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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

Mapping of the interaction interface between Rvb1/2 hexamers based on inaccessible residues.
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f0015: Mapping of the interaction interface between Rvb1/2 hexamers based on inaccessible residues.

Mentions: To demonstrate this feature we repeated a prediction of the interaction interfaces of the Rvb1/2 complex as previously described by Tosi et al. (Tosi et al., 2013) (Fig. 3). In this study, the interaction site between two Rvb1/2 hexamers was predicted based on EM and mono-links without taking the observability of the modified peptides into consideration. Xlink Analyzer automatically identifies modified residues of the Rvb1/2 model and predicts the interaction site straightforwardly and in-line with the aforementioned previous work showing that on the previously predicted interface, the expected to be observed but non-modified residues are enriched comparing to the alternative interface (Fig. 3). However, only the central part of the originally predicted interface contains non-modified residues that are indicators of a buried surface (Fig. 3B, red). Although the outer part contains non-modified residues (yellow), those give rise to peptides that are not likely to be observed by XL-MS and should not be used as indicators. Thus, Xlink Analyzer not only enables locating non-modified residues but also helps in discriminating regions devoid of modifications due to experimental limitations of MS from the regions protected from modification due to interaction interfaces.


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)

Mapping of the interaction interface between Rvb1/2 hexamers based on inaccessible residues.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0015: Mapping of the interaction interface between Rvb1/2 hexamers based on inaccessible residues.
Mentions: To demonstrate this feature we repeated a prediction of the interaction interfaces of the Rvb1/2 complex as previously described by Tosi et al. (Tosi et al., 2013) (Fig. 3). In this study, the interaction site between two Rvb1/2 hexamers was predicted based on EM and mono-links without taking the observability of the modified peptides into consideration. Xlink Analyzer automatically identifies modified residues of the Rvb1/2 model and predicts the interaction site straightforwardly and in-line with the aforementioned previous work showing that on the previously predicted interface, the expected to be observed but non-modified residues are enriched comparing to the alternative interface (Fig. 3). However, only the central part of the originally predicted interface contains non-modified residues that are indicators of a buried surface (Fig. 3B, red). Although the outer part contains non-modified residues (yellow), those give rise to peptides that are not likely to be observed by XL-MS and should not be used as indicators. Thus, Xlink Analyzer not only enables locating non-modified residues but also helps in discriminating regions devoid of modifications due to experimental limitations of MS from the regions protected from modification due to interaction interfaces.

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