Metabolic buffer analysis reveals the simultaneous, independent control of ATP and adenylate energy ratios

Determining the underlying principles behind biological regulation is important for understanding the principles of life, treating complex diseases and creating de novo synthetic biology. Buffering—the use of reservoirs of molecules to maintain molecular concentrations—is a widespread and important mechanism for biological regulation. However, a lack of theory has limited our understanding of its roles and quantified effects. Here, we study buffering in energy metabolism using control theory and novel buffer analysis. We find that buffering can enable the simultaneous, independent control of multiple coupled outputs. In metabolism, adenylate kinase and AMP deaminase enable simultaneous control of ATP and adenylate energy ratios, while feedback on metabolic pathways is fundamentally limited to controlling one of these outputs. We also quantify the regulatory effects of the phosphagen system—the above buffers and creatine kinase—revealing which mechanisms regulate which outputs. The results are supported by human muscle and mouse adipocyte data. Together, these results illustrate the synergy of feedback and buffering in molecular biology to simultaneously control multiple outputs.