Molecular dynamics investigation of cysteine mutations: Effects on calcium ion affinity and structural stability in the RET cysteine-rich domain

The RET receptor tyrosine kinase is essential for cell growth, differentiation, and survival. Its cysteine-rich domain (CRD) is crucial for ligand-induced dimerization, activation, and structural stability, significantly influenced by calcium ion coordination. Mutations in key cysteine residues can disrupt disulfide bonds, alter calcium binding, and destabilize the CRD, leading to oncogenic transformations. This study investigates the impact of cysteine mutations on calcium ion binding and the structural stability of the RET receptor's CRD. Using molecular dynamics simulations and free energy calculations, the research examines the structural effects of specific cysteine mutations (C565F, C581F, and C585S) in the CRD. The findings indicate that these mutations disrupt disulfide bonds, alter calcium binding, and destabilize the CRD. RMSD and RMSF analyses show that each mutant affects structural dynamics and flexibility differently. The C581F mutant exhibited the most significant effect, with average RMSD values of 0.21 nm compared to the wild-type (0.19 nm) and other mutants (C565F, 0.14 nm; C585S, 0.17 nm). Higher residue fluctuations were observed in C581F and C585S, particularly in the calcium-coordinating residues. Binding free energy analysis indicates reduced calcium-binding stability in the mutants, while weighted contact maps reveal altered residue interaction patterns and new contact formations. These results suggest that while global structural changes are minimal, cysteine mutations cause localized destabilization of calcium ion binding sites. The disruption of key disulfide bonds and reduced residue contacts likely contribute to decreased binding stability in the mutants, underscoring the importance of cysteine residues and calcium coordination in maintaining the integrity of the RET-CRD.