Oligomerization

Proteins (or peptides), which are the major constituents of our bodies, are formed by oligomerization of amino acids, which occurs when their peptide bonds are bound together in a specific manner (-CONH-). Although the primary sequence (the linear sequence of amino acids) of a protein is the most important determinant of its shape and function, the secondary structures (conformations) of a protein are also important. The environment in which proteins are found has an impact on their conformation (random coil, -helix, and ß-sheet, for example). The -helix structure is formed by hydrogen bonds that form between the amino acids in the peptide chain. Meanwhile, the ß-sheets (ß-plated sheets) are composed of ß-strands, which are hydrogen-bonded peptide bonds that are laterally connected to one another.

Abstract

When it comes to biological molecules, oligomerization is a common physical characteristic that can be observed in a wide range of proteins, including transcription factors, ion channels, oxygen-carrying macromolecules such as hemocyanin, and enzymes, among others. The formation of pathogenic structures associated with Alzheimer’s disease and other diseases is facilitated by unintentional protein oligomerization, which is undesirable. Peroxiredoxins, a family of thiol peroxidases, have also been shown to self-assemble, which is a well-documented phenomenon. The formation of peroxiredoxin hyperaggregates is the primary mechanism that causes the switch between Prx activity as a peroxidase and that of a chaperone. Understanding the oligomerization process is critical to understanding the function of the multiple peroxiredoxins. Using isothermal titration calorimetry (ITC), the chapter provides a detailed description of typical 2-Cys Peroxiredoxin oligomerization and a recipe for investigating the thermodynamic parameters of peroxiredoxin assembly, including the association and dissociation constants, enthalpy and entropy, as well as the Gibbs free energy of the process, among other things.

Interfaces for Oligomerization that could occur

The term “oligomerization of protein” refers to the interaction of multiple polypeptide chains in a protein. This results in the formation of the quaternary structure, which is generally regarded as the most complex level of organisation within the protein structural hierarchy. Oligomeric proteins can be composed either exclusively of several copies of identical polypeptide chains, in which case they are referred to as homo-oligomers, or alternatively of at least one copy of different polypeptide chains, in which case they are referred to as hetero-oligomers. Homo-oligomers are proteins that are composed exclusively of several copies of identical polypeptide chains, in which case they are referred to as hetero-oligomers (hetero-oligomers).

The oligomerization state is defined as follows

Even though the oligomerization state of microbial Sqr has only been lightly investigated (with the exception of the A. aeolicus enzyme), it is generally accepted that these enzymes are dimeric, similar to enzymes belonging to the same enzyme superfamily. Although it has not been demonstrated, it has been hypothesised that the active form of Sqr in R. capsulatus is a dimer (Griesbeck et al., 2002). When isolated from A. ambivalens, this enzyme is found to be a monomer in solution (Brito et al., 2009). Initially, it was believed that the A. ferrooxidans Sqr was a dimer, but calculations suggest that the equilibrium shifts toward a monomer at low protein concentrations (below 0.01 mM). However, dimers have been observed in the crystal form of both of these last organisms, indicating that the enzyme may be organised in a dimeric fashion within the membrane in both cases. Cherney and colleagues propose that the association of Sqr that exists in solution (dimers interacting via the C-terminal domain) is distinct from the probable biological dimer, which is inserted in the lipid bilayer, as demonstrated by their experiments (Brito et al., 2009; Cherney et al., 2010).

Conclusion

Oligomerization of proteins has been observed in a variety of biological systems. However, it is notoriously difficult to assess the impact of environmental parameters such as ionic strength, pH, and sample matrix using a single methodology due to the complexity of the problem.

When used in conjunction with a variety of assay conditions, the FIDA technology allows for the rapid and accurate determination of the oligomeric state of protein drug targets. Furthermore, it can confirm the oligomeric state of the protein in crude matrices such as plasma, thereby providing important information on the protein’s conformation in physiologically relevant environments.