
- Label: PRIDE project
- Name: An integrative structural biology approach to identify the binding mode of a nanobody towards the pea Ascorbate Peroxidase
