Talk:Glutamate racemase

Team 10 review

Summary: This article talks about the properties that make glutamate racemase a moonlighting protein. The protein’s primarily role (bacterial wall synthesis) and minor role (gyrase inhibition) are described in detail. Furthermore, the article shows that both functions are not related and that their active sites seem to be independent. The main points discussed in this article are stated in the abstract which gives the reader from the start a good sense of what is to be expected in terms of content. Overall it is a well-written, properly structured, and concise article. The information contained in the article was carefully selected, researched, and explained. Major concerns: You might need to clarify the fragment “The minor functions of these unique enzymes are called moonlighting functions, in which a protein can have a second function not dependent upon the main function. The two functions of moonlighting proteins are found in a single polypeptide chain” included in the Background section. This makes the reader think that moonlighting proteins can only have two functions (a main function and a minor function). That is the case for Glutamate racemase, but not for all moonlighting proteins (GAPDH has several roles for example). Minor concerns: We think you should consider revising your citations’ format. It might be more appropriate to follow Wikipedia’s format for citations which consists of numbers inside brackets [ ] referring to the details of the citation listed at the end of your article. We believe that the method that you used (parenthesis with the article’s author and year) is less efficient in linking the text to its source, and also tends to distract the reader. This is the link that explains how to format the citations: http://en.wikipedia.org/wiki/Wikipedia:Citing_sources. It might be helpful to add figures to illustrate some of the concepts and mechanisms described in the article such as bacterial wall synthesis and gyrase inhibition.Saezcab17 (talk) 16:26, 12 April 2011 (UTC) The style of the "Background" section seems to be more of a the style associated with an English paper, introducing a topic. Background generally gives a basis of knowledge for the reader to understand the topics that follow. While the information is good within the background section, some of the language, such as "the active site utilized by Murl will be explored..." sounds out of place. Santosze (talk) 21:38, 12 April 2011 (UTC) Also, in the Bacterial Wall Synthesis section, the sentence "This deprotonation forms an anion and after that there is a reprotonation of the substrate". is very awkwardly worded. It would help the reader understand the process being described if it was reworded in a more clear way. Santosze (talk) 21:38, 12 April 2011 (UTC) This is purely cosmetic, but in the Relationship to the active site section, you used the term kcat, it would look more professional if you either used a symbol for Kcat or if you wrote cat in subscript to emulate the actual symbol. Santosze (talk) 21:38, 12 April 2011 (UTC) The sources cited by the text are accurate to the information cited and are appropriately cited. [The left column of sources was examined for accuracy.] As noted above, however, one might consider using the wikipedia format for citations. Wi lk14 (talk) 23:26, 12 April 2011 (UTC) —Preceding unsigned comment added by 129.2.129.231 (talk)

Team 3 Review

The functions of the moonlighting protein glutamate racemase, also known as Murl, include synthesis of bacterial cell walls and gyrase inhibition. For bacterial wall synthesis, Murl interconverts glutamate enantiomers into D-glutamate in a co-factor process in which the enzyme undergoes deprotonation and then reprononation to form an anion and achieve a conformational change in its domain. This change in domain causes the cysteine residues on either side of the substrate to superimpose at equal positions. The symmetric nature of the domains reveals that this process evolved from gene replication. For gyrase inhibition, Murl reduces activity of DNA gyrase by preventing gyrase from binding to the DNA. Reduction in the production of DNA strands causes existing DNA to become supercoiled, which in turn prevents the reaction that causes the strands to uncoil into RNA. As there is no significant correlation between the concentrations of racemization substrate on gyrase inhibition and because each function is processed on separate active sites, glutamate racemase is a moonlighting protein, or a protein that has more than one function. Abstract Comments Do not use long quoted sections in your article. You do not need to directly quote what Murl is; it is the topic of your article so you should be able to summarize what it is in your own words. You need to use footnotes, not in-text citations. Voice: This is not a persuasive academic paper, it is an informative article. As such, don't say "will be explored to determine" or “will be studied” The abstract is meant to be a general overview of the topic with a little background, the headings in the article make it clear what you will be discussing. Do not label the abstract section “abstract” rather merge it with the background section below to make it the introductory portion of your article, which should be placed above the table of contents, as per Wikipedia formatting.

Background Comments

There is a LOT of repetition here with respect to the abstract. You do not need both an abstract and a background section on Wikipedia. Take out this whole section, and merge whatever isn't repeated with the abstract. You need to clarify what you mean in the portion where you mention that “proteins that are mulitfunctional are not included...” It is not clear. Overall Voice: Again, you do not need to lay out what you're going to talk about. This is not a normal academic paper. Your topic is specific to Murl, you do not need to give too much information on what moonlighting proteins are in general, that is the subject of a different article.

