Computational protocol: Genome-wide identification of antimicrobial peptides in the liver fluke, Clonorchis sinensis

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Protocol publication

[…] AMP candidates were picked according to the previously observed physicochemical properties of reported AMPs. All of the protein-coding genes were calculated using EMBOSS PEPSTATS [] in terms of molecular weight (MW), number of residues (≤ 80-mer), pI (8 ≤ pI ≤ 12) [], and a net positive charge []. In vitro and in vivo aggregation levels were calculated with default parameters using TANGO (AGG ≤ 500, 0 ≤ HELIX ≤ 25, 25 ≤ BETA ≤ 100) [] and AGGRESCAN (-40 ≤ Na4vSS ≤ 60) [], respectively. The continuous sequence of residues in each AMP candidate was determined using AMPA []. These properties reflect the binding of AMPs to negatively charged microbial cell membranes, which results in bacterial cell death via a pore or carpet mechanism []. In order to exclude non-AMP candidates, all Clonorchis sinensis protein sequences were examined using the artificial neural network (ANN) algorithm of CAMP at the default value []. [...] To enhance in vivo stability, C. sinensis protein sequences that had proteolytic cleavage sites were excluded. Proteolytic cleavage sites were identified using PeptideCutter (http://web.expasy.org/peptide_cutter/) for chymotrypsin and EMBOSS EPESTFIND [] for PEST motifs, mainly enriched in proline (P), glutamic acid (E), serine (S), threonine (T). […]

Pipeline specifications

Software tools PeptideCutter, EMBOSS
Databases ExPASy
Application Protein sequence analysis
Organisms Fasciola hepatica, Clonorchis sinensis, Cyclina sinensis
Chemicals Adenosine Monophosphate