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    Modeling protein complexes using restraints from Crosslinking Mass Spectrometry

    Bullock, Joshua M.A. and Sen, N. and Thalassinos, Konstantinos and Topf, Maya (2018) Modeling protein complexes using restraints from Crosslinking Mass Spectrometry. Structure 26 (7), 1015-1024.e2. ISSN 0969-2126.

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    Abstract

    Modeling macromolecular assemblies with restraints from crosslinking mass spectrometry (XL-MS) tends to focus solely on distance violation. Recently, we identified three different modeling features inherent in crosslink data: (1) expected distance between crosslinked residues; (2) violation of the crosslinker's maximum bound; and (3) solvent accessibility of crosslinked residues. Here, we implement these features in a scoring function. cMNXL, and demonstrate that it outperforms the commonlyused crosslink distance violation. We compare the different methods of calculating the distance between crosslinked residues, which shows no significant change in performance when using Euclidean distance compared with the solvent-accessible surface distance. Finally, we create a combined score that incorporates information from 3D electron microscopy maps as well as crosslinking. This achieves, on average, better results than either information type alone and demonstrates the potential of integrative modeling with XL-MS and low-resolution cryoelectron microscopy.

    Metadata

    Item Type: Article
    Keyword(s) / Subject(s): crosslinking, scoring function, crosslinking mass spectrometry, integrative modeling, 3D electron microscopy, cryo-EM, protein structure modelling
    School: School of Science > Biological Sciences
    SWORD Depositor: Mr Joe Tenant
    Depositing User: Mr Joe Tenant
    Date Deposited: 29 May 2018 15:55
    Last Modified: 13 Feb 2021 06:30
    URI: https://eprints.bbk.ac.uk/id/eprint/22562

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