xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints

Abstract

The identification of crosslinks by mass spectrometry has recently been established as an integral part of the hybrid structural analysis of protein complexes and networks. The crosslinking analysis determines distance restraints between two covalently linked amino acids which are typically summarized in a table format that precludes the immediate and comprehensive interpretation of the topological data. xVis displays crosslinks in clear schematic representations in form of a circular, bar or network diagram. The interactive graphs indicate the linkage sites and identification scores, depict the spatial proximity of structurally and functionally annotated protein regions and the evolutionary conservation of amino acids and facilitate clustering of proteins into subcomplexes according to the crosslink density. Furthermore, xVis offers two options for the qualitative assessment of the crosslink identifications by filtering crosslinks according to identification scores or false discovery rates and by displaying the corresponding fragment ion spectrum of each crosslink for the manual validation of the mass spectrometric data. Our web server provides an easy-to-use tool for the fast topological and functional interpretation of distance information on protein complex architectures and for the evaluation of crosslink fragment ion spectra. xVis is available under a Creative Commons Attribution-ShareAlike 4.0 International license at http://xvis.genzentrum.lmu.de/.

Figure 1.

Topological analysis of the INO80 chromatin remodeler in complex with its nucleosome substrate. (A) Identification of subcomplexes and assignment to different structural modules using EM, chemical crosslinking and biochemical assays. (B) Crosslinked INO80 subunits are visualized and alphabetically sorted in a circular representation using xVis. The protein names are colored according to the modules in (A). (C) Hierarchical clustering of INO80 subunits based on crosslinks displayed in a circular diagram by xVis. (D) Hierarchical clustering of INO80 subunits based on crosslinks shown in a bar diagram by xVis. Bars represent InterPro domains (Figure 3A) (inter-protein crosslinks in black, intra-protein crosslinks in red).

Figure 2.

Topological analysis of the INO80 - nucleosome complex by applying the Markov Cluster (MCL) Algorithm in the network diagram. (A) Subunits non-clustered (all proteins blue colored). (B) Subunits clustered with the MCL parameters expansion=2 and inflation=1 separates the Nhp10 subcomplex (light blue). (C) Subunits clustered with expansion=1 and inflation=3 identifies several INO80 subcomplexes. (D) Proteins clustered like in (C) with crosslinks filtered by the identification score (cut-off 27).

Figure 3.

Customized annotations in xVis. (A) Selective representation of the Rvb1/2 and Ino80/Ies2 modules with the subunit Arp8 and histone H2A in a network diagram showing annotations from InterPro (top bars in the protein representation) and user-defined domains (bottom bars). (B) Evolutionary conservation of amino acid positions in the proteins Ino80 and Arp8 (bottom bars) obtained by the ConSurf webserver. (C) InterPro annotation legend used in (A) and (B). (D) User-defined domains displayed in (A).

Figure 4.

Topology of a network of modular PP2A complexes displayed in a network diagram. Proteins were grouped by the MCL algorithm applying the parameters expansion=2 and inflation=2 (STRIPAK, B’’’/striatin-interacting phosphatase and kinase, STRIPAK, complex; TCP1 ring complex, TRiC).