Full ab initio computation of protein-water interaction energies

D. W. Zhang, John Zhang

Research output: Contribution to journalArticle

Abstract

A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.

Original languageEnglish (US)
Pages (from-to)43-49
Number of pages7
JournalJournal of Theoretical and Computational Chemistry
Volume3
Issue number1
DOIs
StatePublished - Mar 2004

Fingerprint

proteins
Proteins
Molecules
Water
fragments
caps
water
molecules
interactions
human immunodeficiency virus
energy
workstations
Fractionation
Macromolecules
macromolecules
fractionation
chemical properties
Chemical properties
Density functional theory
amino acids

Keywords

  • Ab initio calculation
  • Interaction
  • MFCC
  • Protein-water

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Full ab initio computation of protein-water interaction energies. / Zhang, D. W.; Zhang, John.

In: Journal of Theoretical and Computational Chemistry, Vol. 3, No. 1, 03.2004, p. 43-49.

Research output: Contribution to journalArticle

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