Quaternary structure, peptide

FIGURE 1.4 Increasing levels of protein structure. A protein has a given amino acid sequence to make peptide chains. These adopt a 3D structure according to the free energy of the system. Receptor function can change with changes in tertiary or quaternary structure. 

Some proteins contain covalent disulfide (S— S) bonds that link the sulfhydryl groups of cysteinyl residues. Formation of disulfide bonds involves oxidation of the cysteinyl sulfhydryl groups and requires oxygen. Intrapolypeptide disulfide bonds further enhance the stability of the folded conformation of a peptide, while interpolypeptide disulfide bonds stabilize the quaternary structure of certain oligomeric proteins. 

Some proteins are formed by a single chain and are called monomeric, but a large number are formed by several polypeptide chains that associate in a multimeric molecule. The relationships of the peptide chains in a multichain protein are known as the quaternary structure. These subunits may work either independently of each other or cooperatively, i.e. the function of one subunit depends on the functional state of the others11. 

Figure 8.10 The quaternary structure of proteins. The enzyme lactate dehydrogenase (EC 1.1.1.27) has a relative molecular mass of approximately 140 000 and occurs as a tetramer produced by the association of two different globular proteins (A and B), a characteristic that results in five different hybrid forms of the active enzyme. The A and B peptides are enzymically inactive and are often indicated by M (muscle) and H (heart). The A4 tetramer predominates in skeletal muscle while the B4 form predominates in heart muscle but all tissues show most types in varying amounts.

The aromatic rings in the protein absorb ultraviolet light at an absorbance maximum of 280 nm, whereas the peptide bonds absorb at around 205 nm. The unique absorbance property of proteins could be used to estimate the level of proteins. These methods are fairly accurate with the ranges from 20 p,g to 3 mg for absorbance at 280 nm, as compared with 1 to 100 p,g for 205 nm. The assay is non-destructive as the protein in most cases is not consumed and can be recovered. Secondary, tertiary and quaternary structures all affect absorbance therefore, factors such as pH, ionic strength, etc can alter the absorbance spectrum. This assay depends on the presence of a mino acids which absorb UV light (mainly tryptophan, but to a lesser extent also tyrosine). Small peptides that do not contain such a mino acids cannot be measured easily by UV. 

As described in the beginning of this chapter, the peptide bond is rigid, polar, and prefers a planar structure with hydrogen of the amino group and oxygen of the carbonyl almost trans. It is easily understood that this conformational preference and rigidity has profound implications to the tertiary and quaternary structure of proteins and similarly on the binding of smaller peptides to receptors. 

Primary structure of a protein is simply amino acids sequence of the peptide chain. The secondary structure is a result of the different conformations that the chain can take. The tertiary structure refers to the three dimensional shape that results from twisting, bending and folding of protein helix. The quaternary structure refers to the way in which these amino acid chains of a complex protein are associated with each other (oligomer, dimers, trimers, etc.). 

Quaternary structure The structure formed by the association of two or more peptide chains. 

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

These principles are best recognized when studying relatively simple molecular systems that have an ability to exploit weak interactions to create structure. Among many, peptides are the perfect choice for such studies considering their versatility in make up given the 20+ natural and synthetic amino acid residues, and their functional diversity. In addition, the amino acid sequence of the primary structure combined with the ability of forming secondary (3-sheet or a-helix structures provide substantial room for the creation of hierarchical structures based on weak intermolecular forces, mainly hydrogen bonds. A limited sequence of residues also prevents additional complication from tertiary and quaternary structures as seen with proteins. 

---