How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation

A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as Hg^II, Pb^II, and As^III result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that Cd^II forms three-, four- or five-coordinate Cd^IIS₃(OH₂)_x (in which x=0–2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating Cd^IIS₃(OH₂). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming Cd^IIS₃. Residue d -Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding Cd^IIS₃, whereas d -Leu below opens more space, allowing for equal Cd^IIS₃(OH₂) and Cd^IIS₃(OH₂)₂. These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.