Simple Accurate Verification of Enthalpy-Entropy Compensation and Isoequilibrium Relationship

Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments

Hydration plays a key role in the structure-specific stabilization of biomolecules such as nucleic acids. The hydration patterns of biased DNA sequences in the genome, such as GC-repetitive and AT-repetitive regions, are unique to their duplex grooves. As these regions are crucial for maintaining genomic homeostasis and preventing diseases such as cancer and neurodegenerative disorders, the effects of hydration on their stability and functions must be quantitatively analyzed in chemical environments that resemble intracellular conditions. In this study, we systematically investigated duplex formation of biased sequences in cell-like molecularly crowded environments to quantify the effects of groove hydration on their thermodynamics. The interaction of crowders with water molecules in the grooves was found to provide excess stabilization to biased DNAs than to unbiased DNAs, as estimated from the nearest-neighbor prediction model. These hydration effects are sequence-specific and depend on the cation type and cosolute size. Introduction of the "hydration parameters" into the nearest-neighbor model quantifying the effect of groove hydration remarkably enhanced the prediction accuracy for biased DNA stability in crowded environments. Hydration parameters can aid in elucidating the roles of biased sequences in cells such as cation-dependent quadruplex formation in cancer-related genes and regulation of replication initiation by intracellular crowding fluctuations. Additionally, these parameters can predict the free energy changes during the binding of protein to DNA grooves. Overall, our findings can help in realizing and predicting the functions of biased DNAs in cells controlled by variable chemical environments.

Extreme enthalpy‒entropy compensation in the dimerization of small solutes in aqueous solution

This communication summarizes findings from the earliest encounters with extreme enthalpy‒entropy compensation, a phenomenon first detected in the 1950s by a reappraisal of isopiestic and calorimetric measurements on aqueous urea solutions in terms of solute self-association. Because concurrent studies of carboxylic acid association were confined to measurement of the equilibrium constant by conductance, IR spectrophotometry or potentiometric titration measurements, temperature-independence of the dimerization constant was mistakenly taken to signify a value of zero for Δ H o instead of (Δ H o  ‒ TΔ S o ). In those studies of small-solute self-association the extreme enthalpy‒entropy compensation was reflecting the action of water as a reactant whose hydroxyl groups were competing for the solute carbonyl involved in self-association. Such action gives rise to a positive temperature dependence of Δ H o that could well be operating in concert with that responsible for the commonly observed negative dependence for protein‒ligand interactions exhibiting extreme enthalpy‒entropy compensation, where the solvent contribution to the energetics reflects changes in the extent of ordered water structure in hydrophobic environments.

Comment on "Aggregation Interface and Rigid Spots Sustain the Stable Framework of a Thermophilic N-Demethylase"

The thermal properties of proteins are very important in industrial, agricultural, and food chemistry. A recent article (Li, B., et al. J. Agric. Food Chem. 2023, 71, 5614-5629) examines the thermal denaturation of enzymes TrSOX and BSOX by measuring the enthalpy change and melting temperature in the denaturation. In this work, we report the numerical values of entropy in the denaturation of proteins and show that both proteins TrSOX and BSOX exhibit enthalpy-entropy compensation in thermal denaturation, which results in a limited variation of melting temperature in both proteins. Our analysis may serve to improve our understanding of thermal properties in proteins in food chemistry.