Biological and Medicinal Chemistry

Role of Thr199 Residue in Human β-Carbonic Anhydrase-II pH-Dependent Activity Elucidated by Microsecond Simulation Analysis

Hussain Syed Innovative Informatica Technologies
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Abstract

Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate, a reaction required for many functions such as carbon assimilation, pH acid–base homeostasis, respiration and photosynthesis via zinc-hydroxide mechanism for carbon dioxide hydration. In earlier studies, it was revealed that Carbonic anhydrases are inactive at pH 7.5 and active at pH 8.4. This steep pH dependence for its activity led us to design this work in order to understand its mode of action at atomic level detailing. In our microsecond simulation based analysis, it was revealed that the interaction between Glu106 and Thr199 plays a critically important role in its activity. Thr199 co-ordinated loop movement was observed to be acting as a lid, with ‘open’ and ‘close’ mechanism for substrate entry to the core of the catalytic site, where Zn-ion resides and executes its carbon dioxide hydration mechanism. On the other hand, decline in the total secondary structural elements percentage in the protein was observed in correspondence to the pH condition change. Especially, α-helices between Thr125-Gly145 and Val150-Lys170 residues were noticed to be losing their structural integrity responsible for formation of dimer and tetramers. In conclusion, our analysis showed that the interaction between Glu106 and Thr199 is crucial for maintaining the structural integrity of the Thr199 corodinated loop, responsible for allowing substrate towards catalytic site.

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