The receptor binding site of human interleukin-3 defined by mutagenesis and molecular modeling

Interleukin-3 (IL-3) is a member of the cytokine superfamily that promotes multi-potential hematopoietic cell growth by interacting with a cell surface receptor composed of alpha and beta chains. The newly available three-dimensional structure of a variant of human (h) IL-3 allowed us to evaluate new and existing mutagenesis data and to rationally interpret the structure-function relationship of hIL-3 on a structural basis. The amino acid residues that were identified to be important for hIL-3 activity are grouped into two classes. The first class consists of largely hydrophobic residues required for the structural integrity of the protein, including the residues in IL-3 that are largely conserved among 10 mammalian species. These residues form the core of a scaffold for the second class of more rapidly diverging solvent-exposed residues, likely to be required for interaction with the receptor. Ten important and solvent-exposed residues, Asp21, Gly42, Glu43, Gln45, Asp46, Met49, Arg94, Pro96, Phe113, and Lys116, map to one side of the protein and form a putative binding site for the alpha subunit of the receptor. A model of the IL-3.IL-3 receptor complex based on the human growth hormone (hGH).hGH soluble receptor complex structure suggests that the interface between IL-3 and the IL-3 receptor alpha subunit consists of a cluster of hydrophobic residues flanked by electrostatic interactions. Although the IL-3/IL-3 receptor beta subunit interface cannot be uniquely located due to the lack of sufficient experimental data, several residues of the beta subunit that may interact with Glu22 of IL-3 are proposed. The role of these residues can be tested in future mutagenesis studies to define the interaction between IL-3 and IL-3 receptor beta subunit.