Cellular concentrations of enzymes and their substrates

Area of Science:

• Biochemistry
• Metabolic Engineering
• Systems Biology

Background:

• Understanding enzyme-substrate dynamics is crucial for accurate metabolic modeling.
• In vitro enzyme kinetics are often extrapolated to in vivo conditions, necessitating validation.
• Literature data provides a basis for comparing enzyme and metabolite concentrations across various organisms.

Purpose of the Study:

• To compare metabolite concentrations with their cognate enzyme concentrations across diverse organisms.
• To assess the validity of using in vitro enzyme kinetic data for in vivo metabolic simulations.
• To identify metabolic pathways where enzyme-metabolite ratios deviate significantly.

Main Methods:

• Compiled enzyme activity and molecular weight data from literature for multiple organisms.
• Calculated enzyme concentrations based on literature data.
• Determined molar ratios of metabolite concentration to enzyme site concentration.
• Analyzed 140 such ratios to identify trends and exceptions.

Main Results:

• In 88% of cases, metabolite concentrations were found to be equal to or greater than their corresponding enzyme concentrations.
• Enzyme concentrations exceeded metabolite concentrations in 17 instances, with 16 of these occurring within glycolysis.
• The general trend supports the substrate excess hypothesis in most metabolic contexts.

Conclusions:

• The study provides strong evidence that substrate concentrations typically exceed enzyme concentrations in vivo.
• These findings generally validate the application of in vitro enzyme kinetics in constructing dynamic models of in vivo metabolism.
• Glycolysis represents a notable exception where enzyme concentrations may be higher than substrate levels, warranting further investigation.