Multiple molecular dynamics simulations of TEM beta-lactamase: dynamics and water binding of the omega-loop

The Omega-loop of TEM beta-lactamase is involved in substrate recognition and catalysis. Its dynamical properties and interaction with water molecules were investigated by performing multiple molecular dynamics simulations of up to 50 ns. Protein flexibility was assessed by calculating the root mean-square fluctuations and the generalized order parameter, S(2). The residues in secondary structure elements are highly ordered, whereas loop regions are more flexible, which is in agreement with previous experimental observations. Interestingly, the Omega-loop (residues 161-179) is rigid with order parameters similar to secondary structure elements, with the exception of the tip of the loop (residues 173-177) that has a considerably higher flexibility and performs an opening and closing motion on the 50-ns timescale. The rigidity of the main part of the Omega-loop is mediated by stabilizing and highly conserved water bridges inside a cavity lined by the Omega-loop and residues 65-69 of the protein core. In contrast, the flexible tip of the Omega-loop lacks these interactions. Hydration of the cavity and exchange of the water molecules with the bulk solvent occurs via two pathways: the flexible tip that serves as a door to the cavity, and a temporary water channel involving the side chain of Arg(164).