Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study

Uttam Kumar Jana; Gagandeep Singh; Hemant Soni; Brett Pletschke; Naveen Kango

doi:10.1371/journal.pone.0268333

Peer Review History

Original SubmissionNovember 29, 2021
17 Jan 2022 Decision Letter - Sabato D'Auria, Editor PONE-D-21-37808Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation studyPLOS ONE Dear Dr. Kango, 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.Please ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact. Please submit your revised manuscript by Mar 03 2022 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. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. 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, Sabato D'Auria Academic Editor PLOS ONE Journal 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. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files. 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: (Author UKJ is grateful to ICMR, New Delhi for providing financial assistance as Senior Research Fellow. Authors thank Sophisticated Instrumentation Centre (SIC), Dr. Harisingh Gour Vishwavidyalaya, Sagar and DST PURSE (II) scheme for instrumentation facilities and financial support. Authors acknowledge the HPC facility of Indian Institute of Technology, Delhi for providing the computational resources for running the MD simulations.) We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: (The author(s) received no specific funding for this work.) Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes ****** 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. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: No ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript by Naveen Kango et al. entitled “Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study” reports an in-silico approach to study structural and functional aspects of an Aspergillus oryzae β- mannanase (βManAo). Fungal β-mannanases, hydrolyze β-1, 4-glycosidic bonds of mannans and find application in the generation of mannose and prebiotic mannooligosaccharides (MOS). The authors, through homology modeling and secondary structure prevision, created a βManAo model, that was validated and used for the docking, molecular dynamics, and secondary structure prevision studies. From the results obtained, were identified some features of this enzyme, like the binding site, the most important amino acid (Glu244 was found to play a key role in interaction with mannotriose, indicating conserved amino acid for the catalytic reaction), A detailed PCA analysis revealed the very flexible nature of the protein and energy landscapes suggested high conformation sub-states and complex dynamic behavior of the protein. DSSP analysis revealed the major transition of the protein from helix to turn when binding the mannotriose. The authors conclude that a hypothetical model was created, the binding mechanism of A. oryzae β-mannanase with mannotriose was identified where the Glu208 and Glu244 are the key amino acids at the active binding site, and also other amino acids (Asn207, Asp155, and Ser286) are important for the binding with the mannotriose. The manuscript in the present form demands a revision before it can be published, so this reviewer suggests a “minor revision” of the paper. Major issue: 1) The abstract is not very attractive; it should arouse curiosity in the reader and should be clearer. It should include details about the methodologies used to reach the results and in brief some details about the results in terms of numbers. 2) The results sub-section about the docking should be extended. 3) About the conclusion section: it is too simple, in my opinion, needs some improvements, as well as, add all the results obtained and a small perspective paragraph. Minor issue: 1) Please try to improve, in general, the readability of the text helps the reader to better understand the paper. 2) All paper needs an accurate English revision and an accurate formatting check. 3) In Figure 1, panels A and E should be improved in terms of quality. Reviewer #2: In this study, the authors show their results, using in silico approach of structural and functional aspects of an Aspergillus oryzae β- mannanase (βManAo). The manuscript is the interest to the journal, but I suggest publishing after minor revision” of the paper. In particular: 1. The abstract is not clear enough. I suggest the authors rewrite and improve. 2. In my opinion, are needed to improve the conclusion section of the manuscript. In particular, the authors should stress how their results can improve the know-how in the mannanase enzyme and their application in the degradation of mannanase. 3. The quality of Figure 1, panels A and E, is too low. Please, the authors should provide it. 4. The figure legends need more details. Please, the authors should provide it. 5. Accurate English revision of the text is needed. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). 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?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0268333.r001
Revision 1
15 Mar 2022 Author Response Journal 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 Reply: Revised as suggested 2. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files. Reply: Revised as suggested 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. Reply: No, All relevant data are within the paper and its Supporting Information files. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: (Author UKJ is grateful to ICMR, New Delhi for providing financial assistance as Senior Research Fellow. Authors thank Sophisticated Instrumentation Centre (SIC), Dr. Harisingh Gour Vishwavidyalaya, Sagar and DST PURSE (II) scheme for instrumentation facilities and financial support. Authors acknowledge the HPC facility of Indian Institute of Technology, Delhi for providing the computational resources for running the MD simulations.) We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: (The author(s) received no specific funding for this work.) Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Reply: The funding information regarding ‘financial assistance as Senior Research Fellow to UKJ’ has now been removed from the Acknowledgments section. 5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Reply: Not applicable Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes Reply: We are thankful to the reviewers for their kind comments. 