Amoebapore, a 77-residue peptide with pore-forming activity from the human pathogen Entamoeba histolytica, is implicated in the killing of phagocytosed bacteria and in the cytolytic reaction of the amoeba against host cells. Previously, we structurally and functionally characterized three amoebapore isoforms in E. histolytica but recognized only one homolog in the closely related but non-pathogenic species Entamoeba dispar. Here, we identified two novel amoebapore homologs from E. dispar by molecular cloning. Despite strong resemblance of the primary structures of the homologs, molecular modeling predicts a species-specific variance between the peptide structures. Parallel isolation from trophozoite extracts of the two species revealed a lower amount of pore-forming peptides in E. dispar and substantially higher activity of the major isoform from E. histolytica towards natural membranes than that from E. dispar. Differences in abundance and activity of the lytic polypeptides may have an impact on the pathogenicity of amoebae.

Consensus sequence patterns for beta-alpha-beta folds binding FAD, NAD and GTP were constructed on the basis of 11 steric and physicochemical properties. These property patterns permit detection and distinction of the respective nucleotide-binding sites on the basis of amino acid sequence analysis alone. The SWISS-PROT database (release 9) was screened with the three calculated patterns, and nucleotide-binding sites identified are presented. They correspond to existing structure data (if known). For the detected sequence segments we are able to predict the beta-alpha-beta motif as well as the respective binding sites. For some of the proteins so detected a nucleotide-binding capacity has not previously been reported.