Enzyme closure and nucleotide binding structurally lock guanylate kinase.
Résumé
We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of apo-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, apo-versus-holo, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.