Lanmodulin’s EF 2–3 Domain: Insights from Infrared Spectroscopy and Simulations

Abstract

Lanmodulins are small, ∼110-residue proteins with four EF-hand motifs that demonstrate a picomolar affinity for lanthanide ions, making them efficient in the recovery and separation of these technologically important metals. In this study, we examine the thermodynamic and structural complexities of lanthanide ion binding to a 41-residue domain, EF 2–3, that constitutes the two highest-affinity metal-binding sites in the lanmodulin protein from Methylorubrum extorquens. Using a combination of circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics (MD) simulations, we characterize the metal binding capabilities of EF 2–3. ITC demonstrates that binding occurs between peptide and lanthanides with conditional dissociation constants (K_d) in the range 20–30 μM, with no significant differences in the K_d values for La³⁺, Eu³⁺, and Tb³⁺ at pH 7.4. In addition, CD spectroscopy suggests that only one binding site of EF 2–3 undergoes a significant conformational change in the presence of lanthanides. 2D IR spectroscopy demonstrates the presence of both mono- and bidentate binding configurations in EF 2–3 with all three lanthanides. MD simulations, supported by Eu³⁺ luminescence measurements, explore these results, suggesting a competition between water–lanthanide and carboxylate–lanthanide interactions in the EF 2–3 domain. These results underscore the role of the core helical bundle of the protein architecture in influencing binding affinities and communication between the metal-binding sites in the full-length protein.