PURPOSE: To calculate the probability of radiation-induced frank strand breakage (FSB) at each nucleotide in the Escherichia coli lac repressor-lac operator system using a simulation procedure. To compare calculated and experimental results. To asses the contribution of DNA conformational changes and of the masking by the protein to DNA protection by the repressor. MATERIALS AND METHODS: Two structures of the complex were extracted from the PDB databank: crystallography- and NMR-based structures. Calculations were made of the accessibility of the atoms mainly involved in strand breakage (H4' and H5') to O&Hdot; and of the FSB probabilities, along: (1) DNA in the complex; (2) DNA in the complex depleted of the repressor; and (3) a linear DNA having the same sequence. An 80bp fragment bearing the operator was irradiated alone or in presence of the repressor. The relative probabilities of FSB at each nucleotide were determined using sequencing gel electrophoresis. RESULTS: Calculations predict modulation of the accessibility of H4' and H5' atoms and of the probabilities of FSB along the DNA fragments of complexes. This is due to the protein-induced conformational change and to masking by bound protein. The best agreement with the experimental FSB was observed for calculations that use the crystallography-based structure. CONCLUSIONS: For specific DNA-protein complexes, our calculations can predict the protein radiolytic footprints on DNA. They show the significant contribution of the protein-induced DNA conformational change to DNA protection.

• MeSH
• bakteriální proteiny chemie   účinky záření   MeSH
• DNA bakterií chemie   genetika   účinky záření   MeSH
• Escherichia coli genetika   účinky záření   MeSH
• hydroxylový radikál chemie   účinky záření   MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• lac operon účinky záření   MeSH
• lac represory MeSH
• makromolekulární látky MeSH
• metoda Monte Carlo MeSH
• molekulární modely MeSH
• operátorové oblasti (genetika) účinky záření   MeSH
• poškození DNA MeSH
• proteiny z Escherichia coli * MeSH
• represorové proteiny chemie   účinky záření   MeSH
• sekvence nukleotidů MeSH
• tolerance záření MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• DNA bakterií MeSH
• hydroxylový radikál MeSH
• lac represory MeSH
• LacI protein, E coli MeSH Prohlížeč
• makromolekulární látky MeSH
• proteiny z Escherichia coli * MeSH
• represorové proteiny MeSH