Effect of HIV-1 subtype-specific Tat protein polymorphisms on Tat-TAR interaction

Alnara Zhamalbekova; Mahmoud A. A. Ibrahim; Peter A. Sidhom; Syed Hani Abidi

doi:10.1371/journal.pone.0346629

Peer Review History

Original SubmissionSeptember 16, 2025
20 Oct 2025 Decision Letter - Elisabetta Pilotti, Editor Dear Dr. Abidi, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. ============================== The writing is full of jargon that makes it difficult to go through the reading for those not expert of the topic and in particular of methods used. The study provides findings in contrast to or supporting previous ones. The authors largely discuss divergencies and similarities with previous results, losing sight of their key findings whose novelty needs to be highlighted. For this reason, I recommend trimming the discussion. The description of the results requires to be expanded and deepened. I also encourage the authors to address the concerns expressed by the reviewers, comprehensively, particularly when asked to provide additional data to support their conclusions. ============================== Please submit your revised manuscript by Dec 04 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.. 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Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.... We look forward to receiving your revised manuscript. Kind regards, Elisabetta Pilotti Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. 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If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 5. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: No ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.--> Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: The authors carried out a docking and molecular dynamic simulation of HIV Tat protein sequences from subtypes A, A1, A3, A6, B, C, D, CRF01_AE, and CRF02_A with TAR RNA to identify subtype-specific Tat protein polymorphisms. They found that the subtypes A6, C, and CRF02_AG showed higher affinity to TAR while subtypes A3 and A1 had the weakest binding affinity to TAR with a binding energy. The increased and decreased affinity of Tat protein towards the TAR element may be attributed to subtype-specific polymorphisms suggesting that subtype-specific polymorphisms can affect Tat- TAR interactions, allowing certain subtypes to interact much more strongly with TAR as compared to others. This finding may have implications for subtype-specific disease pathogenesis mediated by the Tat protein. However, i have few questions, 1. Have you validated subtype-specific Tat protein polymorphisms on functional cell line based assays? please refer and cite to this paper : PMID: 24465566, PMID: 28484443, PMID: 28468838 and PMID: 31652847. 2. Have you tested subtype-specific other viral genes like VIf protein polymorphisms ? please refer and cite to this paper : PMID: 264941093. does the subtype-specific Tat protein polymorphisms have any effort on host genes like CCR5? please refer and cite to this paper :PMID: 31110236 Reviewer #2: Zhamalbekova et al. present a manuscript to study the variations in HIV Tat and how 3D structures prediction, molecular docking, and molecular dynamics work. However, this study explored Tat polymorphisms and not TAR polymorphisms. Overall, the studies were performed mostly in silico, but there is a highly amount of discrepancy with previously published analyses. I believe this study should be rejected. Major concerns: (i) A substantial body of literature exists regarding the role of the Tat-TAR axis in HIV. For instance, it demonstrates that Tat is both necessary and sufficient for HIV activity, particularly in the context of establishing and reversing latency through TAR mutations. It seems unlikely that the authors intended to overlook this prior research; discussing these earlier studies would provide important context for their results. (ii) The authors should clarify whether the TAR sequences differ among the HIV subtypes they examined. (iii) It is important to consider the disease stage of the subtypes when modeling the predictions and structures. (iv) A 200 ns molecular dynamics run may not adequately capture all relevant long-timescale conformational changes. (v) Generating consensus sequences might overlook intra-subtype diversity and rare but functionally significant variants. (vi) While the authors acknowledge their limitations in the discussion, it should be emphasized that all findings are based on in silico analyses, which can restrict direct biological or clinical relevance. They should clearly indicate that these results are predictions that require further validation. ****** what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? 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If this link does not appear, there are no attachment files.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. https://doi.org/10.1371/journal.pone.0346629.r001
Revision 1
