The Closure Mechanism Of M. Tuberculosis Guanylate Kinase Relates Structural Fluctuations To Enzymatic Function

Abstract

The Allosteric Spring Probe (ASP) technique allowed Zocchi et al. to act on the enzymatic activity of guanylate kinase (GK) by applying tension upon the molecular structure of this enzyme [Choi et al., Biophys. J., 2007]. These experiments raise the question about the underlying conformational modifications leading to such an observation. In order to elucidate the results from these ASP studies, we investigate the conformational dynamics of GK and its mechanical properties. We use both high resolution atomistic molecular dynamics and low resolution Brownian Dynamics simulations. The enzyme is subject to large conformational changes, leading from an open to a closed form, and further influenced by substrate or co-factor docking. A reduction or perturbation of the conformational space available to GK can be related to the activity loss encountered in the ASP experiments. We describe a detailed picture of GK's closure mechanism characterizing the hierarchy and chronology of structural events essential for the enzymatic reaction. Rigidity profiles obtained from simulations of distinct states hint at important differences. We have investigated open vs. closed, apo vs. holo or substrate vs. product-loaded forms of the enzyme.