Size-Dependent Relationships between Protein Stability and Thermal Unfolding Temperature Have Important Implications for Analysis of Protein Energetics and High-Throughput Assays of Protein–Ligand Interactions

Changes in protein stability are commonly reported as changes in the melting temperature, Δ T M, or as changes in unfolding free energy at a particular temperature, ΔΔ G ° . Using data for 866 mutants from 16 proteins, we examine the relationship between ΔΔ G ° and Δ T M . A linear relationship is observed for each protein. The slopes of the plots of Δ T M vs ΔΔ G ° for different proteins scale as N –1, where N is the number of residues in the protein. Thus, a given change in Δ G ° causes a much larger change in T M for a small protein relative to the effect observed for a large protein. The analysis suggests that reasonable estimates of ΔΔ G ° for a mutant can be obtained by interpolating measured values of T M . The relationship between ΔΔ G ° and Δ T M has implications for the design and interpretation of high-throughput assays of protein–ligand binding. So-called thermal shift assays rely upon the increase in stability which results from ligand binding to the folded state. Quantitative relationships are derived which show that the observed thermal shift, Δ T M, scales as N –1 . Hence, thermal shift assays are considerably less sensitive for ligand binding to larger proteins.