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes Reply: We have again checked the requirement for statistical analysis, where relevant. ________________________________________ 3. Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #1: Yes Reviewer #2: Yes Reply: We are thankful to the reviewers for their kind comments. ________________________________________ 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: No Reply: We are thankful to the reviewers for their kind comments. As per the comment of Reviewer #2, we have now revised the manuscript thoroughly with the help of a native English speaker. ________________________________________ 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript by Naveen Kango et al. entitled “Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study” reports an in-silico approach to study structural and functional aspects of an Aspergillus oryzae β- mannanase (βManAo). Fungal β-mannanases, hydrolyze β-1, 4-glycosidic bonds of mannans and find application in the generation of mannose and prebiotic mannooligosaccharides (MOS). The authors, through homology modeling and secondary structure prevision, created a βManAo model, that was validated and used for the docking, molecular dynamics, and secondary structure prevision studies. From the results obtained, were identified some features of this enzyme, like the binding site, the most important amino acid (Glu244 was found to play a key role in interaction with mannotriose, indicating conserved amino acid for the catalytic reaction), A detailed PCA analysis revealed the very flexible nature of the protein and energy landscapes suggested high conformation sub-states and complex dynamic behavior of the protein. DSSP analysis revealed the major transition of the protein from helix to turn when binding the mannotriose. The authors conclude that a hypothetical model was created, the binding mechanism of A. oryzae β-mannanase with mannotriose was identified where the Glu208 and Glu244 are the key amino acids at the active binding site, and also other amino acids (Asn207, Asp155, and Ser286) are important for the binding with the mannotriose. Reply: We are thankful to the reviewers for their kind comments. The manuscript in the present form demands a revision before it can be published, so this reviewer suggests a “minor revision” of the paper. Major issue: 1) The abstract is not very attractive; it should arouse curiosity in the reader and should be clearer. It should include details about the methodologies used to reach the results and in brief some details about the results in terms of numbers. Reply: We thank the reviewer for this very important comment. We have now revised the abstract in order to make it clearer and more interesting for the reader. We have also included details about the methodologies used and provided some brief details of results in numbers. 2) The results sub-section about the docking should be extended. Reply: As suggested, the results sub-section about the docking has now been extended. The extended section is now named as Section 2.5 and Section 2.6. 3) About the conclusion section: it is too simple, in my opinion, needs some improvements, as well as, add all the results obtained and a small perspective paragraph. Reply: We have revised the conclusion and added some results, as well as a perspective paragraph. Line 426-427 and Line 432-434 Minor issue: 1) Please try to improve, in general, the readability of the text helps the reader to better understand the paper. Reply: We have revised the text thoroughly so as to improve the readability of the paper. 2) All paper needs an accurate English revision and an accurate formatting check. Reply: We have revised the text in terms of the use of the English language and formatting as suggested. 3) In Figure 1, panels A and E should be improved in terms of quality. Reply: As suggested, the Figure 1, panels A and E are improved in terms of quality now. Reviewer #2: In this study, the authors show their results, using in silico approach of structural and functional aspects of an Aspergillus oryzae β- mannanase (βManAo). The manuscript is the interest to the journal, but I suggest publishing after minor revision” of the paper. In particular: Reply: We thank the esteemed reviewer for going through the manuscript and kind comments. 1. The abstract is not clear enough. I suggest the authors rewrite and improve. Reply: We thank the reviewer for this comment. We have re-written the abstract to make it clearer. 2. In my opinion, are needed to improve the conclusion section of the manuscript. In particular, the authors should stress how their results can improve the know-how in the mannanase enzyme and their application in the degradation of mannanase. Reply: We have re-written the conclusion section to provide know-how on the mannanase enzymes and their application in the degradation of mannan. 3. The quality of Figure 1, panels A and E, is too low. Please, the authors should provide it. Reply: As suggested, the Figure 1, panels A and E are improved in terms of quality now. 4. The figure legends need more details. Please, the authors should provide it. Reply: Thank you for this very important comment. The figure legends have now been revised to render them complete and informative. 5. Accurate English revision of the text is needed. Reply: We have revised the English language in the text as suggested. Attachments Attachment Submitted filename: Reviewers Reply.doc https://doi.org/10.1371/journal.pone.0268333.r002
4 Apr 2022 Decision Letter - Sabato D'Auria, Editor PONE-D-21-37808R1Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation studyPLOS ONE Dear Dr. Naveen Kango 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. In particular, as required by PLOS policy, the authors should submit a full version of the original submission (included figures and legends to figures) as well as a full version of the revised manuscript (included figured and legend to figures). Please submit your revised manuscript by May 19 2022 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. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. 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, Sabato D'Auria Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments (if provided): As required by PLOS policy, the authors should include the full version of the original submission (included Figures and legends to figures) as well as the full version of the revised manuscript (included figures and legends to figures). [Note: HTML markup is below. Please do not edit.] [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0268333.r003
