Effects of Site-Directed Mutations on the Communicability between Local Segments and Binding Pocket Distortion of Engineered GH11 Xylanases Visualized through Network Topology Analysis
Round 1
Reviewer 1 Report
The work expands the range of network topology analysis used to characterize and visualize the changers of interaction networks, and will be very interesting for the audiences of enzyme catalysis chemistry. Some minor revisions might be done for improving the manuscript for publication.
Line 48 , the word “Bacillus sp.”should be changed to “Bacillus sp.”
Line 72, all of the word “Bacillus firmus” in the entire article should be changed to “Bacillus firmus”.
Line 106, the word “but” should be changed to “ , while”
Line 107, the word “mechanical signal” should be changed to “mechanical signals”
Line 151, the word “represent” should be changed to “represented”
Line 187, the word “sheet” should changed to “sheets”
Author Response
The work expands the range of network topology analysis used to characterize and visualize the changers of interaction networks, and will be very interesting for the audiences of enzyme catalysis chemistry. Some minor revisions might be done for improving the manuscript for publication.
Line 48 , the word “Bacillus sp.”should be changed to “Bacillus sp.”
Line 72, all of the word “Bacillus firmus” in the entire article should be changed to “Bacillus firmus”.
Line 106, the word “but” should be changed to “ , while”
Line 107, the word “mechanical signal” should be changed to “mechanical signals”
Line 151, the word “represent” should be changed to “represented”
Line 187, the word “sheet” should changed to “sheets”
Answer: Thank you for your suggestions, we have addressed all these issues and highlighted them in the new version.
Reviewer 2 Report
The work is devoted to the topical issue of site-directed mutations of industrially significant enzymes.
Major comments:
1. Despite the fact that the term "Catalytic efficiency" is mentioned in the Abstract and Introduction in relation to the studied enzyme, in the work itself, the results of Engineered GH11 Xylanases in this context are not available. There is no information on an increase in activity, a change in substrate specificity, or an increase in thermal stability. This information would undoubtedly decorate the perception of the material. In any case, authors who wish to publish in catalysts should pay more attention to this issue.
2. What new authors wanted to demonstrate in Fig. 1 versus 6 of references? Considering that this article is short, information from previous works does not in any way enhance the presentation of the material.
3. The list of references contains only 10 sources, is this due to the lack of relevance of the topic or have the authors done little work on already published reviews and experimental articles?
Minor comments:
1. The structure of the article is non-standard for catalysts, there is no section Materials and Methods, instead the section Methodology and it is located before the Results.
2. Figure or table captions are not capitalized (except for Fig. 1).
3. Line 63 Bacillus firmus not in italics.
4. Line 39 The terms “glycosidase hydrolase” are not quite correct, check, please.
Author Response
The work is devoted to the topical issue of site-directed mutations of industrially significant enzymes.
Major comments:
- Despite the fact that the term "Catalytic efficiency" is mentioned in the Abstract and Introduction in relation to the studied enzyme, in the work itself, the results of Engineered GH11 Xylanases in this context are not available. There is no information on an increase in activity, a change in substrate specificity, or an increase in thermal stability. This information would undoubtedly decorate the perception of the material. In any case, authors who wish to publish in catalysts should pay more attention to this issue.
Answer: An additional paragraph (line 64) that further explained our previous experiments was added to the Intro, describing a synergistic effects from two distal mutated sites.
- What new authors wanted to demonstrate in Fig. 1 versus 6 of references? Considering that this article is short, information from previous works does not in any way enhance the presentation of the material.
Answer: In our newly added paragraph (line 64), we pointed that the rationally-designed mutations from our previous study (Figure 1) were similar to others references in the way that site-directed mutations were performed near the N-terminal region, while the difference was that synergistic effects from Figure 1 were from distal sites.
- The list of references contains only 10 sources, is this due to the lack of relevance of the topic or have the authors done little work on already published reviews and experimental articles?
Answer: We have done more literature reviews on the review articles to provide more backgrounds, both on protein engineering and previous uses of network topology on other protein structures.
Minor comments:
- The structure of the article is non-standard for catalysts, there is no section Materials and Methods, instead the section Methodology and it is located before the Results.
Answer: We have now swapped the material and methods section with the results. However, we found it hard to separate the Results and the Discussion sections in this manuscript as the discussions are based-on the result figures and cross references are needed.
- Figure or table captions are not capitalized (except for Fig. 1).
Answer: This has been fixed in the revised version.
- Line 63 Bacillus firmus not in italics.
Answer: This has been fixed and highlighted in the revised version.
- Line 39 The terms “glycosidase hydrolase” are not quite correct, check, please.
Answer: This has been fixed and highlighted in the revised version.
Round 2
Reviewer 2 Report
The authors have made corrections to the manuscript. In general, this study can be published.
Minor remarks:
-In the abstract it is better to use (line 21) "Xylooligosaccharide" instead of "oligo-xylose"
- The word "xylooligosaccharide" does not need a hyphen in line 43
- If, nevertheless, the authors decided to leave Fig.1, then it makes sense to improve its quality, and perhaps the location of individual pictures.
Author Response
Dear reviewer,
Thank you again for your suggestions. We have now made following corrections according to your comments.
- Typos in Lines 21 and 43 have been corrected and highlighted
- The resolution of proteins in Figure 1 was improved and subfigures were rearranged
Best regards,
