Quantum study of HIV-1 protease-bridge water interaction

Li L. Duan, Yan Tong, Ye Mei, Qing G. Zhang, John Zhang

Research output: Contribution to journalArticle

Abstract

We present a fully quantum mechanical calculation for binding interaction between HIV-1 protease (PR) and the water molecule W301 which bridges the flaps of the protease with the inhibitors of PR. The quantum calculation is made possible by applying a recently developed molecular fractionation with conjugate caps (MFCC) method which divides a protein molecule into capped amino acid-based fragments and their conjugate caps. These individual fragments are properly treated to preserve the chemical property of bonds that are cut. Ab initio methods at HF, B3LYP, and MP2 levels with a fixed basis set 6-31+ G* have been employed in the present calculation. The MFCC calculation produces a quantum mechanical interaction "map" representing interactions between individual residues of PR and W301. This enables a detailed quantitative analysis on binding of W301 to specific residues of PR at quantum mechanical level.

Original languageEnglish (US)
Article number145101
JournalJournal of Chemical Physics
Volume127
Issue number14
DOIs
StatePublished - 2007

Fingerprint

protease
human immunodeficiency virus
Peptide Hydrolases
caps
Water
Fractionation
water
fractionation
interactions
Flaps
Molecules
fragments
Protease Inhibitors
Chemical properties
chemical properties
inhibitors
quantitative analysis
amino acids
molecules
Amino Acids

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Quantum study of HIV-1 protease-bridge water interaction. / Duan, Li L.; Tong, Yan; Mei, Ye; Zhang, Qing G.; Zhang, John.

In: Journal of Chemical Physics, Vol. 127, No. 14, 145101, 2007.

Research output: Contribution to journalArticle

Duan, Li L. ; Tong, Yan ; Mei, Ye ; Zhang, Qing G. ; Zhang, John. / Quantum study of HIV-1 protease-bridge water interaction. In: Journal of Chemical Physics. 2007 ; Vol. 127, No. 14.
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