Bacterial Wall Synthesis Comments

This is the third time you have introduced what Murl is, this is highly repetitive and unnecessary. You also repeat what Murl’s function is again, please proofread the whole article for your next submission. “Inter conversion” should be replaced with “interconversion”. You already say it converts L-glutamate to D-glutamate multiple times, don't repeat yourself within the same section. What is an allosteric site? Make it a link to another wikipedia article, or if one does not exist explain. What is the significance of being cofactor independent? “...meaning it can proceed without needing an additional source...” What is the additional source? An enzyme? Replace “‘this enzyme’ involves a two step process” with “murl”. First there is a deproteinization of the substrate, "which forms an anion.." Merge these two sentences. Include a picture of the deproteinization/the conformational changes/superimposition to clarify those processes for the reader. Expand on the evolution of the protein from gene duplication. It's not relevant to this section though so if it is important information put it elsewhere. Expand on the applications of Murl and make it its own section.

Gyrase Inhibition Comments

Break this section into multiple paragraphs, it’s too long. You prove that Murl is a moonlighting protein yet again at the end of this section; this is unnecessary and repetitive. What is the significance of the ability of the mutated Murl being able to perform its gyrase inhibition function? If you were expanding upon an article, you should have done so not by eliminating the original content, but actually expanding upon it. You are missing information from the Gyrase Inhibition section of the wikipedia article “Glutamate Racemase”.

Relationship Between Functions Comments

Include which active site specifically carries out bacterial wall synthesis and gyrase inhibition. Avoid using “this” in the beginning of a sentence; indicate clearly the particular subject that is being referred to. Combine the first and second experiment into one sentence because they both lead to the same conclusion: that there is no correlation between bacterial wall synthesis and gyrase inhibition. The function of Murl, the topic of your article, is not to be a moonlighting protein, so do not keep reaffirming this conclusion. This is the third or fourth time you have done so. It is a moonlighting protein, but this is not its function.

Relationship to Active Site Comments

Discuss the meaning and why the active site is used to undergo racemization before analyzing whether or not the same active site is used for moonlighting function. Replace “‘it employs two active site cysteine residues in catalysis’ as acid/base catalysts” with “it employs two active site cysteine residues as acid/base catalysts” Do not use the phrase “This paragraph aims to determine…” Just say what you need to say and it will become self-evident. Do not end your article with a quote.

Team 10 Second Review

The changes and improvements made to the first draft were noticeable. The second draft is better structured and easier to read. Overall, the major and minor concerns pointed out in the previous review were addressed. Team 9 made the effort to reformat the citations, revise the style and syntax of the article, and clarify the definition of a moonlighting protein. Also, the second draft contains more links to technical terms already defined on Wikipedia. This contributes to the comprehension and coherence of the topic. The article could be further improved by adding pictures or diagrams to complement and facilitate the understanding of the topic as mentioned in the first review. It would be helpful to include some figures illustrating the following: the structure of the enzyme, display of the active sites, and possibly diagrams showing substrate/active site interactions. (Saezcab17 (talk) 16:53, 3 May 2011 (UTC)). One last minor detail: maybe you could briefly explain what the dimensions 35 Å × 40 Å × 45 Å mean. (Saezcab17 (talk) 22:02, 3 May 2011 (UTC))

Team 3 Second Review

Overall, the voice is much more professional, the problems with repetition are clearer, and the organization is much better. However, now that your two articles are merged, it’s hard to tell how much of that work is what you’ve done versus what was already present in the existing glutamate racemase article .While one source was added, more sources are needed to strengthen the article. The original article had 10 sources, so merely adding one or two does not indicate significant research on the part of the project team. They did address the minor concerns that were mentioned. The team did not include a picture of the deproteinization or the conformational changes or superimposition to clarify those processes for the reader. The team expanded on the applications of Murl and made it its own section. The team also took out internal citations. They also did not end the article with a quote anymore, and now has a much better ending with the applications section. The overall article (which was merged with an existing article) is only 1507 words, including headings and charts. The article is well below the minimum word count. The groups additions to the article must have a minimum of 1500 words alone. Since the article was merged our group questions the amount of original work that was put into this article by the team. As a suggestion, the article should be extended thoroughly. Another suggestion would be to use the citation found in your “further reading” section as another possible source.

Sportsfan1292 (talk) 22:51, 2 May 2011 (UTC)

Team 9 Note

Several attempts have been made to add pictures to the article; however, this has been difficult, as citing and gaining access to the pictures has been problematic. Pictures have been posted several times only to be taken out due to copyrights and improper citations. Are there any suggestions as to how to incorporate pictures without them being removed? —Preceding unsigned comment added by 129.2.129.231 (talk) 14:33, 7 May 2011 (UTC)

Inserting images taken from journal articles or books, unless permission is obtained from the publisher, is a copyright violation and is absolutely not permitted. Your only recourse is to obtain permission from the publisher or create your own original graphics. Boghog (talk) 18:38, 7 May 2011 (UTC)

In addition, editing others comments as you did in this edit is not acceptable (see talk page guidelines) and has been reverted. Boghog (talk) 18:50, 7 May 2011 (UTC)