Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site.
Binding cooperativity guides the formation of protein-nucleic acid complexes, in particular those that are highly regulated such as replication origins and transcription sites. Using the DNA binding domain of the origin binding and transcriptional regulator protein E2 from human papillomavirus type 16 as model, and through isothermal titration calorimetry analysis, we determined a positive, entropy-driven cooperativity upon binding of the protein to its cognate tandem double E2 site. This cooperativity is associated with a change in DNA structure, where the overall B conformation is maintained. Two homologous E2 domains, those of HPV18 and HPV11, showed that the enthalpic-entropic components of the reaction and DNA deformation can diverge. Because the DNA binding helix is almost identical in the three domains, the differences must lie dispersed throughout this unique dimeric β-barrel fold. This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition.
Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-Conicet, Patricias Argentinas 435, Buenos Aires, Argentina.
Mariano
M
Dellarole
Ignacio E
IE
Sánchez
Gonzalo
G
de Prat Gay
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D052162:Human papillomavirus 16 / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009856:Oncogene Proteins, Viral / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D018741:Replication Origin / Q000235:genetics*; D013816:Thermodynamics; D014158:Transcription, Genetic / Q000235:genetics*
D004268:DNA-Binding Proteins; C054855:E2 protein, Human papillomavirus type 16; D009856:Oncogene Proteins, Viral; D004247:DNA