Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase

Tarak Karmakar, Sourav Roy, Hemalatha Balaram, Meher K. Prakash, Sundaram Balasubramanian

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Atomistic molecular dynamics (MD) simulations coupled with the metadynamics technique were carried out to delineate the product (PPi.2Mg and IMP) release mechanisms from the active site of both human (Hs) and Plasmodium falciparum (Pf) hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (HG(X)PRT). An early movement of PPi.2Mg from its binding site has been observed. The swinging motion of the Asp side chain (D134/D145) in the binding pocket facilitates the detachment of IMP, which triggers the opening of flexible loop II, the gateway to the bulk solvent. In PfHGXPRT, PPi.2Mg and IMP are seen to be released via the same path in all of the biased MD simulations. In HsHGPRT too, the product molecules follow similar routes from the active site; however, an alternate but minor escape route for PPi.2Mg has been observed in the human enzyme. Tyr 104 and Phe 186 in HsHGPRT and Tyr 116 and Phe 197 in PfHGXPRT are the key residues that mediate the release of IMP, whereas the motion of PPi.2Mg away from the reaction center is guided by the negatively charged Asp and Glu and a few positively charged residues (Lys and Arg) that line the product release channels. Mutations of a few key residues present in loop II of Trypanosoma cruzi (Tc) HGPRT have been shown to reduce the catalytic efficiency of the enzyme. Herein, in silico mutation of corresponding residues in loop II of HsHGPRT and PfHGXPRT resulted in partial opening of the flexible loop (loop II), thus exposing the active site to bulk water, which offers a rationale for the reduced catalytic activity of these two mutant enzymes. Investigations of the product release from these HsHGPRT and PfHGXPRT mutants delineate the role of these important residues in the enzymatic turnover.

Original languageEnglish (US)
Pages (from-to)1528-1538
Number of pages11
JournalJournal of Chemical Information and Modeling
Volume56
Issue number8
DOIs
StatePublished - Aug 22 2016
Externally publishedYes

Fingerprint

Inosine Monophosphate
Enzymes
Molecular dynamics
Computer simulation
Binding sites
Memantine
Hypoxanthine Phosphoribosyltransferase
simulation
Catalyst activity
turnover
Molecules
Binding Sites
water
efficiency
Water
present

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

Cite this

Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase. / Karmakar, Tarak; Roy, Sourav; Balaram, Hemalatha; Prakash, Meher K.; Balasubramanian, Sundaram.

In: Journal of Chemical Information and Modeling, Vol. 56, No. 8, 22.08.2016, p. 1528-1538.

Research output: Contribution to journalArticle

Karmakar, Tarak ; Roy, Sourav ; Balaram, Hemalatha ; Prakash, Meher K. ; Balasubramanian, Sundaram. / Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase. In: Journal of Chemical Information and Modeling. 2016 ; Vol. 56, No. 8. pp. 1528-1538.
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abstract = "Atomistic molecular dynamics (MD) simulations coupled with the metadynamics technique were carried out to delineate the product (PPi.2Mg and IMP) release mechanisms from the active site of both human (Hs) and Plasmodium falciparum (Pf) hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (HG(X)PRT). An early movement of PPi.2Mg from its binding site has been observed. The swinging motion of the Asp side chain (D134/D145) in the binding pocket facilitates the detachment of IMP, which triggers the opening of flexible loop II, the gateway to the bulk solvent. In PfHGXPRT, PPi.2Mg and IMP are seen to be released via the same path in all of the biased MD simulations. In HsHGPRT too, the product molecules follow similar routes from the active site; however, an alternate but minor escape route for PPi.2Mg has been observed in the human enzyme. Tyr 104 and Phe 186 in HsHGPRT and Tyr 116 and Phe 197 in PfHGXPRT are the key residues that mediate the release of IMP, whereas the motion of PPi.2Mg away from the reaction center is guided by the negatively charged Asp and Glu and a few positively charged residues (Lys and Arg) that line the product release channels. Mutations of a few key residues present in loop II of Trypanosoma cruzi (Tc) HGPRT have been shown to reduce the catalytic efficiency of the enzyme. Herein, in silico mutation of corresponding residues in loop II of HsHGPRT and PfHGXPRT resulted in partial opening of the flexible loop (loop II), thus exposing the active site to bulk water, which offers a rationale for the reduced catalytic activity of these two mutant enzymes. Investigations of the product release from these HsHGPRT and PfHGXPRT mutants delineate the role of these important residues in the enzymatic turnover.",
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