Challenging the assumptions in estimating protein fractional synthesis rate using a model of rodent protein turnover

Published estimates of protein fractional synthetic rate vary widely (Johnson et al., 1999a). Contributing to the large standard deviation for FSR are physiological and methodological differences that do not account for changes in specific radioactivities of I, E, T, and P. Current methods for estimating FSR are based on four assumptions which may not be valid. The first assumption, that the free amino acid pool is homogenous and reflects the specific radioactivity of the true precursor pool (aminoacyl tRNA), can cause FSR estimates to increase by up to 8%/d. The second assumption, that recycling has an insignificant effect on FSR estimates, could result in decreases in estimates of FSR from 10 to 20%/d. The third assumption, that the protein pool is homogeneous and will not change over time, results in a 4-10%/d change using the flooding dose method. The fourth assumption, that growth will not affect estimated FSR over a short experimental time, is true if aminoacyl tRNA specific radioactivity is used to estimate FSR. Otherwise, estimates can vary 4-5%/d. Although specific radioactivity of aminoacyl tRNA is difficult to measure, the first and fourth assumptions are valid if aminoacyl tRNA specific radioactivity is used. Using a model of protein turnover, as described in this paper, to interpret specific radioactivity data allows the inclusion of all four assumptions and the potential to better quantify changes in FSR under different physiological conditions.