https://libjncir.jncasr.ac.in/xmlui/handle/10572/1498 2026-04-04T05:31:27Z 2026-04-04T05:31:27Z Karmakar, Tarak Roy, Sourav Balararn, Hemalatha Prakash, Meher K. Balasubramanian, Sundaram https://libjncir.jncasr.ac.in/xmlui/handle/10572/2177 2017-02-21T10:22:48Z 2016-01-01T00:00:00Z

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

2016-01-01T00:00:00Z Palazzesi, Ferruccio Prakash, Meher K. Bonomi, Massimiliano Barducci, Alessandro https://libjncir.jncasr.ac.in/xmlui/handle/10572/2037 2017-02-21T10:22:16Z 2015-01-01T00:00:00Z

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States Palazzesi, Ferruccio; Prakash, Meher K.; Bonomi, Massimiliano; Barducci, Alessandro Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w [Best and Mittal J. Phys. Chem. B 2010, 114, 14916-14923] provides the best agreement with experiments, which is further improved by adding the ILDN corrections [Lindorff-Larsen et al. Proteins 2010, 78, 1950-1958]. Restricted access

2015-01-01T00:00:00Z