Talk:Nucleoside-diphosphate kinase

Peer review and responses during the educational assignment in Fall 2015

Peer Review 1

When first learning about a protein, I think that it is useful for the reader to be able to see a three-dimensional schematic representations of the protein structure, so I would include a ribbon diagram of the Nucleoside-diphosphate kinase in the introduction. This would also make for a more visually appealing Wikipedia page, as there are currently no visual aids. In this same vein, when detailing how NDPK utilizes specific enzyme kinetics for the multi-substrate reaction, it might be useful to depict it in a simplified visual model so that the reader can visualize the step-by-step reaction. As of now, there are only three references cited at the bottom of the sandbox page. It would be beneficial to expand the references to back up the extensive information they have provided and reassure readers that it is credible, as well as give credit to the owners of the original research and ideas. For example, the information regarding the Nm23 gene’s involvement in normal development and differentiation in prokaryotes and its relation to the nonspecific nucleoside diphosphate activity should be attributed to a specific author. Additionally, while interesting points are made in this section, the authors mention that “the biomolecular mechanism by which Nm23 suppresses metastasis and/or differentiates in cells is currently unknown” and then report findings that the nucleoside diphosphate kinase "seems to be essential for M. xanthus growth”. As this is an encyclopedia page, and not an area to discuss or summarize the findings of primary research, it might be advantageous to find a prokaryotic system in which the function of nucleoside diphosphate activity is better understood so that the average reader can understand its significance. Alternatively, other examples of nucleoside diphosphate activity in prokaryotes could be incorporated so that the focus of this section is not rooted in one paper’s findings and a more holistic picture can be painted. I would apply this same line of thought to the specific examples of NDPK in humans, NDPK in Cancer, and NDPK in Cardiovascular Disease, and Nme1 as a suppressor of metastasis. Citations should also be added for these sections. In the NDPK in humans section, the sentences "Required for neural development including neural patterning and cell fate determination” and "During GZMA-mediated cell death, works in concert with TREX1” read as bullet points and the subjects of the sentences should be established. There is also a "In Plants and Fungi" section at the very bottom of the page which has no information. This would be very relevant to the topic and I would be interested to read this section if the authors choose to develop it. Overall, the page is successful in leaving the reader with a clear understanding of NDPK’s general function, as well as its biological relevance through their use of specific examples. I believe the aforementioned changes would only serve to further strengthen their well organized and thought out page. Brenmich (talk) 02:27, 19 October 2015 (UTC)Brenmich

Peer Review 2 from Qingze

After group 9’s modification of the wikipedia page on nucleoside-diphosphate kinases (NDKs), the introduction now has more defined description of the function of NDKs and more activities of NDKs. The major modifications includes a sentence to introduce the structure of NDKs and further enrichment of the contents under prokaryotic and eukaryotic systems. Overall, group 9 successfully expanded on the existing topics and added in many relevants resources to facilitate a holistic view on nucleoside-diphosphate kinases. Below are several suggestions for revision.

→·It is not clear at the beginning how many different acronyms can stand for nucleoside-diphosphate kinases. It is confusing whether NDKs and NDPK mean the same thing. So I suggest either using one of them or make sure those two terms are introduced clearly at the very beginning. →·Under the Function section, I recommend creating a graph for the multiple-step mechanism, which will make it easier to understand. →·Under the prokaryotic and eukaryotic systems, it may help to first introduce the relationship between NDKs and Nm23 gene since Nm23 gene took a majority of the lines under those sections. I recommend adding a transition paragraph before Nm23 gene function under the topic of prokaryotic system. →·The structure of the sub topics under eukaryotic system can be further improved. For instance, there can be one introduction for the general function of NDKs in human and group those diseases (cancer and cardiovascular disease) into one single group. Meanwhile, the plant and fungi section still needs additional contents. There are about three literatures cited for this page, I suggest looking further to find relative literatures to add into the page.

In summary, you guys did a very good start on this project. The draft has already drastically improved the original page. As we all know, there is always space to improve, so I hope my comments are helpful for the revision. — Preceding unsigned comment added by Lüqingze (talk • contribs) 19:24, 20 October 2015 (UTC)

Peer Review of Group 9 (NDKs)

Dear Group 9,

This article is overall well written and discusses topics in the appropriate level of technical detail for this assignment. In the "Structures" section, it may be helpful to add a visual diagram to aid the concise descriptions of the structure of NDKs. The "Fuctions" Section is also written very clearly, the bullet pointed step by step mechanism is easy to understand and explains the ping pong mechanism well. The sentences following this bullet pointed mechanism in so many words reiterates what the section has already done a great job explaining. Consider removing some of the redundant explanation in this section as the point is properly made in this section, but also overstated. In the "NDPKs in Cancer" section, consider removing the first sentence as this is a fairly specific section and the general notions of NDKs have already been introduced. Additionally, consider rearranging the page so that the section on "Nme1 suppressing metastasis" is either adjacent to or combined with the "NDKs in Cancer" section.

