title: Structural and dynamical correlations in PfHGXPRT oligomers: A molecular dynamics simulation study.
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.
authors.affiliation: a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India .
authors.forename: Tarak
authors.initials: T
authors.lastname: Karmakar
authors.affiliation: b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India .
authors.forename: Sourav
authors.initials: S
authors.lastname: Roy
authors.affiliation: b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India .
authors.forename: Hemalatha
authors.initials: H
authors.lastname: Balaram
authors.affiliation: a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India .
authors.forename: Sundaram
authors.initials: S
authors.lastname: Balasubramanian
mesh_terms: D056004:Molecular Dynamics Simulation; D010430:Pentosyltransferases / Q000737:chemistry*; D010963:Plasmodium falciparum / Q000201:enzymology*; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D021122:Protein Subunits; D013329:Structure-Activity Relationship
chemical_list: D021122:Protein Subunits; D010430:Pentosyltransferases; C083867:hypoxanthine-guanine-xanthine phosphoribosyltransferase
keywords: PfHGXPRT; inter-subunit interactions; loop opening; oligomers; remote loop