Im currently working on a methicillin-resistant Staphylococcus aureus whole genome based in silico vaccine. I finished the reverse vaccinology steps and I filtered 27 protein candidates out of 2748 proteins to construct the vaccine. My question is on what basic should I choose the proper proteins to start the steps of b cell or t cell epitopes?! Is there any guidline or a protocol for choosing the proper protein candidates for the vaccine design or should I work independently for all the 27 proteins?
According to the literature, it was found that after filtration according to the genome annotations using Rast (https://rast.nmpdr.org/rast.cgi) to recognise the virulent factors responsible for diseases as the first step.
Then to align the annotated genome/proteome to the human "homo-sapien" genome/proteome using blastp tool of ncbi (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) using the output in a fasta format to determine homologous and non-homologous proteins and to exclude homologous proteins to the human proteome.
Then to exclude proteins with transmembrane helices more than one using (https://services.healthtech.dtu.dk/services/TMHMM-2.0/).
Furthermore we used protoparam tool to check for protein physical and chemical characteristics important for vaccine or drug design as (protein stability, Molecular weight) . (https://web.expasy.org/protparam/). We excluded all unstable proteins "those with instability index >40, and those with molecular weight >110 Kda. Then we addressed the antigenicity of proteins using vaxijen 2.0
(http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) the threshold used was 0.4 all non-probable antigens were excluded.
Then the corner stone of the question is how to further address the rest of proteins?
To identify essential genes, proteome using geptop (http://guolab.whu.edu.cn/geptop/) , and to exclude non-essential genes. The yield is a target for vaccine and drug design. Lastly to differentiate between vaccine and drug targets, it is important to localise protein functions subcellularly using PSORTb software (https://www.psort.org/psortb/)
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