Molecular Biology: Protein Structure and Function - Stepanov V.M. 2005

Quaternary Protein Structure
Subunit interactions stabilizing the quaternary structure

Subunit contacts, which determine the existence of The quaternary Structure, represent a highly developed system of non-covalent interactions. Covalent Disulfide Bonds are rarely used to stabilize the quaternary structure (for example, they link the light and heavy chains in IMMUNOGLOBULINS), and even in these cases, they play a subordinate role, complementing non-covalent contacts.

Hydrogen Bonds play a crucial role in organizing the network of subunit contacts. Very often, a system of such bonds unites the ß-pleated sheets of interacting subunits into a single, highly extended structure. If the terminal segment of a ß-pleated sheet emerges On the surface of a subunit, an identical segment will occupy the corresponding position in the other subunit. Rotating the latter by 180° brings these segments into close proximity, establishing a system of hydrogen bonds characteristic of an antiparallel ß-Structure between them. For instance, in the Quaternary Structure of horse Liver Alcohol dehydrogenase (an enzyme catalyzing The conversion of various alcohols into aldehydes), two subunits contact to form an extended ß-pleated layer consisting of 12 peptide segments. Within the contact zone, a total of 8 Hydrogen bonds are established between the C=O and N—H groups of the main chain:

In addition to this system, individual hydrogen bonds may also form between the Functional groups of different subunits.

Significant as The Role of hydrogen bonds may be, they alone cannot ensure a sufficiently stable quaternary structure, especially In aqueous solutions. As in The formation of the tertiary structure, contacts between hydrophobic groups and entire hydrophobic patches on The surface of interacting subunits are of great importance here. It has already been mentioned that about half of the hydrophobic amino acid residues are localized in the surface layer of the protein, which makes The Emergence of such contacts entirely plausible. Thus, aside from hydrogen bonds, the quaternary structure of alcohol dehydrogenase is stabilized by hydrophobic contacts involving, from each of the two subunits, two Methionine residues, one leucine, three isoleucines, two prolines, and one Tryptophan—totalling 18 residues spread across an area of 600 A². In the isolated subunit, the hydrophobic side chains of these residues would form thermodynamically unfavorable contacts with Water, ordering its structure. Therefore, the Formation of the subunit contact leads to an increase in the Entropy of the system, shifting the equilibrium toward the oligomer.

The combination of the hydrogen bonding system and hydrophobic contacts makes the binding of alcohol dehydrogenase subunits extremely strong. Dissociation of this protein's quaternary structure is achieved only in 8 M urea.

Subunit interfaces frequently contain ion pairs that establish Electrostatic Interactions between oppositely charged functional groups of the subunits—for example, between the carboxylate ions of glutamic and aspartic acid residues and the cationic groups of Lysine or Arginine side chains. Furthermore, the formation is not limited to simple ion pairs; entire systems or clusters of spatially close opposite charges frequently arise. The exclusion of water from the subunit contact makes these interactions, which are otherwise relatively unstable on the protein surface, highly significant.

Analysis of the quaternary structure of several Proteins has shown that among The amino acid residues providing subunit contacts, 67% are non-polar, 20% are polar, and 13% bear charged groups.

Overall, the contact zone between subunits constitutes a cooperative system of non-covalent interactions, the stability of which heavily depends on external conditions and, notably, even on minor Changes in the Spatial Structure of each interacting subunit. This conceals the Molecular Basis of one of the most specific Functions of the quaternary structure: its ability to transmit structural rearrangements from one subunit to others.

The strength of the quaternary structure can vary over a wide range. It is sometimes measured by the fraction of the subunit surface that participates in the intersubunit contact and becomes sequestered from water during structure formation.

It should be noted that the stabilization of the quaternary structure is driven by qualitatively the same non-covalent interactions that govern the Stability of the tertiary structure, although THE CONTRIBUTION OF hydrophobic contacts is somewhat smaller. The difference is largely quantitative: as a rule, the tertiary structure is considerably more robust than the quaternary. Consequently, when exposed to factors that disrupt these bonds, the quaternary structure is typically lost first, dissociating into native subunits. This rule has exceptions; however, the relatively lower stability of the quaternary structure provides significant advantages by allowing its modifications to serve as regulatory factors for the Functional Properties of proteins.