Economic principles in cell metabolism
|Protein allocation||Optimal states||Enzyme cost||Flux cost||Rate and yield|
|Value structure||Kinetic models||Flux analysis||Optimal adaptation||Enzyme rhythms|
Protein investment in cellular functions
Proteomics techniques generate an avalanche of data and promise to satisfy biologists’ long-held desire to measure absolute protein abundances on a genome-wide scale. However, can this knowl- edge be translated into a clearer picture of how cells invest their protein resources? This article aims to give a broad perspective on the composition of proteomes as gleaned from recent quantitative proteomics studies. We describe proteomaps, an approach for visualizing the composition of proteomes with a focus on protein abundances and functions. In proteomaps, each protein is shown as a polygon-shaped tile, with an area representing protein abun- dance. Functionally related proteins appear in adjacent regions. General trends in proteomes, such as the dominance of metabo- lism and protein production, become easily visible. We make interactive visualizations of published proteome datasets accessible at www.proteomaps.net. We suggest that evaluating the way protein resources are allocated by various organisms and cell types in different conditions will sharpen our understanding of how and why cells regulate the composition of their proteomes.