Structural insights into temperature-dependent dynamics of METPsc1, a miniaturized electron-transfer protein

• Published in: Journal of inorganic biochemistry 2025-03, Vol.264, p.112810, Article 112810
• Main Authors: Di Costanzo, Luigi F., Sgueglia, Gianmattia, Orlando, Carla, Polentarutti, Maurizio, Leone, Linda, La Gatta, Salvatore, De Fenza, Maria, De Gioia, Luca, Lombardi, Angela, Arrigoni, Federica, Chino, Marco
• Format: Article
• Language: English
• Subjects: Artificial metalloprotein; Cadmium - chemistry; Cadmium coordination; Crystallography, X-Ray; Electron transfer; Electron Transport; Hydrogen Bonding; Metalloproteins - chemistry; Metalloproteins - metabolism; Molecular Dynamics Simulation; Protein Conformation; Protein design; Protein dynamics; Temperature; Temperature-dependent crystallography
• ISSN: 0162-0134; 1873-3344; 1873-3344
• DOI: 10.1016/j.jinorgbio.2024.112810

The design of protein-metal complexes is rapidly advancing, with applications spanning catalysis, sensing, and bioremediation. We report a comprehensive investigation of METPsc1, a Miniaturized Electron Transfer Protein, in complex with cadmium. This study elucidates the impact of metal coordination on protein folding and structural dynamics across temperatures from 100 K to 300 K. Our findings reveal that METPsc1, composed of two similar halves stabilized by intramolecular hydrogen bonds, exhibits a unique “clothespin-like” recoil mechanism. This allows it to adapt to metal ions of varying radii, mirroring the flexibility observed in natural rubredoxins. High-resolution crystallography and molecular dynamics simulations unveil concerted backbone motions and subtle temperature-dependent shifts in side-chain conformations, particularly for residues involved in crystal packing. Notably, CdS bond lengths increase with temperature, correlating with anisotropic motions of the sulfur atoms involved in second-shell hydrogen bonding. This suggests a dynamic role of protein matrix upon redox cycling. These insights into METPsc1 highlight its potential for catalysis and contribute to the designing of artificial metalloproteins with functional plasticity. The METPsc1 (Miniaturized Electron Transfer Protein single chain) designed protein adapts to different metal ion sizes through its unique backbone motion as shown by temperature-dependent experimental and computational analyses. [Display omitted] •METPsc1, a single-chain Miniaturized Electron Transfer Protein, adapts to metals of varying radii through a “clothespin-like” recoil mechanism.•Temperature-dependent X-ray diffraction reveals subtle conformational changes.•Molecular dynamics simulations reveal a glass transition around 190 K in aqueous solution.•METPsc1 demonstrates adaptability similar to natural rubredoxins.•Findings validate the design approach for creating functional protein-metal complexes.