Structural invariants of antigen binding: comparison of immunoglobulin VL-VH and VL-VL domain dimers

Abstract

Antigen-combining site arises by noncovalent association of the variable domain of the immunoglobulin heavy chain (VH) with that of the light chain (VL). To analyze the invariant features of the binding region (VL-VH domain interface), we compared the known immunoglobulin three-dimensional structures by a variety of methods. The interface forms a close-packed, twisted, prism-shaped "beta-barrel" characterized by cross-sectional dimensions 1.04 X 0.66 nm and a top-to-bottom twist angle of 212 degrees. The geometry of the interface is preserved via invariance of some 15 side chains, both inside the domains and on their surface. Buried polar residues form a conserved hydrogen-bonding network that has a similar topological connectivity in the two domain types; two hydrogen bonds contributed by invariant side chains extend across the interface and anchor the beta-sheets in their relative orientation. Invariant aromatic residues close-pack at the bottom of the binding-site beta-barrel with their ring planes oriented perpendicularly in the characteristic "herringbone" packing mode. Electrostatic computations that implicitly include solvent effects show the domains to be stabilized by large electrostatic forces. However, structures that were crystallized at lower pH have their electrostatic energies appropriately lowered, implying that full ionization of carboxyl side chains is essential for efficient electrostatic stabilization. The unusual mode of domain-domain association in the VL-VL dimer RHE correlates with its overall repulsive electrostatic energy (+54 kJ/mol), as opposed to negative (i.e., stabilizing) energy values (-263 to -543 kJ/mol) found in the domains of the other structures. The VL-VL dimer REI mimics closely the interface geometry of VL-VH dimers although its domain-domain contact area is lower by 18%.