Determination of protein-bound palmitate turnover rates using a three-compartment model that formally incorporates...

The observation that the palmitoylation state of certain proteins can be biologically modulated led to the proposal that it could, much like phosphorylation, be an important dynamic regulator of protein function. However, based on single-phase exponential decay analysis of data from [(3)H]palmitate pulse/chase experiments, the measured protein-bound palmitate turnover rates were often found to be too slow to account for rapid physiological responses. This paper reports that exponential decay does not adequately describe the results of such experiments because it fails to account for the recycling of [(3)H]palmitate from cellular lipids to palmitoyl CoA. Taking this recycling into account, a three-compartment model was used to deduce the time-dependent changes of cellular [(3)H]palmitoyl CoA and to infer the time course for the incorporation of [(3)H]palmitate into proteins. The validity of the inferences made by the model was checked against data obtained by metabolic labeling of endogenous HEK293 cell proteins. In addition, the model could account for reported anomalies, discrepancies, and apparently paradoxical observations obtained by traditional analysis of data from pulse/chase experiments. Including the recycling of cellular palmitate in the formal description of the system offers a new tool for quantitative assessment of protein-bound palmitate turnover rates. Through the re-evaluation of these rates, the model provides a means for the reassessment of the potential physiological implications of dynamic palmitoylation. The model may also be generally applicable to other areas of research where recycling of tracer is a concern.