Xlink Analyzer

Xlink Analyzer integrates cross-linking mass spectrometry (XL-MS) data with three-dimensional protein structures to support structural characterization of large multi-subunit protein complexes.

Key Features:

• Visualization of Cross-Links: Overlays XL-MS-derived cross-links onto three-dimensional protein structures to reveal spatial relationships between proximal residues.
• Analysis of Spatial Restraints: Identifies cross-links that violate predefined spatial (distance) restraints and calculates violation statistics to quantify discrepancies.
• Mapping Chemically Modified Surfaces: Maps chemically modified surfaces onto protein structures to localize functional regions and interaction interfaces.
• Interactive Manipulation: Provides interactive analysis capabilities to explore and manipulate XL-MS data in the structural context.
• Integration with UCSF Chimera: Implements as a UCSF Chimera plugin and supports fitting X-ray crystallography structures to electron microscopy (EM) maps.

Scientific Applications:

• Mapping interaction sites in multi-subunit assemblies: Maps interaction sites and subunit arrangements within protein complexes, demonstrated on RNA polymerase I and the Rvb1/2 complex.

Methodology:

Integrates XL-MS data with existing three-dimensional structural information, identifies and quantifies spatial restraint violations, maps chemically modified surfaces, and operates as a UCSF Chimera plugin enabling fitting of X-ray crystallography structures to electron microscopy (EM) maps.