PyXlinkViewer

PyXlinkViewer visualizes protein chemical crosslinking-mass spectrometry (XL-MS) data by mapping intra-protein, inter-protein and dead-end crosslinks onto protein structures or models to calculate inter-residue distances and assess consistency with high-resolution structural information.

Key Features:

• PyMOL integration: Integrates with PyMOL v2 to operate within the PyMOL molecular graphics environment.
• Mapping capabilities: Maps intra-protein, inter-protein and dead-end crosslinks onto protein structures or structural models.
• Automated distance calculations: Automatically calculates inter-residue distances for detected crosslinks.
• Structural assessment: Assesses whether detected crosslinks are consistent with existing structural data and identifies distances exceeding the crosslinker spacer-arm.
• Image production: Produces images of mapped crosslinks on structures suitable for publication.

Scientific Applications:

• Structural modeling: Uses XL-MS-derived crosslinks as restraints to support generation or evaluation of structural models when high-resolution structures are absent.
• Elucidation of macromolecular organization: Maps crosslinks to reveal interaction interfaces and organization within protein complexes.
• Exploration of protein dynamics: Identifies crosslinks with distances greater than the crosslinker spacer-arm to reveal lowly populated or "excited" protein states.
• Validation of XL-MS data: Compares detected crosslinks against structural information to validate experimental XL-MS results.

Methodology:

Maps XL-MS crosslink lists onto PDB structures or models and automates calculation of inter-residue distances to compare against crosslinker spacer-arm constraints.