Abstract
Why and how do enzymes undergo conformational changes in order to perform their function?
The protein Adenylate Kinase (ADK) has two major conformations, the open and closed states. The conformational transition is important for the biological function of the protein in that, 1) the protein has to transform between the two conformations for catalytic function, and 2) the conformational transition is the rate limiting step during the catalytic cycle as shown by NMR experiments. The goal of our computational studies is to answer the questions about “why and how” these conformational transitions happen. We approach this problem indirectly by analyzing how different external pressure conditions affect the dynamics and functions of both P. profundum ADK (Padk), which lives at 700 atm pressure in the deep sea, and its homologue E. coli ADK (Eadk) living at ambient pressures.
Using NMR, we showed the rate of opening/closing transition in Padk increases with increasing pressures indicating that the protein possesses smaller partial molar volume in the transition state compared to its open and closed conformational states. MD simulations under pressure and TMD simulations we used to evaluate pathways of transitions in atomistic detail. Volume and surface accessible solvent area calculations per residue basis revealed physical principles underlying the different adaptations under pressure. Solvent exposure of charged residues combined with formation of ionic bridges was found to be the mechanism of the transition. The predicted pathways were verified by testing how mutations of key residues affected the enzyme conformational dynamics. The initially found steep pressure dependence of Padk in contrast to Eadk was mimicked by both the experiments with mutations and high-pressure simulations, the latter extending the conformational energy landscape to the folding/unfolding region by obtaining atomic scale detail of core hydrophobic interactions.