Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Chemical cross-linking provides insights into protein structures in native environments.
• XLinkDB maps cross-links to structures using sequence homology.
• Euclidean distance is a common but less accurate metric for cross-link consistency.

Purpose of the Study:

• To introduce automatic Solvent Accessible Surface Distance (SASD) calculation in XLinkDB version 4.0.
• To establish empirical maximum SASD spans for common cross-linkers.
• To enhance the inference of protein conformations and ligand occupancy from cross-linking data.

Main Methods:

• Implemented automatic SASD calculation using Jwalk in XLinkDB.
• Calculated SASDs for cross-links with and without considering ligands.
• Derived empirical maximum SASD spans for BDP-NHP (51 Å) and DSSO (43 Å) cross-linkers.

Main Results:

• SASD is a more accurate predictor of cross-link consistency than Euclidean distance.
• Publicly available SASD calculations for cross-linked protein structures.
• Documented ligands proximal to cross-links and demonstrated SASD's utility in inferring ligand occupancy.

Conclusions:

• XLinkDB 4.0 provides enhanced structural analysis of cross-linked proteins through automatic SASD calculation.
• SASD analysis aids in understanding protein dynamics and ligand binding.
• The study highlights SASD's role in identifying conformational changes, such as ADP binding in mitochondria.