Computational insights into substrate-assisted citrullination mechanisms of PAD2 isozyme: A comparative analysis of reaction pathways

Citrullination, catalyzed by protein arginine deiminase enzymes, involves the conversion of peptidyl-arginine to peptidyl-citrulline, disrupting protein interactions and leading to functional alterations. Despite the experimental studies on PAD2 indicating calcium dependence and substrate specificity, the catalytic mechanism remains contentious, with conflicting evidence regarding the roles of active site residues such as Cys647 and His471. The present study is an expansion of prior molecular dynamics simulations that investigated the dynamics of the enzyme PAD2, which indicated that Asp473 may function as a general acid/base, thereby challenging the experimentally proposed pathways. To further elucidate this controversial issue, quantum mechanical methods were employed to examine the protonation states of key residues and their roles in catalysis. Herein, three different pathways have been studied for the substrate-assisted citrullination mechanism of PAD2 isozyme using a model structure that includes the active site residues Asp351, His471, Val472, Asp473, and Cys647 and a water molecule. The highest barriers for two of the designed mechanisms, RM1 and RM3 are comparable: the choice of a single mechanism is not possible since the differences in barriers fall within the error margins in DFT calculations. These findings offer insights into PAD2's enzymatic activity, thereby advancing our understanding of its biological significance.