Communications: Electron polarization critically stabilizes the Mg 2+ complex in the catalytic core domain of HIV-1 integrase

Yunpeng Lu, Ye Mei, John Z.H. Zhang, Dawei Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

In this paper, we present a detailed dynamics study of the catalytic core domain (CCD) of HIV-1 integrase using both polarized and nonpolarized force fields. The numerical results reveal the critical role of protein polarization in stabilizing Mg2+ coordination complex in CCD. Specifically, when nonpolarized force field is used, a remarkable drift of the Mg2+ complex away from its equilibrium position is observed, which causes the binding site blocked by the Mg2+ complex. In contrast, when polarized force field is employed in MD simulation, HIV-1 integrase CCD structure is stabilized and both the position of the Mg2+ complex and the binding site are well preserved. The detailed analysis shows the transition of α-helix to 310-helix adjacent to the catalytic loop (residues 139-147), which correlates with the dislocation of the Mg2+ complex. The current study demonstrates the importance of electronic polarization of protein in stabilizing the metal complex in the catalytic core domain of HIV-1 integrase.

Original languageEnglish (US)
Article number131101
JournalJournal of Chemical Physics
Volume132
Issue number13
DOIs
StatePublished - Apr 7 2010

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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