Genome-wide identification and comparative analysis of coiled-coil proteins

The α-helical coiled-coil domain is a protein structure motif with a characteristic repeat pattern well suited for computer-based prediction. Long coiled-coil proteins play an important role in organizational and regulatory processes within cells and have been implicated in a number of human diseases. Knowledge about plant or prokaryotic long coiled-coil proteins however has been limited to a few isolated findings. For a more comprehensive overview of the occurrence of coiled-coil proteins, we have computationally identified and clustered long coiled-coil proteins from 23 fully-sequenced genomes. Our results indicate that long coiled-coil proteins occur with higher frequency in eukaryotes than prokaryotes, with kingdom-specific families observed in plants and animals. We have established searchable protein databases containing prediction data for Arabidopsis, rice and the green algae Chlamydomonas to facilitate further investigation of plant long coiled-coil proteins.