PXD036833
PXD036833 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | AlphaLink: bringing protein structure prediction in situ with in-cell photo-crosslinking mass spectrometry, crosslinking mass spectrometry, XL-MS, |
| Description | The protein structure prediction problem has been revolutionised by AlphaFold2, an algorithm that uses neural networks and evolutionary information to predict accurate models from the primary sequence. However, some proteins remain difficult to predict. Moreover, proteins are dynamic entities that exist in complex environments in vivo. Here, we use the noncanonical amino acid Photo-Leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. We then introduce AlphaLink, a modified version of the AlphaFold2 algorithm that synergistically incorporates experimental distance restraint information into its network architecture. AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets in both synthetic and real-world scenarios by employing sparse experimental contacts as anchor points. The program can predict individual conformations of proteins based on the distance restraints provided. The noise-tolerant framework presented here for integrating data in protein structure prediction opens a path to accurate characterisation of protein structures from in-cell data. |
| HostingRepository | jPOST |
| AnnounceDate | 2023-02-22 |
| AnnouncementXML | Submission_2023-02-21_07:00:05.402.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD036833 |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Andrea Graziadei |
| SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
| ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; deamidated L-asparagine; unknown modification; unknown modification; unknown modification |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2022-09-18 13:47:01 | ID requested | |
| ⏵ 1 | 2023-02-21 07:00:05 | announced |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: photo-amino acid, crosslinking, photo-leucine,alphafold |
Contact List
| Juri Rappsilber | |
|---|---|
| lab head | |
| Andrea Graziadei | |
| contact affiliation | Technische Universitaet Berlin |
| dataset submitter | |
Full Dataset Link List
| jPOST dataset URI |
| 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.jpostdb.org/JPST001851/ |
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