Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis

Area of Science:

• Proteomics
• Molecular Biology
• Biochemistry

Background:

• Protein degradation is crucial for cellular function and regulation.
• Targeted proteolysis is a promising therapeutic strategy.
• Existing technologies for studying protein degradation dynamics are limited.

Purpose of the Study:

• To develop a novel proteome-wide technology for analyzing protein degradation and synthesis dynamics.
• To apply this technology to uncover cellular responses to specific stimuli and molecular perturbations.

Main Methods:

• Developed multiplexed proteome dynamics profiling (mPDP), a mass spectrometry-based technique.
• Combined dynamic stable isotope labeling by amino acids in cell culture (SILAC) with isobaric mass tagging.
• Applied mPDP to analyze protein turnover in response to drug treatments and molecular modulators.

Main Results:

• mPDP successfully differentiated responses to a bromodomain inhibitor and a proteolysis targeting chimera.
• Elucidated distinct mechanisms of action for estrogen receptor modulators.
• Classified HSP90 clients based on their dependence on the chaperone, revealing distinct properties of constitutive clients.

Conclusions:

• mPDP is a powerful tool for dissecting protein degradation and synthesis dynamics.
• The study identified novel insights into protein homeostasis and chaperone interactions.
• mPDP has the potential to advance the understanding of disease mechanisms and drug development.