The Design of Metal Ion-Induced Dimers Suggestive of 3D Domain Swapping
Shota Shiga1, Seiya Sugiyama1, Satoshi Ito2
1Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, Japan.
Abstract:
Expanding strategies for the design of artificial protein dimers induced by metal ions is important for creating proteins with novel functions as well as useful research tools. In this study, we extended our previously established polyproline-based design and developed a method to induce dimerization suggestive of 3D domain swapping in a metal ion-dependent manner. Variants with six residues deleted from a loop in the C-terminal domain of outer surface protein A and containing His-Pro repeats formed dimers in the presence of divalent first-row transition metal ions. The formation and dissociation of the Zn2+-induced dimer occurred slowly, suggesting that dimerization requires substantial structural rearrangements. Moreover, the structure of the Zn2+-induced dimer predicted by AlphaFold3 was consistent with a 3D domain-swapped dimer stabilized by intermolecular coordination between Zn2+ and the histidine residues within the His-Pro repeats. This predicted structure remained stable during 100-ns molecular dynamics simulations. These experimental and computational evaluations suggest that the insertion of His-Pro repeats into loops is an effective strategy for designing metal ion-induced dimers suggestive of 3D domain-swapped dimers. Our results provide insights into expanding the design space of artificial metal ion-dependent protein dimers and advancing our understanding of the structural principles of metalloproteins.
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