Structure of cytokine hydrophobic cores

Diagrams were constructed that describe, using a common frame of reference, the interactions that occur within the hydrophobic cores of the left-handed four-helix bundles of interleukin-2, -4, -5, granulocyte/macrophage-, granulocyte-, macrophage-colony-stimulating factor, beta- and gamma-interferon, growth hormone, and leukemia inhibitory factor. Based on the assumption that the topologies of the ligand-receptor complexes are similar, analogous patterns were obtained from these diagrams and lead to the detailed comparison of the hydrophobic cores. These patterns were then used to obtain pairwise rigid-body superpositions among all of the four-helix bundles; values of the root-mean-square deviations (C alpha-atoms) over the four alpha-helices of the bundles range from 1.14 A to 3.22 A. Two distinct groups are formed after clustering based on structural superposition of the ten cytokines.