Ligand binding is central to most functions of proteins such as allostery, cooperativity and enzyme regulation etc. Allostery is when the ligand binds at a remote site and can alter the binding affinity of a substrate bound to the active site. Such allosteric modulation of binding affinity may occur not only through structural changes but also predominantly via entropy change and favorable or unfavorable shifts in protonation equilibrium. The latter two factors can also drive the enhancement in binding affinity for cooperativity. In this work, the target protein is E. coli glycinamide ribonucleotide transformylase (GAR Tfase), a regulatory enzyme for de novo purine biosynthesis, which has been proven to be an anticancer target. This protein exhibits pH-dependent conformational changes and catalytic activity. To study pH-dependent protein functions, we use pH replica exchange molecular dynamics (pH-REMD) simulations implemented in the AMBER suite to run on GPUs. Simulation analyses show how pH-change alters the conformation of loops and optimizes it for the ligand binding. We have computed the pH-dependent relative free energy of ligand binding through the double-mutant cycle for the ligand; results imply bidirectional modulation of ligand affinity. This work illustrates the mechanism for ligand binding-induced conformational change at the atomistic level; how protonation equilibrium shifts induced by the ligand to favor another ligand binding. It aids in understanding immediate and long-range electrostatic environments for optimizing drug inhibition.

Bidirectional allosteric modulation in E. coli glycinamide ribonucleotide transformylase (GAR Tfase)

255th National Meeting (2018)

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