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Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M - J. Struct. Biol. (2015)

Bottom Line: Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques.To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures.We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

No MeSH data available.


Related in: MedlinePlus

Assignment of cross-links in homo-oligomeric mode. (A) Schematic illustration of possible residue pair combinations in standard and homo-oligomeric mode. For each cross-link there are four possible residue pair combinations (left). Based on residue distances, Xlink Analyzer automatically determines which pairs more likely correspond to the observed cross-links (right). (B) Cross-linked Rvb1/2 displayed in standard mode. Rvb1/2 hetero-hexamer is composed of three copies each, Rvb1 and Rvb2 subunits that give rise to a large number of residue pair combinations as displayed in standard mode. (C) Same as (B) but displayed in homo-oligomeric mode. The model of Rvb1/2 hexamer was reproduced based on Tosi et al. (Tosi et al., 2013). The remaining cross-links violating the 30 Å distance threshold (Merkley et al., 2014) might indicate an inwards domain movement (see also Fig. 3).
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f0020: Assignment of cross-links in homo-oligomeric mode. (A) Schematic illustration of possible residue pair combinations in standard and homo-oligomeric mode. For each cross-link there are four possible residue pair combinations (left). Based on residue distances, Xlink Analyzer automatically determines which pairs more likely correspond to the observed cross-links (right). (B) Cross-linked Rvb1/2 displayed in standard mode. Rvb1/2 hetero-hexamer is composed of three copies each, Rvb1 and Rvb2 subunits that give rise to a large number of residue pair combinations as displayed in standard mode. (C) Same as (B) but displayed in homo-oligomeric mode. The model of Rvb1/2 hexamer was reproduced based on Tosi et al. (Tosi et al., 2013). The remaining cross-links violating the 30 Å distance threshold (Merkley et al., 2014) might indicate an inwards domain movement (see also Fig. 3).

Mentions: A ‘Homo-oligomeric’ mode is available in Xlink Analyzer that is dedicated to cross-link analysis of homo-oligomeric complexes or complexes containing multiple copies of at least one subunit. In these cases, multiple residue pair combinations can be assigned to cross-links that derive from the subunits that are present in multiple copies (Fig. 4A), making the identification of cross-links in structure and statistical analysis of cross-link violations inherently difficult. In ‘Homo-oligomeric’ mode, given a structure or a theoretical model of the oligomer, Xlink Analyzer automatically identifies the non-violated fraction of every possible set of equivalent residue pairs across the oligomeric interfaces and within the subunits. If no pair within the set satisfies the cross-link, the pair with the shortest distance is selected for display. Violation statistics can be subsequently recalculated. As we demonstrate in Fig. 4, the automatic ‘Homo-oligomeric’ mode significantly increases the visualization and interpretation of the cross-links data on homo-oligomers.


Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M - J. Struct. Biol. (2015)

Assignment of cross-links in homo-oligomeric mode. (A) Schematic illustration of possible residue pair combinations in standard and homo-oligomeric mode. For each cross-link there are four possible residue pair combinations (left). Based on residue distances, Xlink Analyzer automatically determines which pairs more likely correspond to the observed cross-links (right). (B) Cross-linked Rvb1/2 displayed in standard mode. Rvb1/2 hetero-hexamer is composed of three copies each, Rvb1 and Rvb2 subunits that give rise to a large number of residue pair combinations as displayed in standard mode. (C) Same as (B) but displayed in homo-oligomeric mode. The model of Rvb1/2 hexamer was reproduced based on Tosi et al. (Tosi et al., 2013). The remaining cross-links violating the 30 Å distance threshold (Merkley et al., 2014) might indicate an inwards domain movement (see also Fig. 3).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4359615&req=5

f0020: Assignment of cross-links in homo-oligomeric mode. (A) Schematic illustration of possible residue pair combinations in standard and homo-oligomeric mode. For each cross-link there are four possible residue pair combinations (left). Based on residue distances, Xlink Analyzer automatically determines which pairs more likely correspond to the observed cross-links (right). (B) Cross-linked Rvb1/2 displayed in standard mode. Rvb1/2 hetero-hexamer is composed of three copies each, Rvb1 and Rvb2 subunits that give rise to a large number of residue pair combinations as displayed in standard mode. (C) Same as (B) but displayed in homo-oligomeric mode. The model of Rvb1/2 hexamer was reproduced based on Tosi et al. (Tosi et al., 2013). The remaining cross-links violating the 30 Å distance threshold (Merkley et al., 2014) might indicate an inwards domain movement (see also Fig. 3).
Mentions: A ‘Homo-oligomeric’ mode is available in Xlink Analyzer that is dedicated to cross-link analysis of homo-oligomeric complexes or complexes containing multiple copies of at least one subunit. In these cases, multiple residue pair combinations can be assigned to cross-links that derive from the subunits that are present in multiple copies (Fig. 4A), making the identification of cross-links in structure and statistical analysis of cross-link violations inherently difficult. In ‘Homo-oligomeric’ mode, given a structure or a theoretical model of the oligomer, Xlink Analyzer automatically identifies the non-violated fraction of every possible set of equivalent residue pairs across the oligomeric interfaces and within the subunits. If no pair within the set satisfies the cross-link, the pair with the shortest distance is selected for display. Violation statistics can be subsequently recalculated. As we demonstrate in Fig. 4, the automatic ‘Homo-oligomeric’ mode significantly increases the visualization and interpretation of the cross-links data on homo-oligomers.

Bottom Line: Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques.To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures.We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

No MeSH data available.


Related in: MedlinePlus