Toward a Halophenol Dehalogenase from Iodotyrosine Deiodinase via Computational Design

Reductive dehalogenation offers an attractive approach for removing halogenated pollutants from the environment, and iodotyrosine deiodinase (IYD) may contribute to this process after it can be engineered to accept a broad range of substrates. The selectivity of IYD is controlled in part by an active site loop of ∼26 amino acids. In the absence of a substrate, the loop is disordered and only folds into a compact helix-turn-helix upon halotyrosine association. The design algorithm of Rosetta was applied to redesign this loop for response to 2-iodophenol rather than iodotyrosine. One strategy using a restricted number of substitutions for increasing the inherent stability of the helical regions failed to generate variants with the desired properties. A series of point mutations identified strong epistatic interactions that impeded adaptation of IYD. This limitation was overcome by a second strategy that placed no restrictions on side-chain substitution by Rosetta. Nine representative designs containing between 14 and 18 substitutions over 26 contiguous sites were evaluated experimentally. The top performing catalyst (UD08) supported a 4.5-fold increase in turnover of 2-iodophenol and suppressed turnover of iodotyrosine by 2000-fold relative to the native enzyme. The active site loop of UD08 appeared less disordered than the native sequence in the absence of substrate, as evident from their relative sensitivity to proteolysis. Protection from proteolysis increased 9-fold for UD08 in the presence of 2-iodophenol and nearly rivaled the equivalent response of wild-type IYD to iodotyrosine. Thus, the Rosetta designs achieved the goal of creating an active site sequence that gained structure in the presence of iodophenol. Although a limited number of point mutations was sufficient to increase the catalytic efficiency for 2-iodophenol dehalogenation, only Rosetta successfully created a loop structure responsive to this substrate.