A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways.
The DNA-binding mechanism of the dimeric C-terminal domain of the papillomavirus E2 protein with its specific DNA target was investigated and shown to proceed through two parallel pathways. A sequential multi-step reaction is initiated by the diffusion-controlled formation of an encounter complex, with no evidence of base sequence discrimination capacity. Following a substantial conformational rearrangement of the protein, a solvent exclusion step leading to the formation of a final protein-DNA complex was identified. This last step involves the largest burial of surface area from the interface and involves the consolidation of the direct readout of the DNA bases. Double-jump stopped-flow experiments allowed us to characterize the sequence of events and demonstrated that a fast-formed consolidated complex can take place through a parallel route. We present the simplest model for the overall mechanism with a description of all the intermediate species in energetic terms.
Ferreiro
Diego U
DU
Instituto Leloir, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET. Patricias Argentinas 435, (1405), Buenos Aires, Argentina.
de Prat-Gay
Gonzalo
G
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004058:Diffusion; D007700:Kinetics; D009856:Oncogene Proteins, Viral / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012997:Solvents / Q000737:chemistry; D013057:Spectrum Analysis; D013379:Substrate Specificity; D013816:Thermodynamics
D004268:DNA-Binding Proteins; C054855:E2 protein, Human papillomavirus type 16; D009856:Oncogene Proteins, Viral; D012997:Solvents; D004247:DNA