Article
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration.
Biophysical journal - 7 Sept 2011
Beierlein Frank R, Kneale G Geoff, Clark Timothy
Abstract excerpt
Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a protein-binding DNA operator sequence. A guanine-cytosine basepair that interacts strongly with the...
Topics
- Base Pairing
- Computational Biology
- DNA
- Molecular Dynamics Simulation
- Mutation
- Protein Binding
- Protein Conformation
- Proteins
- Thermodynamics