Role of Zn2+ in Protein Structuralization

Abstract Stabilisation of very small proteins and very small domains (less than 50 aa) requires special methods. The stability of the III-order structure is ensured by the presence of hydrophobic core and/or SS-bonds. The contribution of the aqueous environment directing the formation of the III-order structure leads to a structure with a centric hydrophobic core and a polar surface. In similar fashion, the membrane environment directs the structuring of active proteins in the membrane envelope towards the exposure of hydrophobic residues on the surface with polar residues in the centre (ion channel). In addition to these two environments, other factors are identified critical to the formation of the III-order structure. These are chaperone proteins—chaperones or chaperonins. A very short polypeptide chain (below 50 aa) has a much lower number of degrees of freedom in achieving a stable three-dimensional structure. An example of proteins and domains with such a low composition are proteins/domains interacting with DNA referred to as Zn-fingers. Representatives of these proteins/domains (and others requiring the presence of Zn2 + ions) are analysed for hydrophobicity distribution in this paper. In these systems, the Zn2 + ion coordinating mainly Cys and His provides the presence of a centric hydrophobic core stabilising the system with exposed polarity. This is related to the formation of structures adapted to interact with DNA. For these proteins, a small domain size is additionally required to ensure the ability to interact with the corresponding grooves in the DNA structure. The analysis of protein groups containing Zn2 + ions was performed using a fuzzy oil drop model (FOD-M). A high degree of ordered hydrophobicity was demonstrated with a hydrophobic core present and a polar surface with a micelle-like distribution. This system, or arrangement, stabilises the structure in an aqueous environment in which the proteins operate.