Cold Denaturation of a Repressor-Operator Complex: The Role of Entropy in Protein-DNA Recognition

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 91; no. 17; pp. 8244 - 8247
• Main Authors: Foguel, Debora, Silva, Jerson L.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences of the United States of America 16-08-1994; National Acad Sciences; National Academy of Sciences
• Subjects: Bacteriophage P22 - metabolism; Biochemistry; Calorimetry; Cloning, Molecular; Cold Temperature; Deoxyribonucleic acid; Dimers; DNA; DNA - chemistry; DNA - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; Entropy; Escherichia coli; Fluorescence; Models, Structural; Monomers; Nucleic Acid Conformation; Nucleotide sequences; Protein Binding; Protein Conformation; Protein Denaturation; Protein Folding; Proteins; Recombinant Proteins - chemistry; Recombinant Proteins - isolation & purification; Recombinant Proteins - metabolism; Repressor Proteins - chemistry; Repressor Proteins - isolation & purification; Repressor Proteins - metabolism; Solvents; Spectrophotometry, Ultraviolet; Thermodynamics; Viral Proteins - chemistry; Viral Proteins - isolation & purification; Viral Proteins - metabolism; Viral Regulatory and Accessory Proteins; Water pressure
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.91.17.8244

The mechanisms by which regulatory proteins recognize specific DNA sequences are not fully understood. Here we examine the basis for the stability of a protein-DNA complex, using hydrostatic pressure and low temperature. Pressure converts the DNA-binding Arc repressor protein from a native state to a denatured, molten-globule state. Our data show that the folding and dimerization of Arc repressor in the temperature range 0-20⚬C are favored by a large positive entropy value, so that the reaction proceeds in spite of an unfavorable positive enthalpy. On binding operator DNA, Arc repressor becomes extremely stable against denaturation. However, the Arc repressor-operator DNA complex is cold-denatured at subzero temperatures under pressure, demonstrating that the favorable entropy increases greatly when Arc repressor binds tightly to its operator sequence but not a nonspecific sequence. We show how an increase in entropy may operate to provide the protein with a mechanism to distinguish between a specific and a nonspecific DNA sequence. It is postulated that the formation of the Arc-operator DNA complex is followed by an increase in apolar interactions and release of solvent which would explain its entropy-driven character, whereas this solvent would not be displaced in nonspecific complexes.