Sequence conservation in families whose members have little or no sequence similarity: The four-helical cytokines and cytochromes

Proteins for which there are good structural, functional and genetic Similarities that imply a common evolutionary origin, can have sequences whose similarities are low or undetectable by conventional sequence comparison procedures. Do these proteins have sequence conservation beyond the simple conservation of hydrophobic and hydrophilic character at specific sites and if they do what is its nature? To answer these questions we have analysed the structures and sequences of two superfamilies: the four-helical cytokines and cytochromes c'-b(562). Members of these superfamilies have sequence similarities that are either very low or not detectable. The cytokine superfamily has within it a long chain family and a short chain family. The sequences of known representative structures of the two families were aligned using structural information. From these alignments we identified the regions that conserve the same main-chain conformation: the common core (CC). For members of the same family, the CC comprises some 50% of the individual structures; for the combination of both families it is 30%. We added homologous sequences to the structural alignment. Analysis of the residues occurring at sites within the CCs showed that 30% have little or no conservation, whereas about 40% conserve the polar/neutral or hydrophobic/neutral character of their residues. The remaining 30% conserve hydrophobic residues with strong or medium limitations on their volume variations. Almost all of these residues are found at sites that form the buried spine of each helix (at sites i, i + 3, i + 7, i + 10, etc., or i, i + 4, i + 7, i + 11, etc.) and they pack together at the centre of each structure to give a pattern of residue-residue contacts that is almost absolutely conserved. These CC conserved hydrophobic residues form only 10-15% of all the residues in the individual structures. A similar analysis of the cytochromes c'-b562, which bind haem and have a very different function to that of the cytokines, gave very similar results. Again some 30% of the CC residues have hydrophobic residues with strong or medium conservation. Most of these form the buried spine of each helix and play the same role as those in the cytokines. The others, and some spine residues bind the haem co-factor. (C) 2002 Elsevier Science Ltd. All rights reserved.