19 Mar 2026 Author Response Response to the Reviewers' Comments: The authors would like to thank the Reviewers for their time and effort in reviewing our manuscript. The authors sincerely appreciate all the valuable comments and suggestions, which helped us to improve the quality of the manuscript. We have tried our best to address all comments and suggestions. The reply to each comment is given below, while the changes have been highlighted in yellow in the manuscript. Reviewer 1 Comment #1: Have you validated subtype-specific Tat protein polymorphisms on functional cell line based assays? please refer and cite to this paper : PMID: 24465566, PMID: 28484443, PMID: 28468838 and PMID: 31652847. Reply: We thank the reviewer for pointing out the issue about the functional validation of Tat polymorphisms. In our paper, we have incorporated findings from PMID: 28484443, PMID: 24465566, PMID: 28468838, and PMID: 31652847. Please see lines can be checked in lines 376-399. Comment #2: Have you tested subtype-specific other viral genes like VIf protein polymorphisms ? please refer and cite to this paper : PMID: 26494109. does the subtype-specific Tat protein polymorphisms have any effort on host genes like CCR5? please refer and cite to this paper :PMID: 31110236 Reply: We thank the reviewer for suggesting these papers! As suggested, we have incorporated the findings from PMID: 31110236 and PMID: 26494109. Please see lines 92-96 and 376-380. Reviewer 2: Comment #1: A substantial body of literature exists regarding the role of the Tat-TAR axis in HIV. For instance, it demonstrates that Tat is both necessary and sufficient for HIV activity, particularly in the context of establishing and reversing latency through TAR mutations. It seems unlikely that the authors intended to overlook this prior research; discussing these earlier studies would provide important context for their results. Reply: We thank the reviewer for the comment, and we agree that discussing the role of the Tat-TAR axis in latency provides important context for our findings. Thus, we have addressed this point in the revised manuscript, lines 128-136. We have reviewed key studies demonstrating Tat's role in establishing and reversing viral latency. We believe that the impact of genetic variations in Tat across subtypes (aim of our paper) beyond B and C on the Tat-TAR interaction remains underexplored. Comment #2: The authors should clarify whether the TAR sequences differ among the HIV subtypes they examined. Reply: We used a single and highly conserved TAR sequence across all subtypes analysis to ensure that observed differences in binding were attributable specifically to Tat protein polymorphisms. Please see lines 178-180. Comment #3: It is important to consider the disease stage of the subtypes when modeling the predictions and structures. Reply: We thank the reviewer for raising this point. We completely agree that disease stage is a critical factor when interpreting functional consequences of Tat polymorphisms. In the revised manuscript, we have accounted for disease stage by stratifying comparisons into acute, chronic, and AIDS stages for each subtype. We observed that different HIV-1 subtypes accumulate distinct polymorphisms as the disease progresses, as summarized in Table 2 and in the discussion section. Please see Table 2 and lines 437-442. Comment #4: A 200 ns molecular dynamics run may not adequately capture all relevant long-timescale conformational changes. Reply: We thank the reviewer for his valuable comment. While 200 ns molecular dynamics simulations are commonly sufficient to capture the equilibration and stability of protein-RNA complexes, the authors agree that longer simulations can further validate the robustness of the observed trends. Therefore, the authors performed extended molecular dynamics simulations of 500 ns for two representative systems: the A6-TAR complex (strongest binding) and the A1-TAR complex (weakest binding). The extended trajectories exhibited stable RMSD profiles and consistent MM-GBSA binding energies (ΔGbinding = −140.6 kcal/mol for A6-TAR and −73.4 kcal/mol for A1-TAR), in agreement with the trends observed in the 200 ns MDS. These results confirmed that the conclusions derived from the 200 ns trajectories remain valid. Please see figure S2, and lines 218-223, 290-295, and 314-318. Comment #5: Generating consensus sequences might overlook intra-subtype diversity and rare but functionally significant variants. Reply: We acknowledge that the consensus-sequence approach can mask specific mutations within a single subtype. To address this concern, we have built out a consensus using a threshold of more than 50% amino acid frequency at each position. We found that a substantial sequence conservation across all 9 subtypes: 90% of amino acid residues met the 50% threshold, ranging from 60-95%. The remaining amino acid residues (10%) exhibited variability, but none of these polymorphic sites corresponded to previously investigated polymorphisms that influence Tat-TAR binding affinity. Please see lines 158-165. Comment #6: While the authors acknowledge their limitations in the discussion, it should be emphasized that all findings are based on in silico analyses, which can restrict direct biological or clinical relevance. They should clearly indicate that these results are predictions that require further validation. Reply: We thank the reviewer for this important clarification. We agree that our study needs experimental validation. Accordingly, we have expanded the limitations section to address this point. Please see lines 453-458. Attachments Attachment Submitted filename: Response_R4.docx https://doi.org/10.1371/journal.pone.0346629.r002
22 Mar 2026 Decision Letter - Elisabetta Pilotti, Editor Effect of HIV-1 subtype-specific Tat protein polymorphisms on Tat-TAR interaction PONE-D-25-50484R1 Dear Dr. Abidi, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support.... If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Elisabetta Pilotti Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0346629.r003
Formally Accepted
Acceptance Letter - Elisabetta Pilotti, Editor PONE-D-25-50484R1 PLOS One Dear Dr. Abidi, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Elisabetta Pilotti Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0346629.r004

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