Fig. 1: Quantitative modeling of multi-species metabolic labeling experiments identifies limits and possibilities of the approach.
a In a steady-state system with interconverting species, such as proteins with or without a PTM, an introduced metabolic label equilibrates into both unmodified and modified protein species through writing and erasing of the PTM (yellow circle). b Previous pulse-labeling experiments have shown that clearance of modified peptides can differ substantially from the rest of the protein. Shown are archetypal clearance profiles (logarithm of fraction of old protein remaining, φ, over time, t) for the entire protein pool (gray) and the modified species (yellow). c In the simplest, single-species model for protein turnover, the slope of the clearance profile is directly defined by the protein degradation rate constant, kdeg. Models are named “Model x:y” (e.g., Model 0:1) indicating the number of modified species (x), and the number of species altogether (y). In the small cartoons, the size and opacity of the arrows reflect the magnitude of the rate constant. The size of the circle reflects the steady-state amount of the species. d Two-species model (Model 1:2) including protein modification. The slopes of the clearance profiles are complex functions of the model parameters (all but the synthesis rate ksyn), and change over time (see Supplementary Note 1 for full analytical description). In Model 1:2 clearance of the modified species PP can never be faster than the clearance of the entire protein pool P. Parameter combinations with distinct biological interpretation have practically indistinguishable clearance profiles. e Alternative (reverse, r) two-species model, Model 1:2r, in which a protein is synthesized as a modified species, allows faster clearance of the modified species PP compared to the entire protein pool P. The relative order of clearance profiles is defined by the order of species (or “wiring” of the modification network) during a protein’s lifetime. See also https://apps.embl.de/pptop for an interactive web application of the models.
