Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational...

Area of Science:

• Biochemistry
• Structural Biology
• Proteomics

Background:

• Proteins exist in multiple conformations in vivo, influencing their functions.
• Conformational states are affected by post-translational modifications (PTMs) and binding partners.
• Quantitative cross-linking mass spectrometry (XMS) measures protein states but requires careful interpretation.

Purpose of the Study:

• To develop a method for clustering intraprotein cross-links based on their quantitative abundance across diverse samples.
• To provide a large-scale view of cross-links associated with specific protein conformational states.
• To enable the assessment of cross-links' origins from protein structures.

Main Methods:

• Utilized quantitative cross-linking data from the public XLinkDB database.
• Clustered intraprotein cross-links based on their quantitation across multiple compared samples.
• Developed a method to align clustered cross-links with protein structures.

Main Results:

• Successfully clustered intraprotein cross-links according to their predominant originating conformational states.
• Provided the first wide-scale glimpse of cross-links grouped by protein conformational ensembles.
• Demonstrated alignment of clustered cross-links with protein structures to assess their likelihood.

Conclusions:

• Quantitative cross-linking data can be leveraged to systematically group cross-links by protein conformational states.
• This clustering approach offers insights into protein dynamics and structural heterogeneity.
• The developed method facilitates the interpretation of cross-linking data in structural biology and proteomics.