Ionizable residues present in a protein core can lead to a conformational change in response to its environment. The charged states of these residues are essential to many protein functions such as ligand binding and catalysis. Ionizable residues could tune proteins to give a completely different pH range of catalysis than the usual pH-range based on its pKa in solution. This is because of the delicate interplay of three factors: protein’s hydrophobic interior, electrostatic interaction with its neighboring residues and conformational change of receptor. Most of the drugs and its receptors contain ionizable residues which restrict ligand binding into a specific pH range. The knowledge of the pH-range and the interactions between protein and ligand at the transition state would help in designing an effective inhibitor. In our 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. Given its biological and pharmaceutical importance, a lot of relevant experimental information along with crystal structures at different pH values are available. To analyze its pH-dependent functions, we have used pH-replica exchange molecular dynamics (pH-REMD) to get pH-equilibrated protein-ligand structures. We find that conformational change occurs at low pH and this matches well with the previous experimental and theoretical study. We have also computed the pH-activity profile by calculating the conditional probability of correct protonation states of catalytically important residues and it matches well with experiment. We delved deeper into finding the reason for catalytic inactivity at low pH and found that the experimentally proposed model doesn’t show the whole picture. This study will help in finding the catalytic mechanism which is essential for designing effective inhibitors.

pH-dependent conformational change and its impact on E.coli glycinamide ribonucleotide transformylase catalytic activity

253rd National Meeting (2017)

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