Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Conformational Transition of Catalytic Domain in hGMPR enzyme from Native to Ligand Bound State: A MD Simulation Study

The human Guanosine-5’-Monophosphate Reductase (hGMPR) enzyme involves in inosine biosynthesis pathway by converting GMP to IMP and ammonia with concomitant oxidation of NADPH and plays a vital role in re-utilization of free intracellular bases. Type I hGMPR is expressed in all cells whereas isoform-II can promote monocytic differentiation of HL-60 leukaemia cells. So, hGMPR-II attracts an excellent potential target for design of isoform specific antileukemic agent. The catalytic domain of hGMPR is a homo-tetramer with 37-kDa subunits and monomer of this enzyme has a (α/β) 8 structure of TIM barrel. The polypeptide chain of this domain has folded to form two separate nucleotide binding pockets (Fig.A). One of them accommodates cofactor NADP (di-nucleotide) and the other binds to substrate GMP (mono- nucleotide). Few crystal structures of hGMPR are observed in different conformations. The analysis of crystal structures explores that active site residue or Cys186 attacks C2 of substrate (GMP) to create an intermediate (Cys186SG ---C2 GMP) whereas ammonia leaving group is activated by proton relay through Thr188 and Glu289 dyad. So, interaction between Cys186 and Thr188/Glu289 is Cys186---GMP---Glu289/Thr188 in ligand bound state (Fig.D).Consequently, cofactor or NADPH is stabilized by Lys78, Thr105, Ser270 and Arg286/Tyr285 (Fig. B). In spite of this distinction, no studies have been carried out on catalytic domain to identify the new conformation of native state of hGMPR enzyme. To investigate the dynamic behavior of native conformation of catalytic domain, molecular dynamics simulation was carried out using CHARMM27 force field with Nanoscale Molecular Dynamics (v.2.9) program In fact, MD result suggest that 22 water molecules are observed to occupy at position of GMP and NADPH binding region (in unliganded form). The Cys186, Thr188, Glu289 of substrate and Lys78, Glu289, Ser270, Arg286/Tyr285 of cofactor binding residues move away from their respective binding pocket during MD simulation and stabilized by conserved water mediated interactions. Four water molecules (Cys186---W1---W2---W3---W4---Thr188/Glu289) at substrate binding region (Fig.E) and eighteen water molecules (Lys78---W5---W6---W7(---Thr105)---W8---W9---W10---W11---W12---W13---OB(Arg286)---W14---W15---W16---W17---W18---W19---OG(Ser270)---W20---W21---W22---Lys78) at cofactor binding pocket (Fig.C) are observed to stabilize in unliganded state of catalytic domain, but they move and vacate those positions when enzyme (hGMPR)-substrate cofactor-complex is formed. Our computational study highlights structural and functional importance of water molecules in catalytic domain of hGMPR enzme and suggests a rethink of conventional definition of chemical geometry of inhibitor binding site.

This research has been supported by C.S.I.R. for Senior Research Associateship (Pool Scientist scheme).


Figure. A is GMP with NADPH bound conformation. B and D indicate residues of NADPH and IMP binding pocket in X-ray structure. C and D are water mediated H-bonding interaction of NADPH and IMP binding pocket in native conformation of MD structures.

Hridoy R. Bairagya

Department of Biophysics
All India Institute of Medical Sciences
New Delhi-110029, India

Ph: (91)8277145815
Email: hbairagya@gmail.com