Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.

Area of Science:

• Biochemistry
• Biophysics
• Computational Biology

Background:

• Phosphorylation sites are abundant in eukaryotic disordered proteomes.
• Kinase-substrate interactions are influenced by conformational fluctuations.
• Substrate selectivity may depend on conformational ensembles.

Purpose of the Study:

• To investigate the role of equilibrium fluctuations in phosphorylation.
• To develop a framework for predicting phosphorylation sites.
• To understand the biophysical basis of kinase-substrate selectivity.

Main Methods:

• Developed a statistical-thermodynamics-based informatics framework.
• Decomposed substrate sequence information into vertical and horizontal components.
• Analyzed the contribution of conformational fluctuations to phosphorylation site prediction.

Main Results:

• Conformational fluctuations are a major, dominant contributor to substrate selectivity.
• The change in local chain compaction upon phosphorylation is a key classifier.
• Successfully predicted Ser/Thr/Tyr phosphorylation sites in the disordered proteome.

Conclusions:

• Equilibrium fluctuations significantly impact kinase-substrate interactions.
• Phosphorylation's effect on protein conformation is crucial for selectivity.
• The framework offers a strategy for sequence-based searches in proteomics.