Packing motifs as predictors of the propensity of antibody fragments to crystallize

A recurring theme in the crystallization of antibody fragments in our labor atory has been a packing pattern involving formation of intermolecular, ant iparallel beta-pleated sheets across two-fold axes. The most common motif i s the antiparallel stacking of constant (C) domains of light (L) chain dime rs or Fab molecules. Here, cross-molecule six-stranded sheets are produced by hydrogen-bonding interactions of three-residue polypeptide segments (tri ads), in the i, i + 2 and i + 4 positions of the final strands (designated 3-3) of the three-chain layers from two adjacent molecules. In the variable (V) domains the triads are supplied by the first strands (4-1) of the four -chain layers and the resulting cross-molecule sheets contain eight strands . The latter type of packing is more likely to be seen in crystals of Fv fr agments (V domains only) than in those of L chain dimers or Fabs. Amongst t he triads from either the V or C domains, there are on average four sets of backbone carbonyl and amide groups within hydrogen bonding distance (< 3.2 Angstrom) of each other. In at least one example, the adjacent antiparalle l strands are sterically aligned, but only two of the appropriate sets of a toms are sufficiently close to meet the distance criteria for intermolecula r hydrogen bonding. These observations have been used to construct a list o f rules for predicting which types of L chain dimers, Fab and Fvs are likel y to crystallize in these packing patterns. (C) 1999 Elsevier Science B.V. All rights reserved.