Turnover rates of human muscle proteins in vivo reported in fractional, mole and absolute units

Abstract

Protein fractional turnover rates (FTR) represent measurements of flux through a protein pool, i.e. net abundance (ABD) of the protein. If protein abundance is not measured or is different between experimental conditions the interpretation of FTR data may be confounded. This project investigates the consequences of reporting turnover rates of human muscle proteins in vivo in mole and absolute units (that incorporate protein abundance data) compared to fractional (%/d) data that ignore protein abundance. Three physically active males (21 +/- 1 years) were recruited and underwent a 12-d protocol of daily deuterium oxide (D2O) consumption and biopsies of vastus lateralis on days 8 and 12. Protein abundances were normalised to yeast alcohol dehydrogenase, added during sample preparation, and FTR was calculated from time-dependent changes in peptide mass isotopomer profiles. FTR and abundance data (fmol/ug protein) were combined to calculate mole turnover rates (MTR; fmol/ug protein/ d) and absolute turnover rates (ATR; ng/ug protein/ d). Abundance data were collected for 1,772 proteins and FTR data were calculated from 3,944 peptides representing 935 proteins (average 3 peptides per protein). The median (M), lower- (Q1) and upper-quartile (Q3) values for protein FTR (%/d) were M = 4.3, Q1 = 2.52, Q3 = 7.84. Our analyses suggest MTR data is preferred over FTR, particularly for studies on multiprotein complexes, wherein MTR takes account of potential differences amongst the molecular weight of the component subunits. ATR data may be preferred over MTR and FTR, particularly when comparing samples with different abundance profiles.