Research Projects

The proposed work focuses on the enzyme human carbonic anhydrase (HCA) IX that is a known target in cancer diagnosis and therapeutics. The research group of the PI has performed extensive classical molecular dynamics (MD) and enhanced sampling studies on the non-reactive, yet functionally important, reorganizations of this enzyme in its monomeric and dimeric catalytic domains in water for a wide range of pH, with and without a glycan chain covalently attached to it. These studies provide (i) multiple initial and end structures with varying conformation and charge, corresponding to the reactant and product states, and (ii) a large number dynamic hydrogen bonded networks as putative reaction paths for the rate determining proton transfer step. In this project, we aim at using these data to construct a reaction network for the catalysis by glycosylated catalytic domain of HCA IX at different pH (a) in water and (b) when attached to a disordered proteoglycan (PG)-like domain. The main objectives are (i) to derive the underlying variation in the charge transfer mechanism, energetics and kinetics with changing pH; (ii) understanding the role of glycosylation and membrane anchoring at each pH. In each of the systems mentioned above, the following computational steps are proposed. (i) The first step would involve using the nudged elastic band method to identify different potential intermediates between the reactant and product states, including both proton and hydroxide ion transfer. (ii) In the second step, an optimal number of ‘best’ pathways will be derived connecting the terminal and intermediate states, optimized using both energetic and kinetic data. (iii) In the final step, along a few top ranked pathways, we propose to perform QM-MM MD interfaced with OPES metadynamics and transition path sampling to compute the committor (reaction coordinate) along which the free energy and kinetics will be estimated. In view of the lack of any dynamical information on this enzyme system, the proposed project is expected to explore the complex reaction network and provide a much needed quantitative basis for the structure and dynamics based drug design in this therapeutically important enzyme.