Effect of interprotein polarization on protein-protein binding energy

Chang G. Ji, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

Molecular dynamics simulation in explicit water for the binding of the benchmark barnase-barstar complex was carried out to investigate the effect polarization of interprotein hydrogen bonds on its binding free energy. Our study is based on the AMBER force field but with polarized atomic charges derived from fragment quantum mechanical calculation for the protein complex. The quantum-derived atomic charges include the effect of polarization of interprotein hydrogen bonds, which was absent in the standard force fields that were used in previous theoretical calculations of barnase-barstar binding energy. This study shows that this polarization effect impacts both the static (electronic) and dynamic interprotein electrostatic interactions and significantly lowers the free energy of the barnase-barstar complex.

Original languageEnglish (US)
Pages (from-to)1416-1420
Number of pages5
JournalJournal of Computational Chemistry
Volume33
Issue number16
DOIs
StatePublished - 2012

Keywords

  • Binding energy
  • Electrostatic interaction
  • Hydrogen bond
  • Molecular dynamics simulation
  • Polarization
  • Protein-protein interactions

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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