Structural basis of immune response mechanisms
Antibody-antigen (Ab-Ag) interaction forms the basis of adaptive immune response mechanisms of a vertebrate. When bacteria or viruses infect the human body and introduce toxic substances (antigen) into it, specialized cells (B-lymphocytes) of the body responds by producing antibody (Ab) molecules to destroy the infecting agent.
Two functions of an antibody
Two functions of an antibody molecule are responsible for immune response – the ability to bind specifically to its target antigen (Ag) and recruit other cells and molecules to encounter the bound Ag. Evidently, there must be sites on both the Ab and Ag to bind to each other. The binding site on the Ag is called the epitope while that on the Ab is called the paratope.
The binding of Ag and Ab involves different types of noncovalent interactions between the epitope and the paratope. The diversity in the binding potentials of Ab molecules is indeed remarkable – they can bind to almost any ‘non-self’ surface with high affinity and specificity, notwithstanding the fact that all Abs are structurally similar. With the availability of an increasing amount of structural data, the mechanisms of Ab-Ag interaction are becoming ever more comprehensible.
The structure of an Ab molecule.
Ab structure
As shown in the figure above, an Ab molecule consists of two identical heavy (H) chain and two identical light (L) chains. The four chains are held together by disulfide bonds to form a Y-shaped structure. Each arm of the structure is known as a Fab (fragment of antigen-binding). The Fab is composed of two variable domains (VH and VL) and two constant domains (CH1 and CL), where the subscripts H and L represent the heavy and light chains respectively. Each H-chain contains two additional domains CH2 and CH3 in the FC region.
The two variable domains, VH and VL, dimerize to form the FV fragment that contains the Ag binding site. Three hypervariable loops (H1, H2, and H3) are present in VH while three (L1, L2, and L3) are in VL. Intervening sequences between the hypervariable regions, called Framework residues (FRs), are more or less conserved. VH and VL fold in such a manner as to bring the hypervariable loops together and form the Ag binding site or paratope. The hypervariable regions are also sometimes called complementarity determining regions (CDRs).
Any part of Ag surface - epitopic
For the Ag, there are no clear rules that would differentiate between epitopic and nonepitopic residues. In fact, under appropriate conditions, any part of the Ag surface has the potential to become an epitope. It is likely that the epitope is Ab-dependent. This is illustrated in figure below which shows that three epitopes on the surface of the antigen hen egg-white lysozyme bind to three different Abs.
Three Abs (Ab1, Ab2 and Ab3) bound to three different epitopes (colored coral, gold and purple) in antigen (Ag) egg-white lysozyme.
Ag-Ab interaction interface
Interaction interface of a human IL15 Ag-anti-IL15 Ab complex. Hypervariable region L2 colored red. Some of the H-bonds shown by black lines.
The exact boundaries of the CDRs still remain uncertain as contacts with the Ag occur even outside the hypervariable loops. However, all Ag-binding residues are located in regions of ‘structural consensus’ across antibodies. Sometimes the Ag-binding residues outside the conventionally defined CDRs have a greater energetic contribution towards the stability of the Ag-Ab complex than the ones within. The figure on the left shows the interaction interface of a human IL15 Ag-anti-IL15 Ab complex. Of the seven Ab L-chain residues that interact with the Ag, L46 and Y49 are outside the hypervariable region L2.
Structural flexibility of Ab
Like other ligand-binding proteins, Abs demonstrate necessary flexibility for their function. Upon Ag binding, structural changes occur within and far from the binding site. A comparison of the free and Ag-bound structures of the anti-epidermal growth factor receptor (EGFR) Ab (figure on the right) shows that a significant binding-related conformational change occurs at the hypervariable region (CDR) H3. An even larger change occurs in a loop region in the CH1 domain. It has been speculated that epitope recognition may be allosterically influenced by changes in the constant domains.
Comparison of free (light / hot pink) and Ag-bound (light blue / cyan) structures of anti-EGFR Ab. Regions with significant changes have been indicated by dotted circles.
From the pages of Fundamentals of Molecular Structural Biology
