The structural context of posttranslational modifications at a proteome-wide scale

Area of Science:

• Proteomics
• Structural Biology
• Computational Biology

Background:

• Advancements in protein structure prediction enable integration with large-scale experimental data.
• Mass spectrometry (MS)-based proteomics has identified numerous posttranslational modifications (PTMs) with unclear functional roles.

Purpose of the Study:

• To determine the structural context of PTMs.
• To leverage structural information for identifying regulatory sites.
• To differentiate regulatory PTMs from those associated with protein misfolding.

Main Methods:

• Integration of computational protein folding models with MS-based proteomics data.
• Analysis of PTM occurrence in folded versus intrinsically disordered protein regions.
• Three-dimensional proximity analysis to identify spatial coregulation and PTM crosstalk.

Main Results:

• Global patterns of PTMs in folded and disordered regions were uncovered.
• Regulatory PTMs can be distinguished from those marking improperly folded proteins.
• Thousands of human proteins feature disordered regions enriched in regulatory phosphosites, including kinase activation loops.
• This regulatory mechanism extends beyond phosphorylation to ubiquitination and acetylation.
• Spatial coregulation and potential PTM crosstalk were identified through 3D proximity analysis.

Conclusions:

• Structural context is crucial for understanding PTM function.
• Disordered regions act as key regulatory hubs for PTMs, particularly phosphorylation.
• The findings reveal widespread regulatory mechanisms involving PTMs across diverse protein families.
• Tools for PTM visualization and data processing are provided for community use.