ANTIGENICITY OF EBOLA VIRUS VP40 PROTEIN

EBOLA VIRUS

• Ebola, is a disease of humans and other primates caused by Ebola virus. Ebola virus disease (EVD), formerly known as Ebola haemorrhagic fever, is a severe, often fatal illness in humans. 
• The virus is transmitted to people from wild animals and spreads in the human population through human-to-human transmission.

TRANSMISSION

• It is thought that fruit bats of the Pteropodidae family are natural Ebola virus hosts. Ebola is introduced into the human population through close contact with the blood, secretions, organs or other bodily fluids of infected animals such as chimpanzees, gorillas, fruit bats, monkeys, forest antelope and porcupines found ill or dead or in the rainforest. 

VIROLOGY

• Ebolaviruses contain single-stranded, non-infectious RNA genomes. Ebolavirus genomes are approximately 19 kilo base pairs long and contain seven genes in the order 3 UTR-NP-VP35-VP40-GP-VP30-VP24-L-5 UTR.The genomes of the five different ebolaviruses (BDBV, EBOV, RESTV, SUDV and TAFV) differ in sequence and the number and location of gene overlaps. As all filo viruses ebola virions are filamentous particles that may appear in the shape of a shepherd's crook, of a "U" or of a "6," and they may be coiled, toroid or branched. In general, ebolavirions are 80 nanometers (nm) in width and may be as long as 14,000nm.
• In this present blog my emphasis is on VP40 gene of ebolavirus and would like to describe ANTIGENICITY of its protein.  

 STRUCTURE OF EBOLA VP-40 PROTEIN

  

•  Fig Represents 3D Structure of VP-40 protein obtained from PDB Database

FUNCTION

• Promotes virus assembly and budding by interacting with host proteins of the multivesicular body pathway. May facilitate virus budding by interacting with the nucleocapsid and the plasma membrane. 
• Specific interactions with membrane-associated GP and VP24 during the budding process may also occur. The hexamer form seems to be involved in budding.
•  The octamer form binds RNA, and may play a role in genome replication.

 ANTIGENICITY

• Antigenicity is the capacity of a chemical structure (either an antigen or Hapten) to bind specifically with a group of certain products that have adaptive immunity: T cell receptors or antibodies (a.k.a. B cell receptors).
• We can determine antigenicity is a protein sequence in protein sequence using DNA STAR using PROTEAN 3D module.
• We perform this experiment using DNA STAR and we obtain regions in the protein showing high level of antigenicity.
• We can even obtain the B-cell epitope, MHC II epitopes and T cell epitopes.

Fig Represents the output of antigenicity obtained from DNASTAR

Fig Represents the epitope predicted by DNASTAR

• The above figure represents the regions in the protein sequence which exhibits antigenicity. The above mentioned protein is obtained from patient.
• This is done by using NCBI BIO PROJECT module were we can find information regarding the  ebolavirus and its outbreaks on some patients.
•  For the T-cell epitope prediction DNASTAR uses Roth bard-Taylor algorithm which uses amino acid window of 4 or 5 and this predicts the epitopes.
• The epitopes should be int he following re-occurring pattern
• If there are four AA then it should have charged/P, hydrophobic, hydrophobic and polar/G.
• In the above example we could see that there are four amino acids in the figure which are selected G,A,L,R which follows the above mentioned pattern.

IEDB T-CELL EPITOPE PREDICTION

• Every patient has an ID so we obtained a patient with a particular ID KM233090.1 then we analyze VP40 protein.
• We obtain the sequence of VP40 sequence from particular patient then we try to obtain the epitopes from IEDB for one particular HLA allele.
• In this case I choose HLA-A*01 allele for a 9 AA length epitope to be predicted. We can determine epitope to be a good binder if it has low percentile score.
• So by this procedure I found that epitope "WTDDTPTGS" with percentile rank of 0.9.
• The best peptide binder would be the one with the least percentile rank.