Schiffrin, B, Radford, SE orcid.org/0000-0002-3079-8039, Brockwell, DJ orcid.org/0000-0002-0802-5937 et al. (1 more author) (2020) PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system. Protein Science, 29 (8). pp. 1851-1857. ISSN 0961-8368
Abstract
Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yield inter-residue restraints that can be compared with high-resolution structural data. Distances greater than the crosslinker spacer-arm can reveal lowly populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL-MS, there are few tools to enable rapid and facile mapping of XL-MS data onto high-resolution structures or structural models. PyXlinkViewer is a user-friendly plugin for PyMOL v2 that maps intra-protein, inter-protein, and dead-end crosslinks onto protein structures/models and automates the calculation of inter-residue distances for the detected crosslinks. This enables rapid visualization of XL-MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high-quality images for publication.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2020 The Authors. Protein Science published by Wiley Periodicals LLC. on behalf of The Protein Society. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) > Biomolecular Mass Spectroscopy (Leeds) The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) > Structural Molecular Biology (Leeds) |
Funding Information: | Funder Grant number BBSRC (Biotechnology & Biological Sciences Research Council) BB/N007603/1 BBSRC (Biotechnology & Biological Sciences Research Council) BB/P000037/1 BBSRC (Biotechnology & Biological Sciences Research Council) BB/T000635/1 |
Depositing User: | Symplectic Publications |
Date Deposited: | 16 Jul 2020 13:59 |
Last Modified: | 25 Jun 2023 22:18 |
Status: | Published |
Publisher: | Wiley |
Identification Number: | 10.1002/pro.3902 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:162022 |