Structural and dynamical correlations in PfHGXPRT oligomers: A molecular dynamics simulation study

Tarak Karmakar, Sourav Roy, Hemalatha Balaram, Sundaram Balasubramanian

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

PfHGXPRT is a key enzyme involved in purine nucleotide salvage pathway of the malarial parasite, Plasmodium falciparum. Atomistic molecular dynamics simulations have been performed on two types of PfHGXPRT dimers (D1 and D3) and its tetramer in their apo and ligand-bound states. A significant event in the catalytic cycle is the dynamics of a gate that provides access for the ligand molecules to the reaction center. The gate is formed by loops II and IV, the former being the most flexible. Large amplitude conformational changes have been observed in active site loop II. Upon complete occupancy of the active site, loop II gets stabilized due to specific interactions between its residues and the ligand molecules. Remote loop, X, is seen to be less fluxional in the D3 dimer than in D1 which is rationalized as due to the greater number of inter-subunit contacts in the former. The presence of ligand molecules in subunits of the tetramer further reduces the flexibility of loop X epitomizing a communication between this region and the active sites in the tetramer. These observations are in accordance with the outcomes of several experimental investigations. Participation of loop X in the oligomerization process has also been discerned. Between the two types of dimers in solution, D1 tetramerizes readily and thus would not be present as free dimers. We conjecture an equilibrium to exist between D3 and the tetramer in solution; upon binding of the ligand molecules to the D3 dimer, this equilibrium shifts toward the tetramer.

Original languageEnglish (US)
Pages (from-to)1-16
Number of pages16
JournalJournal of Biomolecular Structure and Dynamics
DOIs
StateAccepted/In press - Apr 24 2016
Externally publishedYes

Fingerprint

Molecular Dynamics Simulation
Ligands
Catalytic Domain
Purine Nucleotides
Plasmodium falciparum
Parasites
Communication
Enzymes

Keywords

  • inter-subunit interactions
  • loop opening
  • oligomers
  • PfHGXPRT
  • remote loop

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Structural and dynamical correlations in PfHGXPRT oligomers : A molecular dynamics simulation study. / Karmakar, Tarak; Roy, Sourav; Balaram, Hemalatha; Balasubramanian, Sundaram.

In: Journal of Biomolecular Structure and Dynamics, 24.04.2016, p. 1-16.

Research output: Contribution to journalArticle

Karmakar, Tarak ; Roy, Sourav ; Balaram, Hemalatha ; Balasubramanian, Sundaram. / Structural and dynamical correlations in PfHGXPRT oligomers : A molecular dynamics simulation study. In: Journal of Biomolecular Structure and Dynamics. 2016 ; pp. 1-16.
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