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Issue 5, 2014
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QM/MM simulations indicate that Asp185 is the likely catalytic base in the enzymatic reaction of HIV-1 reverse transcriptase

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Abstract

Alternative possible mechanisms of reaction in HIV-1 reverse transcriptase are studied here by QM/MM molecular dynamics umbrella sampling simulations. Two protonation states of the dTTP substrate are tested. Among three different pathways, Asp185 is the probable base for deprotonation of the 3′-primer terminus prior to nucleotide addition on fully-deprotonated dTTP with formation of the stable final product complex of DNAn+1 and PPi. In contrast, the reactions via dTTP or Asp186 as the base show higher energy barriers for either deprotonation or nucleotide addition.

Graphical abstract: QM/MM simulations indicate that Asp185 is the likely catalytic base in the enzymatic reaction of HIV-1 reverse transcriptase

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Publication details

The article was received on 24 Oct 2013, accepted on 14 Feb 2014 and first published on 17 Feb 2014


Article type: Concise Article
DOI: 10.1039/C3MD00319A
Citation: Med. Chem. Commun., 2014,5, 593-596
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    QM/MM simulations indicate that Asp185 is the likely catalytic base in the enzymatic reaction of HIV-1 reverse transcriptase

    T. Rungrotmongkol, A. J. Mulholland and S. Hannongbua, Med. Chem. Commun., 2014, 5, 593
    DOI: 10.1039/C3MD00319A

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