Uncomplexed antibodies and `induced fit' movements

The topographies of the uncomplexed antibody combining sites (Tables 2.2 and 2.5) are less clearly correlated with antigen type. However, for many of these antibodies it has been more difficult to identify the true nature of the antigen and therefore know which type of combining site to expect.

It is possible that a combining site `relaxes' in the absence of antigen (induced fit) or is distorted by crystal contacts. We have investigated the former possibility by determining the topographic classes of the combining site surfaces of both the complexed and uncomplexed antibody structures where available. The topographies of the 10 pairs of complexed/uncomplexed antibody are given in Table 2.6. In these cases, the assigned topographic class is that of the closest topography profile in Figure 2.6(c) (minimum Euclidean distance). Four antibodies change their topographic class between complexed and uncomplexed forms; two of the ridged-type antibodies (17/9[Schulzegahmen et al., 1993] and BV04-01[Herron et al., 1991]) become concave-type, and two moderately concave-type antibodies (McPC603[Satow et al., 1986] and 50.1[Rini et al., 1993]) become ridged-type. However, none of the concave-type anti-hapten antibodies `relax' to moderately concave, nor do the planar-type antibodies change their gross topography.

**Table 2.6:** Combining site topographies compared between complexed and uncomplexed antibody crystal structures.
antibody	antigen	complexed		uncomplexed
name	type	PDB code	topography	PDB code	topography
DB3	hapten	1dbb	concave	1dba	concave
26-10	hapten	1igj	concave	1igi	concave
`2cgr'	hapten	2cgr	concave	1cgs	concave
McPC603	hapten	2mcp	mod. concave	1mcp	ridged
50.1	peptide	1ggi	mod. concave	1ggb	ridged
17/9	peptide	1him	ridged	1hil	concave
B1312	peptide	2igf	ridged	1igf	ridged
BV04-01	dna	1cbv	ridged	1nbv	concave
D1.3	protein	1vfb	planar	1vfa	planar
D44.1	protein	1mlc	planar	1mlb	planar