UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures

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. Green open access

[thumbnail of MonoLinks_paper_revised_withfigs_withsupp.pdf]
Preview
Text
MonoLinks_paper_revised_withfigs_withsupp.pdf - Accepted Version

Download (3MB) | Preview

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
Downloads since deposit
41Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item