Will Quantitative Proteomics Redefine Some of the Key Concepts in Skeletal Muscle Physiology?

Abstract

Molecular and cellular biology methodology is traditionally based on the reasoning called "the mechanistic explanation". In practice, this means identifying and selecting correlations between biological processes which result from our manipulation of a biological system. In theory, a successful application of this approach requires precise knowledge about all parameters of a studied system. However, in practice, due to the systems' complexity, this requirement is rarely, if ever, accomplished. Typically, it is limited to a quantitative or semi-quantitative measurements of selected parameters (e.g., concentrations of some metabolites), and a qualitative or semi-quantitative description of expression/post-translational modifications changes within selected proteins. A quantitative proteomics approach gives a possibility of quantitative characterization of the entire proteome of a biological system, in the context of the titer of proteins as well as their post-translational modifications. This enables not only more accurate testing of novel hypotheses but also provides tools that can be used to verify some of the most fundamental dogmas of modern biology. In this short review, we discuss some of the consequences of using quantitative proteomics to verify several key concepts in skeletal muscle physiology.

Keywords: C2C12 cells; glycolysis regulation; glyconeogenesis; kcat; lysine acetylation; skeletal muscle.

Figure 1

Total activities of glycolytic enzymes in red and white skeletal muscles calculated on the basis of kcat (taken from the BRENDA database) and proteomic data on the concentrations of glycolytic enzymes in skeletal muscles [6]. HK—Hexokinase; GPI—phosphoglucoisomerase; PFKM—muscle phosphofructokinase; ALDOA—aldolase A; TPI—triosephosphate isomerase; GAPDH—glyceraldehyde-3-phosphate dehydrogenase; PGK1—phosphoglycerate kinase 1; PGAM2—muscle phosphoglycerate mutase; ENO—enolase; PKM—muscle pyruvate kinase.

Figure 2

Schematic summary of the new, unexpected findings on the skeletal muscle metabolism obtained with the use of quantitative proteomics. AC—acetylation; F1,6P2—fructose-1,6-bisphosphate; F2,6P2—fructose-2,6-bisphosphate; F6P—fructose-6-phosphate; K—lysyl residues of glycolytic enzymes; PEP—phosphoenolpyruvate; PFK—phosphofructokinase; PKM—muscle isoform of pyruvate kinase.