The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI
| Autor: | Sadie C. Piatt, Allen C. Price, Joseph J. Loparo |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Binding energy
Biophysics EcoRI Plasma protein binding Deoxyribonuclease EcoRI Diffusion 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Binding site Quantum 030304 developmental biology Sequence (medicine) 0303 health sciences Binding Sites biology Base Sequence Energy landscape DNA Articles chemistry Chemical physics biology.protein 030217 neurology & neurosurgery Protein Binding |
| Zdroj: | Biophys J |
| ISSN: | 1542-0086 |
| Popis: | A one-dimensional (1D) search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of 1D diffusion can help resolve the competing demands of a fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies. In this work, we report observations of a 1D search by quantum dot-labeled EcoRI. Our data supports the view that proteins search DNA via rotation-coupled sliding over a corrugated energy landscape. We observed that whereas EcoRI primarily slides along DNA at low salt concentrations, at higher concentrations, its diffusion is a combination of sliding and hopping. We also observed long-lived pauses at genomic star sites, which differ by a single nucleotide from the target sequence. To reconcile these observations with prior biochemical and structural data, we propose a model of search in which the protein slides over a sequence-independent energy landscape during fast search but rapidly interconverts with a "hemispecific" binding mode in which a half site is probed. This half site interaction stabilizes the transition to a fully specific mode of binding, which can then lead to target recognition. |
| Databáze: | OpenAIRE |
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