Journal of Proteomics & Bioinformatics
Open Access

Abstract

Helical Parameters and Correlations of Tandem Leucine Rich Repeats in Proteins

Purevjav Enkhbayar, Hiroki Miyashita, Robert H Kretsinger and Norio Matsushima

Leucine rich repeats (LRRs) are present in over 20,000 proteins from viruses to eukaryotes. Most LRR units are 20-30 residues long and can be divided into a highly conserved segment and a variable segment. Eight classes have been recognized. Two to sixty-two units occur in tandem to form an LRR structure. The tertiary structures of these LRRs are helical, in which the β-strands of the highly conserved segments stack in parallel. This helix consists of a super helical arrangement of repeating structural units. We call it a coil of solenoids. We have used our program HELFIT to assign helical parameters to 642 LRRs of known structures of 114 proteins. We report these parameters and their correlations with eight classes of LRR, with the number of repeat units in the LRR, with oligomerization, and with ligand state of the LRR. The helical parameters of the eight LRR classes frequently overlap one another. However, the constant distance between parallel β-strands is the primary determinant of the helical parameters of the LRRs. When the repeat number, n, in LRRs is small, the LRR structures are more variable and, by inference, more flexible. In the LRRs with n ≥ 10, Δz (the rise per repeat unit) of the “RI-like” and “Cysteine-containing” classes is smaller than those of “SDS22-like”, and “Plant-specific” classes, This difference is ascribed mainly to the difference in the structural units. The helical parameters of the LRRs unambiguously describe both right handed and left handed helices, helical dimers, and subdomains if they exist. Moreover, the helical parameters sensitively detect structural changes induced by protein, protein interactions, glycosylation, and/or mutation.