Radiosensitivity of DNA in a specific protein-DNA complex: the lac repressor-lac operator complex

Citation
M. Begusove et al., Radiosensitivity of DNA in a specific protein-DNA complex: the lac repressor-lac operator complex, INT J RAD B, 77(6), 2001, pp. 645-654
Citations number
30
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Experimental Biology
Journal title
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
ISSN journal
0955-3002 → ACNP
Volume
77
Issue
6
Year of publication
2001
Pages
645 - 654
Database
ISI
SICI code
0955-3002(200106)77:6<645:RODIAS>2.0.ZU;2-0
Abstract
Purpose: To calculate the probability of radiation-induced frank strand bre akage (FSB) at each nucleotide in the Escherichia coli lac repressor-lac op erator system using a simulation procedure. To compare calculated and exper imental results. To asses the contribution of DNA conformational changes an d of the masking by the protein to DNA protection by the repressor. Materials and methods: Two structures of the complex were extracted from th e PDB databank: crystallography- and NMR-based structures. Calculations wer e made of the accessibility of the atoms mainly involved in strand breakage (H4' and H5') to OH* and of the FSB probabilities, along: (1) DNA in the c omplex; (2) DNA in the complex depleted of the repressor; and (3) a linear DNA having the same sequence. An 80 bp fragment bearing the operator was ir radiated alone or in presence of the repressor. The relative probabilities of FSB at each nucleotide were determined using sequencing gel electrophore sis. Results: Calculations predict modulation of the accessibility of H4' and H5 ' atoms and of the probabilities of FSB along the DNA fragments of complexe s. 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 pred ict the protein radiolytic footprints on DNA. They show the significant con tribution of the protein-induced DNA conformational change to DNA protectio n.