Additional file 1 of Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains
Creators: name: Shafaghi, Mona
name: Bahadori, Zohreh
name: Madanchi, Hamid
name: Ranjbar, Mohammad Mehdi
name: Shabani, Ali Akbar
name: Mousavi, Seyed Fazlollah
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Table S1. Protein sequences of PspA1-5 (clades 1 to 5), PhtD and Ply. A region of PspA clade 2, B and C region of PspA clades 1 to 5 are underlined and shown in blue, red and green color, respectively. The C-terminal of PhtD (amino acid 383 to 853) and domain 4 of Ply (amino acid 360 to 471) are shown in color and underlined. In Ply4, the amino acids D385, C428 and W433, which must be replaced with N, G and F, respectively, are presented in blue color. Signal peptide is represented in lowercase italics. Table S2. The predicted B cell epitopes of A region of PspA2. Table S3. The predicted B cell epitopes of B region of PspA1. Table S4. The predicted B cell epitopes of B region of PspA2. Table S5. The predicted B cell epitopes of B region of PspA3. Table S6. The predicted B cell epitopes of B region of PspA4. Table S7. The predicted B cell epitopes of B region of PspA5. Table S8. The experimentally verified B cell epitopes from C region of PspAs. Table S9. The predicted linear B cell epitopes of PhtD-C. Table S10. The predicted discontinuous B cell epitopes of PhtD-C. Table S11. Prediction of MHC-II epitopes of PspA2-A and PspA1-5-B. The peptides with IEDB percentile rank &lt;10.0 and NetMHCIIpan rank value &lt;1.0 were considered for the next analysis. Table S12. Prediction of MHC-II epitopes of PhtD-C. The epitopes with IEDB percentile rank &lt;10.0 and NetMHCIIpan rank value &lt;1.0 were considered for the further analysis. Figure S1. Domain structure of PspA protein. Major domains of PspA are α-helical charged domain (amino acids 1-288) consisting of A, Aˊ and B regions, proline-rich domain (amino acids 289-370, C region), and choline-binding domain (amino acids 371-571). Within the α-HD, region B is a clade-defining region of the PspA molecule, which is represented by the stippled box. Figure S2. The results of transmembrane helices prediction. A and B show the prediction results of transmembrane helices in PspA2 and PhtD-C, respectively. The pink lines indicate the domains facing outside. Figure S3. The 3D models of PspA2 and PhtD-C. The predicted and refined 3D structures were visualized by the Discovery Studio Visualizer. Figure S4. The validation of refined model of PspA2 (A) and PhtD-C (B) with PROCHECK and ERRAT. Ramachandran plot of the structure of PspA2 or PhtD-C represents 82.1% or 87.2% residues in favored regions, respectively. In the ERRAT plot, the overall quality factor of structure of PspA2 or PhtD-C is 88.69% or 85.23%, respectively. Figure S5. The 3D models of B regions of PspA1-5. The homology modeled structures of B regions of PspA clades 1 to 5 (B1 to 5, respectively) visualized by Discovery Studio Visualizer. Figure S6. Codon optimization results of the designed construct. Codon optimization was performed using JCAT and codons were adapted for efficient expression in E.coli K12. The CAI index and GC content of the optimized sequence were 0.99 and 53.27%, respectively.