Computational protocol: Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against Corynebacterium pseudotuberculosis

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Protocol publication

[…] Initially, the endoglycosidase Corynebacterium (CP40) (accession number GenBank NC_017730.1), as a component of the virulence factors of C pseudotuberculosis and presenting an immune profile previously reported, was used to map epitopes of immunodominant B cells using BepiPred software which is based on propensity scale methods (http://www.cbs.dtu.dk/services/BepiPred/). Furthermore, ABCPred, based on learning methods of the machine, applies recurrent neural network (http://www.imtech.res.in/raghava/abcpred), and BCPreds, which are also based on the learning ability of the machine, applies to support vector machines (http://ailab.cs.iastate.edu/bcpreds/) and the Immune Epitope Database and Analysis Resource (IEDB) (http://www.iedb.org/). The epitopes were predicted in different major histocompatibility complex (MHC) class II alleles (Iab, Iad, Ias, Ied, and Ies). [...] To analyze allergenic of the selected targets, software AlgPred (http://www.imtech.res.in/raghava/algpred/index.html) was used. The server executes prediction based on 6 different approaches. Combinations of the 6 approaches can be used to predict the allergenic proteins with high precision. [...] To verify antigenicity of the proteins and the peptides predicted by the tools, 2 software were applied. The VaxiJen v2.0 software (available at http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) works based on independent alignment prediction of protective antigens. This software was developed to allow antigen classification based solely on the physical-chemical properties of the proteins without considering the sequence alignment. The server precision varies from 70% to 89% based on the target organism. The other tool used was ANTIGENpro (available at http://scratch.proteomics.ics.uci.edu/). The server is an independent free alignment predictor based on the sequence of 5 pathogens, which predict antigenicity based on the results obtained from the protein data by microarray. [...] For the determination of tridimensional protein structure, 2 software were used: the 3Dpro (http://scratch.proteomics.ics.uci.edu) and the Galaxy TBM (http://galaxy.seoklab.org/index.html). 3Dpro uses predicted structural features, and the APB knowledge is based on statistic data considering energy. The conformational research uses a set of movements consisting on fragment substitution (using a fragment library built from the Protein Data Bank [PDB]), as well as random disturbance for the model. The Galaxy TBM develops modeling based on 2 stages. On the first stage, the more reliable structures are created selecting models that are aligned with the PROMALS3D and MODELLERCSA models. In the second stage, the loop areas or less reliable areas (called ULR, nonreliable local areas) are detected and remodeled using a refining method based on optimizations. [...] The refinement process was performed using a selected model by the 3Dpro and introduced in the server GalaxyRefine (http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE) to refine the entire protein, using the mild and aggressive relaxation methods. [...] To identify the possible error in the 3-dimensional (3D) structures predicted, the ProSA-web server and the Ramachandran validation were used. The ProSA-web calculates the general quality score for a 3D structure. If the calculated scores are outside the natural protein range, an error in the predicted structure is indicated. The Ramachandran validation is based on estimation of torsion angles for each residue in the structure, and these residues are classified as favorable, allowed, and isolated. [...] To verify the anchoring between the protein and the toll-like receptor type 2 (TLR2) the SwarmDock software (http://bmm.crick.ac.uk/~SwarmDock/index.html) was used. This software uses a flexible protein-protein complex model. The server is divided into the following stages:Entrance structure minimization and preprocessing.Docking using a hybrid particle swam optimization/local research.Minimization, reclassification, and anchored pose grouping.The preprocessing stage involves the disordered bond mending, modeling absent atoms, posttransduction modifications, and using the CHARMM mechanics after minimizing the entrance structures. [...] Seeking to verify the interaction between the predicted peptides and the design of an efficient vaccine, it was necessary to identify the peptides that present interactions with the TLR2 receptor. Therefore, the GalaxyPepDock was used, which predicts the protein-peptide complex structures and uses the 3D structure of the receptor and the peptide sequence combining information of the similar interactions found in the structure and optimization data based on energy (). […]

Pipeline specifications

Software tools PROMALS3D, GalaxyRefine, ProSA-web
Applications Protein structure analysis, Amino acid sequence alignment
Organisms Corynebacterium pseudotuberculosis, Escherichia coli, Ovis aries, Capra hircus
Chemicals Amino Acids