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Updated: Jul 11, 2026
06:48
CD Spectroscopy to Study DNA-Protein Interactions
Published on: February 10, 2022
Intradomain LexA rotation is a prerequisite for DNA binding specificity
Matej Butala1, Milan Hodoscek, Gregor Anderluh
1Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, Ljubljana, Slovenia. matej.butala@bf.uni-lj.si
FEBS Letters
|September 22, 2007
Summary
The LexA protein controls the bacterial SOS DNA repair system. Blocking its DNA binding domain reorientation prevents LexA from binding DNA, offering new drug design possibilities.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- The LexA protein is a key repressor of the bacterial SOS DNA damage response system.
- Understanding LexA's DNA binding mechanism is crucial for comprehending bacterial stress responses.
Purpose of the Study:
- To elucidate the mechanism of LexA protein's selective DNA binding.
- To investigate the role of domain reorientation in LexA-operator interactions.
- To explore potential therapeutic targets for modulating bacterial DNA repair.
Main Methods:
- Molecular dynamic simulations were employed to model LexA dimers bound to DNA operators.
- Engineered LexA mutants with double and quadruple cysteine substitutions were created.
- Electrophoretic mobility-shift assays (EMSA) and surface plasmon resonance (SPR) were used to assess DNA binding.
Main Results:
- Molecular dynamics simulations predicted that LexA DNA binding requires rotation of the DNA binding domain relative to the dimerized C-terminal domain.
- Disulfide bond formation in engineered cysteine mutants blocked this essential domain reorientation.
- Mutant LexA proteins with blocked domain rotation failed to bind DNA specifically, confirming the model's prediction.
Conclusions:
- The study confirms that selective DNA binding by LexA is dependent on the reorientation of its DNA binding domain.
- Interfering with this domain reorientation effectively inhibits LexA DNA binding.
- The findings provide a structural basis for designing novel drugs targeting bacterial DNA repair mechanisms.
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