Antigenicity analysis of Ebola Group Project
I Noshaba Bakht colloborated with Xi Wang and Sai Krishna .
We selected three patients from the Bio project with the I.D # KM 233115.1, KM 233091.1, KM 233042.1 from Zaire ebolavirus sample sequencing from the 2014 outbreak in Sierra Leone, West Africa.
I analyzed the VP-30 gene, Xi Wang analyzed VP-24 and Sai Krishna analyzed VP-40 in IEDB and DNASTAR.
http://www.saikirshnacb.blogspot.com
http://www.missxiwangbioinformatics.wordpress.com
I analyzed the VP-30 gene, Xi Wang analyzed VP-24 and Sai Krishna analyzed VP-40 in IEDB and DNASTAR.
http://www.saikirshnacb.blogspot.com
http://www.missxiwangbioinformatics.wordpress.com
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| The Three patients |
I selected VP-30 gene from the three patients Ebola Virus sequence and did analysis in the DNASTAR and IEDB.
IEDB the Immune Epitope database prediction tools are used to detect the T Cell Epitopes and for MHC Binding Prediction.
Peptide binding to MHC class I molecules take in an amino acid sequence, or set
of sequences and determine each subsequence's ability to bind to a specific MHC
class I molecule. These tools predict IC50 values for peptides binding to specific MHC molecules. Binding to MHC is necessary but not sufficient for recognition by T cells.
I analysed the T cell Epitope affinity for the three patients in the following way.
- Individually and
- Collectively.
- For all the frequently occurring alleles:
- For the 05 Alleles HLA-A*01:01, HLA-B*07:02, HLA-C*01:02, HLA-E*01:01, HLA-G*01:01.
The VP-30 is a gene consisting of nucleotide 8464..9330 and 288 amino acids.
The notepad description of the VP-30 for the three patients with their outputs for all the alleles.
The notepad description of the VP-30 for the three patients with their outputs for all the alleles.
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| Three-vp-30-sequences-and the output of-all-alleles-format |
Individual Analysis:
I.D # KM 233115.1.
For all the Alleles; The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03
For all the Alleles; The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03
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| KM 233115.1-ALL-Alleles |
The analysis for the 05 alleles: HLA-A*01:01, HLA-B*07:02, HLA-C*01:02, HLA-E*01:01, HLA-G*01:01. The allele " HLA-B*07:02" of 10 peptide length with the sequence of "RPRAARQHSR" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.25" and Ann IC(50nm) score 34 and Smm IC (50nm) score 25.28.
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| KM233115.1-05-Alleles |
I.D # KM 2330421.1
For all the Alleles; The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03
For all the Alleles; The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03
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| KM233042-AllAlleles |
Analysis of 05 Alleles:The allele " HLA-B*07:02" of 10 peptide length with the sequence of "RPRAARQHSR" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.25" and Ann IC(50nm) score 34 and Smm IC (50nm) score 25.28.
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| KM233042.1-05Alleles |
I.D # KM 233091.1
For all the Alleles; The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03
For all the Alleles; The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03
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| KM233091-AllAlleles |
Analysis of 05 Alleles:The allele " HLA-B*07:02" of 10 peptide length with the sequence of "RPRAARQHSR" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.25" and Ann IC(50nm) score 34 and Smm IC (50nm) score 25.28.
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| KM233091-05Alleles |
The allele " HLA-B*07:02" of 10 peptide length with the sequence of "RPRAARQHSR" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.25" and Ann IC(50nm) score 34 and Smm IC (50nm) score 25.28.
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| KM2330-115-042-091-05Alleles |
I analyzed the VP-30 of the three patients in the IEDB
for all the alleles.
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| KM2330-115-042-091-Alleles |
The result of analysis of the all-alleles showed :
The allele " HLA-B*44:02" of 10 peptide length with the sequence of "FEAALWQQW" analysed via the method "Consensus (ann/smm)" had the lowest percentile rank of "0.1" and Ann IC(50nm) score 13 and Smm IC (50nm) score 20.03 had the highest T-cell antigenicity.
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| Three-vp-30-sequences-fasta-format |
The VP-30 gene analysis via the DNASTAR software for the presence of T-cell epitopes.
Brief description of three Algorithms from the help section of DNASTAR is as following.
T-Cell Epitopes – AMPHI
The T-Cell Epitopes – AMPHI method uses the model of Margalit and Berzofsky (1987) to predict
immunodominant helper T-lymphocyte antigenic sites from primary sequence data. The underlying assumption of the AMPHI method is that T-cell antigenic sites are composed of amphipathic helices. The method is useful only for T-cell epitopes and not B-cell epitopes (the latter normally requires greater knowledge of the tertiary structure of the binding site).
Method results is displayed as a hydrophobicity graph, an AMPHI region graph, an alpha-helix graph, a 3-10 helix graph (scaled for the amphipathic index) and/or an AMPHI intensity graph.
MHC II Epitopes (Sette)
The MHC II Epitopes (Sette) method predicts peptide antigenic sites which interact with mouse MHC II haplotype d proteins. There are separate motifs for IAd and IEd haplotypes, and Sette et al. (1989) reports that this method finds more than 75% of known epitope sites for each. It can be used to design peptide epitopes when used in conjunction with the T-Cell Epitopes – AMPHI and the T-Cell Epitopes – Rothbard-Taylor methods.
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| KM233115-vp30-Rothbard-Taylor-AMPHI-SETTE |
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| KM233042-vp30-Rothbard-Taylor-AMPHI-SETTE |
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| KM233091-vp30-Rothbard-Taylor-AMPHI-SETTE |
T-Cell Epitopes – Rothbard-Taylor
The T-Cell Epitopes – Rothbard-Taylor method locates potential T-lymphocyte antigenic determinants which contain a common sequence motif. Although Rothbard and Taylor (1988) found that the method predicted 80% of the antigenic determinants for their peptide database, the presence or absence of the motif is not sufficient to guarantee antigenicity. The method is useful only for T-cell epitopes and not B-cell epitopes, which often require greater knowledge of the tertiary structure of the binding site. This method is used in combination with the T-Cell Epitopes – AMPHI and the MHC II Epitopes (Sette) methods for best results.
The window described by the Rothbard-Taylor method was as following.
Window size 04:
The amino acids Were "RAAR"
R = Arginine a Positive basic Charged amino acid.
A= Alanine a tiny Hydrophibic amino acid.
A= Alanine a tiny Hydrophibic amino acid.
R= Arginine a Positive basic Charged amino acid.
The analysis of all the three variants is the three patients showed similar patterns of T-cell antigenecity when described by the AMPHI, SETTE and Rothbard-Taylor algorithms.
Conclusion:The analysis of all the three variants is the three patients showed similar patterns of T-cell antigenecity when described by the AMPHI, SETTE and Rothbard-Taylor algorithms.
Regarding the T cell antigenic determination there is no difference in the three patients with VP-30 gene.
Xi and Sai conculded that the gene VP-24 and VP-40 T cell antigenic determination is also of the same magnitude.
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