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Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics
Monisha Mohan1, Vishal Pandya1, Roy Anindya1
1Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Hyderabad, 502285, Telangana, India.
Journal of Molecular Graphics & Modelling
|May 27, 2018
Summary
Escherichia coli AlkB enzyme repairs DNA alkylation damage on single-stranded DNA (ssDNA) coated by SSB protein. Molecular dynamics simulations reveal flexible binding of AlkB to SSB-ssDNA complexes, aiding DNA repair.
Area of Science:
- Molecular Biology
- Biochemistry
- Genetics
Background:
- DNA alkylation damage poses a threat to genome integrity.
- The Escherichia coli (E. coli) AlkB enzyme repairs DNA damage via oxidative demethylation.
- Single-stranded DNA binding protein (SSB) binds ssDNA non-sequence-specifically.
Purpose of the Study:
- To elucidate the mechanism of AlkB-mediated DNA repair on SSB-bound DNA.
- To understand the structural basis of AlkB interaction with SSB-coated ssDNA.
Main Methods:
- Generation of a structural model for AlkB-SSB-ssDNA complex.
- Molecular Dynamics (MD) simulations.
- Docking analysis of the AlkB-SSB-ssDNA structure.
Main Results:
- SSB-bound DNA exhibits flexibility, allowing multiple binding modes for AlkB.
- Docking analysis identified Cyt109 base within the AlkB active site hydrophobic cavity.
- Detailed AlkB-SSB interaction patterns were characterized.
Conclusions:
- AlkB can access and repair alkylation damage on SSB-coated ssDNA.
- The flexibility of SSB-bound DNA is crucial for AlkB binding and repair.
- Understanding AlkB-SSB interactions provides insights into alkylated DNA adduct recognition.
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