Protein Turnover / Protein Stability

Motivation

Protein turnover is the apparent outcome of protein synthesis and protein degradation processes within a cell. Protein turnover greatly influences protein abundance and protein half lives and can be a major regulation mechanism of protein function within a cell.

Typically, protein turnover is measured using either pulse-labeling or cycloheximide treatment at defined time points. A popular approach involves pulse-labeling of amino acids utilizing stable isotope labeling by amino acids in cell culture (SILAC) to introduce heavy isotope labeled amino acids which are incorporated in newly synthesized proteins. Changes in protein turnover can be quantified by the ratio between light and heavy labeled peptides provided by mass spectrometry read-out. Another popular method is cycloheximide treatment which blocks protein synthesis in living cells and enables the calculation of protein depletion times. However, this method is useful especially for short lived proteins, since prolonged treatment affects cell viability.

Outcome

The outcome of a protein turnover experiment based on pulsed SILAC is typically a list of quantitative SILAC ratios for each identified protein. Time resolved experiments also provide information about protein synthesis and degradation and enables the calculation of protein half lives.

The outcome of a cycloheximide treatment experiment is a list of identified and quantified proteins and a ratio of intensities depending on the used quantification method. Time resolved experiments facilitate calculation of the depletion rate of proteins.