Polyproline II Helix as a Recognition Motif of Plant Peptide Hormones and Flagellin Peptide flg22

Background: Plant peptide hormones play a crucial role in plant growth and development. A group of these peptide hormones are signaling peptides with 5 - 23 amino acids. Flagellin peptide (flg22) also elicits an immune response in plants. The functions are expressed through recognition of the peptide hormones and flg22. This recognition relies on membrane localized receptor kinases with extracellular leucine rich repeats (LRR-RKs). The structures of plant peptide hormones - AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of flg22 complexed with LRR domains of corresponding LRR-RKs and co-receptors SERKs have been determined. However, their structures are well not analyzed and characterized in detail. The structures of PIP, CEP, CIF, and HypSys are still unknown. Objective: Our motivation is to clarify structural features of these plant, small peptides and Flg22 in their bound states. Methods: In this article, we performed secondary structure assignments and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness) based on the atomic coordinates from the crystal structures of AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of flg22. We also performed sequence analysis of the families of PIP, CEP, CIF, and HypSys in order to predict their secondary structures. Results: Following AtPep1 with 23 residues adopts two left handed polyproline helices (PPIIs) with six and four residues. IDA, IDL1, RGFs 1 - 2, and TDIF/CLE41 with 12 or 13 residues adopt a four residue PPII; RGF3 adopts two PPIIs with four residues. Flg22 with 22 residues also adopts a six residue PPII. The other peptide hormones – PIP, CEP, CIF, and HypSys – that are rich in proline or hydroxyproline presumably prefer PPII. Conclusion: The present analysis indicates that PPII helix in the plant small peptide hormones and in flg22 is crucial for recognition of the LRR domains in receptors.