Recommendations for terminology and databases for biochemical thermodynamics

Biochemical reactions often involve multiple species in equilibrium. Traditional chemical equations balance all atoms and charges. Biochemical equations instead sum species at fixed concentrations, like hydrogen at a given pH. This distinction affects how equilibrium constants are defined. Standard transformed Gibbs energies of reaction Δ(r)G'° are calculated using these summed species. These energies depend on pH and temperature. Existing databases provide Δ(r)G'° and Δ(f)G(i)'° values for many reactions. These databases also include functions for calculating thermodynamic properties. However, gaps remain in how experimental results are reported and interpreted.

This work aims to clarify how biochemical equations should be written for thermodynamic analysis. It addresses the need to distinguish between atomic balance and species sums. The goal is to improve consistency in reporting experimental data. The study also seeks to guide the use of transformed Gibbs energies in biochemical contexts. It emphasizes the importance of pH and temperature in these calculations. The purpose includes promoting accurate interpretation of enzyme kinetics. It also aims to standardize how K' is derived from kinetic measurements. The study highlights the need for clear communication of thermodynamic parameters.

The authors review established practices in biochemical thermodynamics. They examine how equilibrium constants are defined in different contexts. They analyze the role of fixed concentrations in biochemical equations. The study uses existing databases of Δ(r)G'° and Δ(f)G(i)'° values. It evaluates how these databases incorporate pH and temperature dependencies. The authors also consider how kinetic data can inform thermodynamic parameters. They assess the use of apparent equilibrium constants in enzyme kinetics. The methods include comparing traditional chemical equations with biochemical conventions.

Biochemical equations should sum species in equilibrium rather than balance all atoms. Standard transformed Gibbs energies Δ(r)G'° are derived from these summed species. These energies depend on pH and temperature, which are included in available databases. Apparent equilibrium constants K' can be calculated from kinetic data. The study confirms that K' is valid when both forward and reverse velocities are measured. Databases provide Δ(r)G'° and Δ(f)G(i)'° as functions of pH and temperature. The results show that these databases support accurate thermodynamic analysis. The study also recommends specific formats for reporting experimental results.

The authors propose that biochemical equations should sum species in equilibrium rather than balance all atoms. They emphasize the role of fixed concentrations like pH in defining K'. The study concludes that Δ(r)G'° is best calculated from Δ(f)G(i)'° and measured K'. Available databases provide essential data for these calculations. The authors suggest that K' can be derived from kinetic measurements when both directions are known. They recommend standardized formats for reporting experimental data. The conclusions highlight the need for consistent terminology and data presentation. They also stress the importance of pH and temperature in biochemical thermodynamics.