Enterotoxigenic escherichia coli bacteria are one of the major causes of diarrhea in developing countries, that causing deaths of hundreds of thousands of people annually.
some strains of enterotoxicogenic bacteria cause disease in livestock, especially in newborns, as a result, mortality of livestock and cause a lot of economic losses to the livestock breeder.
one of the most important pathogenic factors in enterotoxicogenic e. coli bacteria is colonization factors (binding factors).the colonization factors are often encoded by the plasmid. most etec bacterial binding factors are assembled through the chaperone-usher pathway and are exposed at the bacterial cell surface. examples of these factors in humans include: cfa / i, cs1 -7, cs10-12, cs14, cs17, cs18 and cs20 and in animals are f4 (or k88), f5 (k99), f6 (987p), f17 and f18 (4, 7-9)
due to the etec strains express one or more types of colonization factors at the cell surface, developing effective etec vaccines has encountered by some problems.
The fimbriaes’ data of enterotoxygenic e. coli were retrieved from different sources. then, the amino acid sequences of fimbriaes’ chaperones were extracted from the uniprot database.
the theoretical isoelectric point (pi) and the total number of positive and negative amino acids were calculated using the protparam analysis tool on expasy database.
phylogenetic trees were constructed based on the multiple alignments using treetop server.
3d models of these chaperones were modeled using the modeller 9 & 20 software. the the models were evaluated using procheck and prosa ii servers. the discovery studio software was used to visualize the 3d structures of models. the root-mean-square deviation (rmsd) was calculated using the swiss-pdb-viewer software.
the cons-ppisp server was applied for prediction of protein-protein interfaces.
Characterization of the physicochemical properties of proteins:
determining the physicochemical properties of proteins can be very useful for better understanding of proteins functions. according to table 1, it is seen that all proteins have a lower molecular weight and are not significantly different. it is also observed that the proteins have an isoelectric point higher than 8 which indicates their basic properties. investigation in the table 1 showed the overall positive charge of all proteins predominates over their negative charge.
following homology modeling process, the assessment of the quality of the predicted models are necessary. therefore, the quality of the predicted models were evaluated by the ramachandran plot in procheck program. the result showed that the number of residues in disallowed reagion was very low. also, the quality of the predicted structures was evaluated by the prosa software. the evidence of prosa server also suggest that all protein models are acceptable and of good quality.
the 3d structures (3d-structure) were visualized using the discovery studio software. the images, showed the alpha helix, beta plates and coils (fig. 1). these chaperones have very similar structure, displaying two domains which make a 45 angle relative to one another lending to the protein the shape of a boomerang with a cavity. the results of the analysis with the ppisp cons-server showed that the above-mentioned cavity are in contact with the major subunit of fimbriae.
phylogenetic analysis and structural comparisons of chaperones:
the phylogenetic study based on the sequence similarity suggests a close relationship between the animal and human chaperons’ etec
based on our previous experiences with the cs3-1, the comparison were done against cs3-1.the structure of each single chaperon was constructed with cs3-1 structure. the results of this comparison, shown as rmsd in table 1, which indicate the structural similarity of chaperones protein in different strains of enterotoxicogenic bacteria.
This study showed that the different fimbriaes’ chaperone have similar structures. therefore, it seems it is possible to inhibit several fimbriae assembly systems simultaneously inhibited with limited number of drugs and prevent their presentation at the bacterial cell surface.
Bacterial diarrhea, fimbriae and molecular modeling