Effect of interprotein polarization on protein-protein binding energy

Chang G. Ji, John Zhang

Research output: Contribution to journalArticle

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

Fingerprint

Binding Energy
Binding energy
Polarization
Hydrogen Bonds
Force Field
Proteins
Protein
Free energy
Free Energy
Hydrogen bonds
Charge
Coulomb interactions
Electrostatics
Molecular Dynamics Simulation
Molecular dynamics
Fragment
Electronics
Benchmark
Water
Computer simulation

Keywords

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

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Effect of interprotein polarization on protein-protein binding energy. / Ji, Chang G.; Zhang, John.

In: Journal of Computational Chemistry, Vol. 33, No. 16, 2012, p. 1416-1420.

Research output: Contribution to journalArticle

@article{d2f64ea516f44217ab740efab700fcdd,
title = "Effect of interprotein polarization on protein-protein binding energy",
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.",
keywords = "Binding energy, Electrostatic interaction, Hydrogen bond, Molecular dynamics simulation, Polarization, Protein-protein interactions",
author = "Ji, {Chang G.} and John Zhang",
year = "2012",
doi = "10.1002/jcc.22969",
language = "English (US)",
volume = "33",
pages = "1416--1420",
journal = "Journal of Computational Chemistry",
issn = "0192-8651",
publisher = "John Wiley and Sons Inc.",
number = "16",

}

TY - JOUR

T1 - Effect of interprotein polarization on protein-protein binding energy

AU - Ji, Chang G.

AU - Zhang, John

PY - 2012

Y1 - 2012

N2 - 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.

AB - 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.

KW - Binding energy

KW - Electrostatic interaction

KW - Hydrogen bond

KW - Molecular dynamics simulation

KW - Polarization

KW - Protein-protein interactions

UR - http://www.scopus.com/inward/record.url?scp=84861580646&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84861580646&partnerID=8YFLogxK

U2 - 10.1002/jcc.22969

DO - 10.1002/jcc.22969

M3 - Article

C2 - 22495971

AN - SCOPUS:84861580646

VL - 33

SP - 1416

EP - 1420

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 16

ER -