Thermodynamic Parameters of Specific and Nonspecific Protein-DNA Binding

• Published in: Supramolecular chemistry 2000-10, Vol.12 (2), p.143-160
• Main Authors: Jen-jacobson, Linda, Engler, Lisa E., Ames, Jennifer T., Kurpiewski, Michael R., Grigorescu, Arabela
• Format: Article
• Language: English
• Subjects: enthalpy-entropy compensation; heat capacity change; nonspecific protein-DNA complexes; specific protein-DNA complexes; thermodynamics
• ISSN: 1061-0278; 1029-0478
• DOI: 10.1080/10610270008027446

Proteins that bind preferentially to specific recognition sites on DNA also bind more weakly to nonspecific DNA. We have studied both specific and non-specific binding of the EcoRI and BamHI restriction endonucleases, and determined enthalpic and entropic contributions to binding free energy (ΔG° bind ) using both the van't Hoff method and isothermal titration calorimetry. Specific binding is characterized by a strongly negative ΔC° p and can be either enthalpy-driven or entropy-driven, depending on temperature. Nonspecific binding has ΔC° p ≈ 0 and is enthalpy-driven. A strongly negative ΔC° p is the ,thermodynamic signature' of site-specific binding, because it reflects the characteristics of a tight complementary recognition interface: the burial of previously hydrated nonpolar surface and restriction of configurational-vibrational freedoms of protein, DNA, and water molecules trapped at the protein-DNA interface. These factors are absent in nonspecific complexes. We probed the contributions to ΔC° p by varying the sequence context surrounding the recognition site. As ΔG° bind improves, ΔC° p' ΔH° and ΔS° all become more negative, and there is a linear correlation between ΔH° and ΔS° (enthalpy-entropy compensation). Because these context variations do not change the protein-base or protein-phosphate contacts, the hydrophobic contribution or the number of trapped water molecules at the interface, we conclude that a better sequence context improves the ,goodness of fit' in the interface and and thus increases the magnitude of the negative configurational-vibrational contribution to ΔC° p .