(26d) Structural Underpinnings of Lanmodulin and Its Variants on the Energetics of Rare Earth Metal Binding

Understanding rare earth element (REE) binding to proteins enables the engineering of selective protein-based ligands for precise REE recovery. Lanmodulin (LanM), with notable REE selectivity and picomolar binding affinity, is a promising candidate. This study shows that LanM variants employ distinct inter-residue interactions for REE binding. We detail the thermodynamics and structural aspects of binding events in wild-type (WT) Methylorubrum extorquens LanM and five EF-hand residue variants (4P₂A and 4D₉X, X=N, A, H, M), using AI-based protein structure prediction, molecular docking, dynamics simulations, binding motif exploration, and force-field reweighting. We analyze the agreement between experimental binding measurements (apparent K_d) and in silico binding energy scores of WT, 4P₂A, and 4D₉X LanMs. In silico scores and experimental K_d values align for WT and 4P₂A, but 4D₉X variants show discrepancies. We systematically investigate solvent impact, force field reliability, and initial protein structure on metal ion-binding energetics. Optimal reweighting of energy terms and redefining the interacting domain in LanM elucidates the experimental binding characteristics of 4D₉X variants. This reweighting and redefinition scheme not only yields energetics in agreement with the experimental K_d values – for the first time, to the best of our knowledge, for a computational study of this protein – but it also sheds light on how a point mutation can induce long-range structural perturbations to regulate metal ion-protein interactions.