Bioinformatics analysis of the antigenic epitopes of L7/L12 protein in the B- and T-cells active against Brucella melitensis
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Abstract
The objective is to analyse the physicochemical properties, spatial structure and protein–protein interactions (PPIs) of L7/L12 protein using bioinformatics methods and predict their B- and T-cell epitopes to lay a theoretical foundation for developing a novel multiepitope vaccine (MEV). The National Center for Biotechnology Information (NCBI) database was searched for the amino acid sequences of L7/L12 from Brucella melitensis . In addition, the online softwares, ProtParam and ProtScale, were used to predict the physicochemical properties: NetPhos3.1 and CD-search to predict the phosphorylation sites and conserved domains; SOMPA and SWISS-MODEL to predict the secondary and tertiary structures; the STRING database to analyse the PPIs; and the IEDB, ABCpred, SVMTrip and SYFPEITHI databases to predict the B- and T-cell epitopes. L7/L12 was docked to Toll-like receptor 4 (TLR4), B-cell receptor (BCR), Major histocompatibility complex I-T cell receptor (MHC I-TCR) and MHC II-TCR complexes, respectively, and the binding ability of L7/L12 to the targeted receptors was tested. L7/L12, consisting of 124 amino acids, was determined to be a stable, intracellular, hydrophilic protein containing 6 phosphorylation sites and ribosomal protein-related conserved domains. α-helices accounted for 70.16 %, β-turns for 2.42 %, extended strands for 8.87 % and irregular coils for 18.55 % of the secondary structure. The PPIs indicated that L7/L12 was involved in the constitution of ribosomes and regulating the accuracy of the translation process. Three B-cells, two cytotoxic T lymphocytes and three helper T lymphocyte epitopes were finally screened by comparing multiple databases. L7/L12 binds to TLR4, BCR, MHC I-TCR and MHC II-TCR complexes and forms stable hydrogen bonds, respectively. L7/L12, which governs the translation curate of proteins, possesses several potentially advantageous epitopes, laying a theoretical foundation for designing MEVs.
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I am pleased to tell you that your article has now been accepted for publication in Access Microbiology. Thank you for the thorough revision in response to reviewer comments.
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The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
The article is a solid presentation and discussion of the use of some online tools to inform the development of vaccines, particularly for Brucella melitensis. The article discusses some of the online tools available for the purposes stated and discusses some of the implications of this in vaccine development. Overall, the article is of interest, but needs editing and some of the figures are unnecessary. Some points to address (but there are others). Line 39-43 - Strangely phrased paragraph needs amending. Fig #1 - AA Sequence NOT Figure worthy needs more or to be removed. Line 92 - Need to state why these particular MHC alleles were selected. Line 103 - PRIMARY structure is simply downloaded from NCBI NOT predicted using PortParam. Fig #2 - Unnecessary does not show anything novel? Fig #4 - …
Comments to Author
The article is a solid presentation and discussion of the use of some online tools to inform the development of vaccines, particularly for Brucella melitensis. The article discusses some of the online tools available for the purposes stated and discusses some of the implications of this in vaccine development. Overall, the article is of interest, but needs editing and some of the figures are unnecessary. Some points to address (but there are others). Line 39-43 - Strangely phrased paragraph needs amending. Fig #1 - AA Sequence NOT Figure worthy needs more or to be removed. Line 92 - Need to state why these particular MHC alleles were selected. Line 103 - PRIMARY structure is simply downloaded from NCBI NOT predicted using PortParam. Fig #2 - Unnecessary does not show anything novel? Fig #4 - Unnecessary, what does this show? Table 4,5,6 - Need attention & formatting. Line 178 - "severely Pathogenic" is strange phrasing and the whole sentence needs attention. Line 180-182 - Sentence needs work, does not make sense. Line 187-184 - Sentence does not make sense. Line 189 - "Bottoms up" should read "Bottom up". Line 191 - "Therefore" not explained, why does one point lead to the next? Paragraph line 197-206 - Feels like a restatement of results with no discussion.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
Zhang et.al study evaluates the physicochemical and immunological properties of L7/L12 protein of Brucella melitensis by in Silico methods. I have suggested the following modifications for further consideration of the manuscript which are mandatory for the improvement of the manuscript. 1. Docking and molecular dynamics with human immune system proteins such as toll like receptors should be performed. 2. Blast of L7/L12 should be performed in all human pathogenic species. 3. The reaction of the host's body after injection of the protein should be checked with c-immsim server. 4. Protein expression in appropriate prokaryotic and eukaryotic expression systems should be investigated by in silico methods. 5. Allergenicity and cytotoxicity of protein should be evaluated using in silico methods. 6. In the …
Comments to Author
Zhang et.al study evaluates the physicochemical and immunological properties of L7/L12 protein of Brucella melitensis by in Silico methods. I have suggested the following modifications for further consideration of the manuscript which are mandatory for the improvement of the manuscript. 1. Docking and molecular dynamics with human immune system proteins such as toll like receptors should be performed. 2. Blast of L7/L12 should be performed in all human pathogenic species. 3. The reaction of the host's body after injection of the protein should be checked with c-immsim server. 4. Protein expression in appropriate prokaryotic and eukaryotic expression systems should be investigated by in silico methods. 5. Allergenicity and cytotoxicity of protein should be evaluated using in silico methods. 6. In the discussion section, the previous articles that have evaluated this issue should be mentioned and the difference between the current study and previous studies be said. 7. Experimental evaluation needs to confirm the results.
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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