Interdependence of free zinc changes and protein complex assembly – insights into zinc signal regulation

Abstract

Cellular zinc (Zn(II)) is bound with proteins that are part of the proteomes of all domains of life. It is mostly utilized as a catalytic or structural protein cofactor, which results in a vast number of binding architectures. The Zn(II) ion is also important for the formation of transient protein complexes with a Zn(II)-dependent quaternary structure that is formed upon cellular zinc signals. The mechanisms by which proteins associate with and dissociate from Zn(II) and the connection with cellular Zn(II) changes remain incompletely understood. In this study, we aimed to examine how zinc protein domains with various Zn(II)-binding architectures are formed under free Zn(II) concentration changes and how formation of the Zn(II)-dependent assemblies is related to the protein concentration and reactivity. To accomplish these goals we chose four zinc domains with different Zn(II)-to-protein binding stoichiometries: classical zinc finger (ZnP), LIM domain (Zn₂P), zinc hook (ZnP₂) and zinc clasp (ZnP¹P²) folds. Our research demonstrated a lack of changes in the saturation level of intraprotein zinc binding sites, despite various peptide concentrations, while homo- and heterodimers indicated a concentration-dependent tendency. In other words, at a certain free Zn(II) concentration, the fraction of a formed dimeric complex increases or decreases with subunit concentration changes. Secondly, even small or local changes in free Zn(II) may significantly affect protein saturation depending on its architecture, function and subcellular concentration. In our paper, we indicate the importance of interdependence of free Zn(II) availability and protein subunit concentrations for cellular zinc signal regulation.