3D circle fitting of leucine-rich repeat proteins

Purevjav Enkhbayar1, Norio Matsushima2, Mitsuru Osaki
1penkh@chem.agr.hokudai.ac.jp, Hokkaido University; 2matusima@sapmed.ac.jp, Sapporo Medical University

Leucine-rich repeat (LRR)-containing proteins are present in over 2000 proteins from viruses to eukaryotes. Most of LRRs are 20-30 amino acids long and the repeat number ranges from 2 to 42. The known structures of thirteen LRR proteins with 4 to 17 repeats have revealed that the LRR domains fold into a horseshoe shape (or an arc shape) with a parallel ?-sheet on the concave face and with various secondary structures including ?-helix, 310-helix, and polyproline II (pII) helix on the convex face. We developed least-squares method of three dimensional (3D) circle fitting using atomic coordinate in order to characterize quantitatively the LRR arc shape. The analysis results indicate that there is a regular relationship between the radius of the LRR arc and the rotation angle about the central axis of the arc per repeating unit. The radius of the LRR arc with ?-? structural units was smaller than those with ?-310 or ?-pII units.