Why does the silica-binding protein “Si-tag” bind strongly to silica surfaces? Implications of conformational adaptation of the intrinsically disordered polypeptide to solid surfaces

We recently reported that the bacterial 50S ribosomal protein L2 binds strongly to silica surfaces even in the presence of high salt concentrations, detergents, and denaturants such as 8 M urea. We designated L2 as Si-tag, a fusion tag for immobilizing functional proteins on silica materials. Here we discuss the remarkable properties of the Si-tag polypeptide in order to understand the mechanism underlying this binding. Experimental and theoretical studies have shown that the 60-aa N-terminal region and the 71-aa C-terminal region, both of which are rich in positively charged residues, lack a well-defined three-dimensional structure under physiological conditions. This lack of a stable tertiary structure suggests that Si-tag belongs to a family of intrinsically disordered (ID) proteins that exist as dynamic ensembles of rapidly fluctuating structures in aqueous solution. Because of its inherent flexibility, Si-tag could form a large intermolecular interface and optimize its structure for surface interactions by conformational adaptation at the binding interface. Such conformational adaptation occurring concomitantly with binding is common to many ID proteins and is called “coupled folding and binding”. Through this conformational adaptation, Si-tag could optimize the interactions between its positively charged side chains and ionized surface silanol groups and between its apolar side chains and hydrophobic surface siloxane sites. The cumulative contribution of these contacts would significantly strengthen the binding of Si-tag, resulting in strong, virtually irreversible binding. Our study suggests that flexible ID proteins have tremendous potential for connecting biomolecules to inorganic materials.