Peptide Charge Modulates Ion Binding to EF-Hand Motifs: A Molecular Dynamics Study

Rare earth elements (REEs), particularly lanthanides (Ln), are of significant interest due to their critical roles in modern technology and medicine. However, their extraction, isolation, and purification remain challenging. Lanmodulin (LanM), a recently discovered EF-hand protein, exhibits high affinity and selectivity for binding Ln3+ ions. This enhanced affinity is partly attributed to the presence of additional acidic residues within its EF-hand metal binding loops. Previous studies have demonstrated that reducing the number of ligating acidic residues within EF-hand motifs significantly decreases their binding affinities for La3+. Yet, the underlying molecular mechanisms remain poorly understood. To address this, we performed molecular dynamics (MD) simulations and MMPBSA/MMGBSA analyses on a series of EF-hand motifs with varying numbers of ligating acidic residues. Our results reveal that the number of acidic ligands strongly influences the structure of the peptide–ion complex. Specifically, a decrease in ligating acidic residue leads to increased coordination of water molecules to La3+. We also observed a complex interplay among different ligand types, including ligating acidic and neutral residues, non-ligating acidic residues, backbone carbonyls, and water molecules. Notably, reducing the number of acidic ligands significantly alters the secondary structure of the EF-hand motif, increases its flexibility, and reshapes its free energy landscape. This study provides important molecular insights into how peptide charge modulates ion binding to EF-hand motifs, offering valuable guidance for the rational design of EF-hand proteins with tailored ion-binding properties.