A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways.

Diego U Ferreiro; Gonzalo de Prat-Gay

doi:10.1016/s0022-2836(03)00720-4

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A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways.

Diego U Ferreiro·Gonzalo de Prat-Gay

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Abstract

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.

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Base Sequence DNA DNA-Binding Proteins Diffusion Kinetics Oncogene Proteins, Viral Protein Binding Protein Conformation Protein Structure, Tertiary Solvents Spectrum Analysis Substrate Specificity Thermodynamics Journal Article Research Support, Non-U.S. Gov't

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Diego U Ferreiro, Gonzalo de Prat-Gay. 2003-08-01. A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways.. https://doi.org/10.1016/s0022-2836(03)00720-4

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