UMMS Affiliation
RNA Therapeutics Institute
Publication Date
2017-11-20
Document Type
Article
Disciplines
Amino Acids, Peptides, and Proteins | Biophysics | Investigative Techniques | Research Methods in Life Sciences | Structural Biology
Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigid-body refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein-protein complexes, and is freely available at www.tanglab.org/resources.
Keywords
Chemical cross-linking, DynaXL, Ensemble refinement, Multi-domain protein, Protein–protein complex, Solvent accessible surface distance
Rights and Permissions
Copyright © The Author(s) 2017. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
DOI of Published Version
10.1007/s41048-017-0044-9
Source
Biophys Rep. 2017;3(4):100-108. doi: 10.1007/s41048-017-0044-9. Epub 2017 Nov 20. Link to article on publisher's site
Journal/Book/Conference Title
Biophysics reports
Related Resources
PubMed ID
29238747
Repository Citation
Gong Z, Liu Z, Dong X, Ding Y, Dong M, Tang C. (2017). Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. Open Access Publications by UMMS Authors. https://doi.org/10.1007/s41048-017-0044-9. Retrieved from https://escholarship.umassmed.edu/oapubs/3318
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biophysics Commons, Investigative Techniques Commons, Research Methods in Life Sciences Commons, Structural Biology Commons