Conservation of water molecules in an antibody–antigen interaction

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Abstract
The solvation of the antibody–antigen Fv D1.3–lysozyme complex is investigated through a study of the conservation of water molecules in crystal structures of the wild‐type Fv fragment of antibody D1.3, 5 free lysozyme, the wild‐type Fv D1.3–lysozyme complex, 5 Fv D1.3 mutants complexed with lysozyme and the crystal structure of an idiotope (Fv D1.3)‐abti‐idiotope (Fv E5.2) complex. In all, there are 99 water molecules common to the wild‐type and mutant antibody–lysozyme complexes. The antibody–lysozyme interface includes 25 well‐ordered solvent molecules, conserved among the wild‐type and mutant Fv D1.3–lysozyme complexes, which are bound directly or through other water molecules to both antibody and antigen. In addition to contributing hydrogen bonds to the antibody–antigen interaction the solvent molecules fill many interface cavities. Comparison with x‐ray crystal structures of free Fv D1.3 and free lysozyme shows that 20 of these conserved interface waters in the complex were bound to one of the free proteins. Uo to 23 additional water molecules are also found in the antibody–antigen interface, however these waters do no bridge antibody and antigen and their temperature factors are much higher than those of the 25 well‐ordered waters. Fifteen water molecules are displaced to form the complex, some of which are substituted by hydrophilic protein atoms, and 5 water molecules are added at the antibody–antigen interface with the formation of the complex. While the current crystal models of the D1.3–lysozyme complex do not demonstrate the increase in bound waters found in a physico‐chemical study of the interaction at decreased water activities, the 25 well‐ordered interface water contribute a net gain of 10 hydrogen bonds to complex stability.