Metal-Coordination Specificity and Structural Dynamics of C. elegans Metallothionein I: Insights From 3D Modeling and MD Simulations.

Abstract

Metallothioneins (MTLs) are small, cysteine-rich proteins known for their ability to bind metal ions and exhibit flexible, disordered structures. The structural and functional characteristics of metallothionein I (MTL-1) from Caenorhabditis elegans were investigated, focusing on its behavior in both metal free (MTL-1 Apo) and metal-bond states with Zn²⁺, Cd²⁺, Cu²⁺, Hg²⁺, and Pb²⁺ divalent metal ions. Using molecular dynamics simulations and 3D modeling via AlphaFold, we characterized the flexibility and stability of MTL. The MTL-1 Apo form displayed high flexibility, aligning with its intrinsically disordered protein (IDP) nature, with 89.3% of its structure composed of coils, bends, and turns. Metal binding significantly enhanced the protein's stability, particularly with Zn²⁺, Cd²⁺, Cu²⁺, and Hg²⁺, reducing root mean square deviation (RMSD), root mean square fluctuation (RMSF), accessible surface area (SASA) and radius of gyration (R_g) values, indicating structural compaction. Conversely, Pb²⁺ showed a weaker stabilizing effect, with a more dynamic and less stable structure. Structural analysis revealed that conserved cysteine residues coordinate the metal through strong thiolate interactions, with additional contributions from non-cysteine residues, such as Glu and Lys. The study underscores the importance of incorporating intrinsically disordered protein models in MD simulations to provide deeper insights into how metallothionein's flexibility and stability vary in response to different metal ions, offering a structural perspective on their biological interactions and behavior under diverse environmental conditions. While thermodynamic aspects were not directly assessed, the results reveal consistent conformation trends across different metal coordination states.