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The correct placement of side-chain functional groups that interact with the charged groups of the new substrate is necessary to change an enzyme's selectivity. In order for the functional groups to be positioned correctly, this necessitates sequence alterations that not only add the new functional groups but also modify the structure of the protein backbone. We present a computational design approach for the targeted modification of loops close to the active site to introduce unique enzyme-substrate interactions. The approach can restore native loop lengths and, frequently, native loop conformations, according to benchmark studies on 8 native protein-ligand complexes. Next, we redesign a crucial loop in human guanine deaminase using the technique to ensure that an important side-chain contact is made with the substrate ammelide.
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