User talk:Kkentala/sandbox

Peer review by Heng

Grammar and language

The active site is lined with hydrophobic residues to accommodate the substrate, but Asp-99 and Tyr-14 are within hydrogen bonding distance of O-3. The hydrogen bonds from Tyr-14 and Asp-99 are known to significantly affect the rate of catalysis in KSI.

• This article shows a good neutral atitude on different views. But the begining of the second paragraph is a little bit confusing. The topic is changed to another mechanism too fast. It could be better by starting with "another theory goes that..." or using subheadings.

Warshel, et al. applied statistical mechanical computational methods to previous experimental data to determine that electrostatic preorganization-including ionic residues and fixed dipoles within the active site-contributes most to KSI catalysis.

• This setence may be too long without punctuation. It may be better to say

KSI catalyzes the rearrangement of a carbon-carbon double bond through an enolate intermediate at a diffusion-limited rate.

• It's better to mention the substrate here.

...Tyr-14 and Asp-99 are known to significantly affect the rate of catalysis in KSI. Mutagenesis of this residue to alanine (D99A) or asparagine (D99N) results in a loss in activity at pH 7 of 3000-fold and 27-fold, respectively, implicating Asp-99 as important for enzymatic activity.

• Maybe some evidences for importance of Tyr14 are needed here.

Linkage and references

• This article shows a banlanced citation between different opinions.
• Some citations form other scientists (not only Warshel and Herschlag) about the debate on the mechanism may be better. This can provide a broader view of the debate.
• It will be better if all the references in the original article are also included in this sandbox draft.
• Some terminologies are not that clear to readers, like "base rescue". A wikipeida linkage or some explanation will be good.
• It's also a good idea to link the other mentioned concepts to their wikipedia pages, like "oxyanion hole" and "mutagenesis".
• You don't have to cite one source for several times in the same paragraph. It may be better to put the reference to the end of related content.

Other topics

• Stablizing of the intermediate is a really important topic for this enzyme, but other aspects like RDS, general study of kinetics, substrate study can also be included.
• It will be better to use a figure to show oxyanion hole because there is only a figure of H-bonding in the original article.

--Gbzwg (talk) 16:20, 3 March 2017 (UTC)

Comments Joe S

Overall: This a good summary, with the proper tone and appropriate citations. The Pymol images are very good.

Comments:

1)I would say what type of carbon-carbon double bond it catalyzes the rearrangement of (where they are relevant to the carbonyl carbon).

2) Where is the form KSI from? Residues Asp-38, Asp-99 and Tyr-14 are not in the same positions for all KSIs.

3) I don’t think you should discuss the boxer article without mentioning the critiques contained in the two comments on their paper.

4) What is the substrate scope of this enzyme. What is its native substrate and what other compounds can KSI catalyze the rearrangement of?

5) Maybe include a chemdraw of the structure of Hershlag’s unnatural amino acids. Why did Herschlag investigate this? Wasn’t this to determine whether low barrier hydrogen bonds were important? Should you mention this? Is this article the one that best demonstrates your point about oxyanion hole stabilization? The oxyanion hole is atleast 10^3 and upto 10^6 enhancement based on who is reporting it. Maybe include Hershlags claim of only 10^3 enhancement this and rephrase the last sentence.

6)The numbering of the amino acids is confusing when the crystal structure you used for your pymol has the different positions then number you use in the text. Choose a crystal structure with Asp-38, Asp-99 and Tyr-14 or clarify that these amino acids are conserved but the positions are not the same in all KSIs.

7)The close-up pymol image probably could use labels for the active site amino acids because you rotated it 180 degrees, relative to the other graphic, so it maybe unclear which Aspartic Acid is which.

8) You wrote “These measurements quantified the electrostatic contribution to KSI catalysis(70%),” What do you mean by electrostatic contribution and is this number agreed on by other experts in the field?

9) Maybe include a recent computational study that investigates the contributions of the amino acids.

10) What is KSI bound to in your pymol images?

11) Possibly include a pymol of the D99A or D99N mutant with substrate bound to highlight the differences in active site interactions that lead to this difference in activity. Jsolomon580 (talk) 09:39, 3 March 2017 (UTC)

Comments Michael Burke

Overall I think the article is informative and maintains the proper encyclopedia presentation. However, I think a few things could be done to make things clearer. 1) A few times you introduce the investigating scientist first as opposed to the enzyme. Example: Warshel, et al. applied statistical mechanical computational methods to previous experimental data to determine that electrostatic preorganization-including ionic residues and fixed dipoles within the active site-contributes most to KSI catalysis. To KSI Catalysis is driven primarily by electrostatic preorganization from ionic residues and fixed dipoles within the active site, shown through both applied statistical mechanical computational methods and experimental data [cite warshel] I feel that this brings the focus to the enzyme a little bit more and helps educate the reader on delta-steroid isomerase. 2) There is a large discussion on the purpose of different residues. I think it would be helpful to make a subheading in the mechanism section of “key residues” and then underneath smaller headings, bullets, or in a table could be used to list the residues. And then with each residue you could explain its purpose, how the purpose was determined, and if it’s been accepted as a catalytically relevant residue. 3) The pymol images are helpful and clear, however, I think it would be helpful to maybe label the residues outside of pymol. The names of the residues are rather difficult to read. 4) I think the last paragraph could use some expanding, maybe a section on controversy could be useful?

Mjburke17 (talk) 16:10, 3 March 2017 (UTC)

Jared notes

1. you refer to position 4 of steroid in text -- label any positions mentioned in the chemdraw figure 2. "statistical mechanical computational methods" he typically refers to this as empirical valence bond. is what you said accurate? 3. note: refer to papers as first author et. al. or corresponding author and co-workers. strictly speaking, "al" just means "others", but it seems to imply completion of the author list. 4. "The reader should note that the driving force for KSI catalysis is still debated." not the driving force! the magnitude of energetic contributions of different factors discussed above... — Preceding unsigned comment added by Jared Lewis (talk • contribs) 19:46, 13 March 2017 (UTC)