Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin.

@article{Ji2008DevelopingPP,
  title={Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin.},
  author={Changge Ji and Ye Mei and John Zenghui Zhang},
  journal={Biophysical journal},
  year={2008},
  volume={95 3},
  pages={1080-8}
}
Ab initio quantum mechanical calculation of protein in solution is carried out to generate polarized protein-specific charge(s) (PPC) for molecular dynamics (MD) stimulation of protein. The quantum calculation of protein is made possible by developing a fragment-based quantum chemistry approach in combination with the implicit continuum solvent model. The computed electron density of protein is utilized to derive PPCs that represent the polarized electrostatic state of protein near the native… CONTINUE READING