In an attempt to account for antibody specificity and complementarity in terms of structure, human kappa-, human lambda-, and mouse kappa-Bence Jones proteins and light chains are considered as a single population and the variable and constant regions are compared using the sequence data available. Statistical criteria are used in evaluating each position in the sequence as to whether it is essentially invariant or group-specific, subgroup-specific, species-specific, etc. Examination of the invariant residues of the variable and constant regions confirms the existence of a large number of invariant glycines, no invariant valine, lysine, and histidine, and only one invariant leucine and alanine in the variable region, as compared with the absence of invariant glycines and presence of three each of invariant alanine, leucine, and valine and two each of invariant lysine and histidine in the constant region. The unique role of glycine in the variable region is emphasized. Hydrophobicity of the invariant residues of the two regions is also evaluated. A parameter termed variability is defined and plotted against the position for the 107 residues of the variable region. Three stretches of unusually high variability are noted at residues 24-34, 50-56, and 89-97; variations in length have been found in the first and third of these. It is hypothesized that positions 24-34 and 89-97 contain the complementarity-determining residues of the light chain-those which make contact with the antigenic determinant. The heavy chain also has been reported to have a similar region of very high variability which would also participate in forming the antibody-combining site. It is postulated that the information for site complementarity is contained in some extrachromosomal DNA such as an episome and is incorporated by insertion into the DNA of the structural genes for the variable region of short linear sequences of nucleotides. The advantages and disadvantages of this hypothesis are discussed.

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An analysis of the sequences of the variable regions of bence jones proteins and myeloma light chains and their implications for antibody complementarity

The structure of the Fab′ fragment of a human myeloma immunoglobulin was determined by x-ray crystallographic analysis at 2.8-A resolution. The Fourier map of the electron density was correlated with the aminoacid sequence to obtain a three-dimensional model. Four globular subunits, which correspond to the homology regions of the light and heavy chains, are arranged in a tetrahedral configuration. These subunits closely resemble each other, sharing a basic pattern of polypeptide chain folding. In each subunit, long sequences of tightly packed, hydrogen bonded polypeptide chain run parallel to the major axis of the subunit. No helical conformation can be seen. Different patterns of interchain disulfide linkage and unusual intrachain disulfide bonds that have been observed in other immunoglobulins can be explained with this model. The regions of hypervariable sequences in the light and heavy chains occur at one end of the molecule, in close spatial proximity.

https://www.pnas.org/content/pnas/70/12/3305.full.pdf

Three-Dimensional Structure of the Fab′ Fragment of a Human Immunoglobulin at 2.8-Å Resolution

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%.

https://www.pnas.org/content/pnas/82/14/4592.full.pdf

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

A new test principle for the detection of specific IgM-class antibodies was developed and applied in an Enzyme-Linked Immuno Sorbent Assay (ELISA) for the detection of hepatitis A IgM antibodies. A solid phase coated with anti-IgM was incubated successively with serum sample, specific antigen, and enzyme-labeled F (ab')2 fragments from IgG antibodies against the antigen and enzyme substrate. F(ab')2 fragments were used to avoid interference with rheumatoid factor. Specificity and sensitivity are very high. This test principle appears generally applicable in the diagnosis of infectious and parasitic diseases by testing only one serum sample.

A new principle for the detection of specific IgM antibodies applied in an ELISA for hepatitis A.

The structure of human immunoglobulin Fab′ fragment has been elucidated at a resolution of 6 A. There are two globular subunits, which presumably correspond to the variable and constant regions of the heavy and light polypeptide chains of immunoglobulins

Structure of Fab' New at 6 A resolution.

INFORMATION concerning the three-dimensional structure of an antibody and the contours of its combining site can in theory be derived by X-ray crystallography. In view of the large molecular weight of antibody molecules (150,000 or greater), crystals of fragment Fab, which has a molecular weight of 50,000 and contains the combining site of an antibody, may be of particular value.

G Rossi

Papers

Crystals of fragment Fab': preparation from pepsin digests of human IgG myeloma proteins.