Sinnott, M;
Malhotra, S;
Madhusudhan, MS;
Thalassinos, K;
Topf, M;
(2020)
Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures.
Structure
, 28
(9)
1061-1070.e3.
10.1016/j.str.2020.05.012.
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Abstract
Monolinks are produced in a chemical crosslinking mass spectrometry experiment and are more abundant than crosslinks. They convey residue exposure information, but so far have not been used in the modeling of protein structures. Here, we present the Monolink Depth Score (MoDS), for assessing structural models based on the depth of monolinked residues, corresponding to their distance to the nearest bulk water. Using simulated and reprocessed experimental data from the Proteomic Identification Database, we compare the performance of MoDS to MNXL, our previously developed score for assessing models based on crosslinking data. Our results show that MoDS can be used to effectively score models based on monolinks, and that a crosslink/monolink combined score (XLMO) leads to overall higher performance. The work strongly supports the use of monolink data in the context of integrative structure determination. We also present XLM-Tools, a program to assist in this effort, available at: https://github.com/Topf-Lab/XLM-Tools.
| Type: | Article |
|---|---|
| Title: | Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.str.2020.05.012 |
| Publisher version: | https://doi.org/10.1016/j.str.2020.05.012 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| Keywords: | XLMS, crosslinks, integrative modelling, mass spectrometry, monolinks, protein structure modeling, residue depth, structure prediction |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10103678 |
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