Blake Carlson. — Preceding unsigned comment added by RedwingsWIKI (talk • contribs) 15:55, 22 October 2015 (UTC)

Peer Review 4 - Ankur Gupta

• Ankur Gupta
• Peer review - Group 9
• Nucleoside-diphosphate kinases Peer Review

Wikipedia related corrections:

• Link to the “ping-pong” mechanism so readers understand what the following equation means.
• Correction, you link to the article in the “Function” header, link it in the introduction for added clarity OR have it redirect to the functions header.
• Links [4], [5], and [6] are nonexistent but are in the sandbox
• Is there a source for the multistep mechanism?
• Citations needed for the four Eukaryotic systems subtopics
• In Plants and Fungi needs to be either completed or removed
• Link to gram negative bacteria in Nm23 gene function portion
• Have the same source [Dumas, C; Lascu …] listed twice in references.
• Source listed in original wikipedia entry is not listed in the new entry. Did you remove it and its content entirely?
• Content related feedback:
• Introduction/Structure/Function portions are very clear
• Consider including portion of “ping pong” mechanisms in the functions portion in the introduction instead
• You mention TREX1 in Eukaryotic Systems/NDPK in Humans section. Not clear what this is. Link to another wikipedia article or mention it in the article itself.
• The portions under Eukaryotic systems are very clear.

Conclusion

• Overall, I found this article very concise and strongly written. Clarify a few points by linking to other wikipedia articles and correcting/improving citations will make this article great. If an image is available (perhaps to better visualize the multistep equilibrium) that would be useful, albeit not necessary.

Suggestions from ChemLibrarian

Good job with expanding the article. Here are my suggestions.

1. It's great that you incorporated the content in the original article in your edits.
2. You may want to change the heading levels of 4.1.1.1 and 4.1.1.2. The logic seems confusing there to me.
3. Be consistent with acronyms. Do you want to use NDKs or NDPK?
4. I see that you have not added any images to the article yet. Please check out slide 21 and 37 of the Slides for Wikipedia Editing Basics I posted on the CTools site for link to video tutorials and notices about copyright issues.
5. I see there is a Info Box for Enzyme on the page. It may be a good idea to put a structure in the info box as the image you need to add. Please see Template:Infobox enzyme for how to add images to that box.
6. Your reference 1 seems strange to me. Are you citing the challenge or someone else put it there? Or did you try to add the reference 1 shown up in the original article Nucleoside-diphosphate kinase.
7. It seems to me that you still have problems with formatting your references. Please check the two videos below for help.

ChemLibrarian (talk) 18:17, 23 October 2015 (UTC)

Review from GSI

The article is well written and modified nicely. Here are some suggestions that can make it better.

1. In the introduction, link the term 'Ping-pong mechanism' to the existing wikipedia page as well as explain the notations X and Y in the reaction.

2. A reaction scheme, showing the phosphorylation of histidine by terminal phosphate can provide a better understanding to the readers.

3. Several technical terms in the article like, 'gram negative bacteria' (in Nm23 gene function), 'hematological malignancies' (in NDPK in cancer), 'Gs protein' (in Cardiovascular Disease) etc can be explained more in a general way or be linked to the wikipedia pages if existing.

Soumigchem (talk) 04:00, 24 October 2015 (UTC)

Our tentative changes in response to the Peer Reviews

• Add 3-D structure of NDPK
• Add diagram that illustrates ping-pong diagram under Function section
• Revise and paraphrase the original content of Function section
• Revise citations and references
• Include summary findings from primary resources instead of using review articles
• Add new section Regulation in which we will describe its regulatory functions
• Use general definitions to explain technical terms to be more user-friendly
• Add more information about different NDPK uses in prokaryotes
• Use a variety of sources, including primary sources & secondary sources
• Clarify the acronyms of this protein to NDPK — Preceding unsigned comment added by Anneskim (talk • contribs) 20:12, 17 November 2015 (UTC)