Revision 2
19 Apr 2022 Author Response 1. Please amend your authorship list in your manuscript file to include author Brett Pletschke. Reply: Author Brett Pletschke is added now in the MS. As per the instructions received from the Academic editor, original manuscript with figures and revised marked manuscript with figures is being submitted for kind consideration. Reviewer #1: The manuscript by Naveen Kango et al. entitled “Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study” reports an in-silico approach to study structural and functional aspects of an Aspergillus oryzae β- mannanase (βManAo). Fungal β-mannanases, hydrolyze β-1, 4-glycosidic bonds of mannans and find application in the generation of mannose and prebiotic mannooligosaccharides (MOS). The authors, through homology modeling and secondary structure prevision, created a βManAo model, that was validated and used for the docking, molecular dynamics, and secondary structure prevision studies. From the results obtained, were identified some features of this enzyme, like the binding site, the most important amino acid (Glu244 was found to play a key role in interaction with mannotriose, indicating conserved amino acid for the catalytic reaction), A detailed PCA analysis revealed the very flexible nature of the protein and energy landscapes suggested high conformation sub-states and complex dynamic behavior of the protein. DSSP analysis revealed the major transition of the protein from helix to turn when binding the mannotriose. The authors conclude that a hypothetical model was created, the binding mechanism of A. oryzae β-mannanase with mannotriose was identified where the Glu208 and Glu244 are the key amino acids at the active binding site, and also other amino acids (Asn207, Asp155, and Ser286) are important for the binding with the mannotriose. Reply: We are thankful to the reviewers for their kind comments. The manuscript in the present form demands a revision before it can be published, so this reviewer suggests a “minor revision” of the paper. Major issue: 1) The abstract is not very attractive; it should arouse curiosity in the reader and should be clearer. It should include details about the methodologies used to reach the results and in brief some details about the results in terms of numbers. Reply: We thank the reviewer for this very important comment. We have now revised the abstract in order to make it clearer and more interesting for the reader. We have also included details about the methodologies used and provided some brief details of results in numbers. 2) The results sub-section about the docking should be extended. Reply: As suggested, the results sub-section about the docking has now been extended. The extended section is now named as Section 2.5 and Section 2.6. 3) About the conclusion section: it is too simple, in my opinion, needs some improvements, as well as, add all the results obtained and a small perspective paragraph. Reply: We have revised the conclusion and added some results, as well as a perspective paragraph. Section 4. Minor issue: 1) Please try to improve, in general, the readability of the text helps the reader to better understand the paper. Reply: We have revised the text thoroughly so as to improve the readability of the paper. 2) All paper needs an accurate English revision and an accurate formatting check. Reply: We have revised the text in terms of the use of the English language and formatting as suggested. 3) In Figure 1, panels A and E should be improved in terms of quality. Reply: As suggested, the Figure 1, panels A and E are improved in terms of quality now. Reviewer #2: In this study, the authors show their results, using in silico approach of structural and functional aspects of an Aspergillus oryzae β- mannanase (βManAo). The manuscript is the interest to the journal, but I suggest publishing after minor revision” of the paper. In particular: Reply: We thank the esteemed reviewer for going through the manuscript and kind comments. 1. The abstract is not clear enough. I suggest the authors rewrite and improve. Reply: We thank the reviewer for this comment. We have re-written the abstract to make it clearer. 2. In my opinion, are needed to improve the conclusion section of the manuscript. In particular, the authors should stress how their results can improve the know-how in the mannanase enzyme and their application in the degradation of mannanase. Reply: We have re-written the conclusion section to provide know-how on the mannanase enzymes and their application in the degradation of mannan. 3. The quality of Figure 1, panels A and E, is too low. Please, the authors should provide it. Reply: As suggested, the Figure 1, panels A and E are improved in terms of quality now. 4. The figure legends need more details. Please, the authors should provide it. Reply: Thank you for this very important comment. The figure legends have now been revised to render them complete and informative. 5. Accurate English revision of the text is needed. Reply: We have revised the English language in the text as suggested. Attachments Attachment Submitted filename: Reviewers Reply.doc https://doi.org/10.1371/journal.pone.0268333.r004
28 Apr 2022 Decision Letter - Sabato D'Auria, Editor Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study PONE-D-21-37808R2 Dear Dr.Naveen Kango, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Sabato D'Auria Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0268333.r005
Formally Accepted
19 Aug 2022 Acceptance Letter - Sabato D'Auria, Editor PONE-D-21-37808R2 Molecular insight into Aspergillus oryzae β-mannanase interacting with mannotriose revealed by molecular dynamic simulation study Dear Dr. Kango: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. If we can help with anything else, please email us at plosone@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. Sabato D'Auria Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0268333.r006

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .