Cytokine conformations: Predictive studies

The amino acid sequences of human and murine haemopoietins have been analysed using algorithms predictive for secondary structure. The results for 19 of these proteins (human and murine Interleukins 2, 3, 4, 5, 6, 7 and granulocyte, macrophage and granulocyte macrophage‐colony stimulating factors as well as human erythropoietin) suggest that they each contain a 4‐α‐helical bundle, ca 25 Å long, as a common conformational feature. The most important predictive indicator was considered to be occurrence of quasi‐repeating sequences of seven amino acids of the form ( a ‐ b ‐ c ‐ d ‐ e ‐ f ‐ g ) n with a polar side chains (usually leucine) lying alternately three and four residues apart in the a and d positions. As with other proteins of known secondary structure this periodicity favors the formation of α‐helical elements, each with an a polar external strip, which interdigitate closely with one another when tested appropriately. Molecular models based on these putative 4‐α‐helical bundles are presented – with special references to human granulocyte macrophage‐colony stimulating factor. The extent to which such models are consistent with experiments designed to delineate receptor binding sites is discussed.