Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration

Biophys J. 2011 Sep 7;101(5):1130-8. doi: 10.1016/j.bpj.2011.07.003.


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 DNA-binding protein is mutated into adenine-thymine, cytosine-guanine, and thymine-adenine. It is shown that basepair mutations can be performed using a conservative protocol that gives error estimates of ∼10% of the change in free energy of binding. Despite the high CPU-time requirements, this work opens the exciting opportunity of being able to perform basepair scans to investigate protein-DNA binding specificity in great detail computationally.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing*
  • Computational Biology
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism*
  • Molecular Dynamics Simulation*
  • Mutation*
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry
  • Proteins / metabolism*
  • Thermodynamics


  • Proteins
  • DNA