Talk:Enzyme

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enzyme theory of life[edit]

Many astro-biologies that design 5 stages experiments that introduce the extracts of one experiment as inputs to the next, claim that all life started with enzymes... well it is a great ideal, but experimentally few results were great, but we do not understand the full mechanism of the creation of DNA out of simple mollecules via asteroid and territorial processes... We just don't know... but it's worth mentioning. — Preceding unsigned comment added by 2.84.223.244 (talk) 01:47, 5 April 2015 (UTC)

Possibly FAR[edit]

There's a lot sections or sentence need additional footnotes, consider this article are already been featured for more than 8 years, I think may require FAR.--Jarodalien (talk) 06:40, 5 February 2015 (UTC)

@Jarodalien: Would you like to elaborate? 175.156.125.155 (talk) 13:11, 5 February 2015 (UTC)
"Uncompetitive inhibition", "Non-competitive inhibition", "Mixed inhibition", "Uses of inhibitors", "Control of activity" said there's five main ways that enzyme activity is controlled in the cell, but two sections without any footnotes, other sections, like:

I understand there were big chance those content could be supported by other source that already listed, but as far as I believe, "encyclopedic content must be verifiable" and the word "Featured article" should not require readers get through tens of books just try to locate something they're not even sure is there.

One more thing, I don't know why phrase like "EC numbers", "Enzyme production", "compartmentalized", "activated when localized to a different environment", "covalent modulation" need to be in bold.--Jarodalien (talk) 13:40, 5 February 2015 (UTC)
As for the bold words in the Control of activity section, I think the purpose is to emphasize the five main ways enzyme activity is controlled in the cell. Perhaps the boldface can be removed or they can be italicised. 175.156.125.155 (talk) 12:32, 6 February 2015 (UTC)
Added cn tags to the article. You could submit to FARC if these issues are not addressed. The issues are not very serious so hopefully it can be settled at the FARC stage. HYH.124 (talk) 12:40, 6 February 2015 (UTC)

The pre-FAR enzyme article (as it was on 5 February 2015)

Reverse plagiarism[edit]

For the FAR, I have been trying to locate suitable references to replace the {{cn}} tags. For the passage on parallel enzymes, I was shocked to find this exact copy of the text:

  • van Oort M (2010). "Chapter 1: Enzymes in Food Technology – Introduction". In Whitehurst RJ, van Oort M. Enzymes in Food Technology (2nd ed.). Chichester, U.K.: Wiley-Blackwell. p. 4. ISBN 978-1-4443-0994-2. Several enzymes can work together in a specific order, creating metabolic pathways. In a metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the catalytic reaction, the product is then passed on to another enzyme. Sometimes more than one enzyme can catalyse the same reaction in parallel, this can allow more complex regulation: with for example a low contant activity being provided by one enzyme but an inducible high activity from a second enzyme. 

This text was introduced in part on 4 September 2006 in this edit years before the above book was published. Several other passages in this chapter look like they were also copied from the Wikipedia article. Boghog (talk) 11:10, 14 February 2015 (UTC)

Wow, I didn't think that sort of thing really happened. Are there procedures for contacting the publisher? T.Shafee(Evo﹠Evo)talk 13:15, 14 February 2015 (UTC)
It's happened before in a stats paper by a field heavyweight and in a biotech review paper, but a book!? That's new. Opabinia regalis (talk) 06:03, 15 February 2015 (UTC)
Unfortunately this has happen before:
Boghog (talk) 07:08, 15 February 2015 (UTC)
That's hilarious. Especially OMICS. Of course it was OMICS. Opabinia regalis (talk) 08:56, 16 February 2015 (UTC)
Since the substantive plagiarized text is mostly the work of TimVickers (who I see has been helping out lately with the FAR), perhaps he should decide how to proceed, if at all? A2soup (talk) 06:02, 17 February 2015 (UTC)
Since I try to put everything I write in the public domain, this copying is perfectly fine from my viewpoint. Tim Vickers (talk) 02:07, 20 April 2015 (UTC)

FAR-related discussion[edit]

The following was copied from the FAR page because it is cumbersome to edit without subsections. Opabinia regalis (talk) 06:33, 2 March 2015 (UTC)

Organisation of specificity and mechanism[edit]

Currently the organisation of specificity and mechanism is split a little oddly. What do poeple think of the following structure? Perhaps also move 'allostery' into the 'inhibition' section and rename that section 'regulation'? T.Shafee(Evo﹠Evo)talk 05:48, 1 March 2015 (UTC)

Current:

  • Specificity
  • Mechanism
    • "Lock and key" model
    • Induced fit model
    • Reducing activation energy
    • Dynamics
    • Allosteric modulation

Proposed:

  • Mechanism
    • Binding
      • Specificity
      • Lock and key
      • Induced fit
    • Catalysis
    • Dynamics

New images are really nice! I especially like the surface representations - it's easy to keep showing ribbon diagrams and end up giving people the impression that proteins are strings.

I think the specific points above are now cited (thanks again Boghog, both for the citations and fixing my lazy ref formatting), and there are now a whole bunch of little notes in the giant table of doom (I am betting the click-through rate on these is indistinguishable from zero). In other news, there is a journal called Meat Science.

The only significant text change I made was to go back to the Stryer formulation of the "control of activity" list - which includes a fifth entry for organ and tissue differentiation. If we're consolidating on the Stryer text then it makes sense to be consistent.

I think the proposed reorganization looks good. I'll have to think a little more about the second suggestion; allostery isn't always inhibition and most of the basic kinetics of inhibition stuff here is essentially about in vitro enzyme assay measurements. Opabinia regalis (talk) 09:14, 1 March 2015 (UTC)

Likewise, thanks Evolution for the great graphics and Opabinia regalis for your diligent work in cleaning up the text and finding citations. I agree that the structure of the "Specificity" and "Mechanism" sections are a bit odd and should be reorganized. One minor suggestion is that I don't think we need a separate "Binding" heading. "Specificity" can be used as the first subheading:
  • Mechanism
    • Specificity
      • Lock and key
      • Induced fit
    • Catalysis
    • Dynamics Allosteric modulation
Also the "Dynamics" section is a little oddly placed because it says very little concrete about mechanism. I see a relationship the between "Dynamics" and "Allosteric modulation" sections stronger because dynamics makes allostery possible (see Monod-Wyman-Changeux model) Enzymes exist in dynamic equilibrium between several states (e.g., active and inactive) and an allosteric regulator can shift the equilibrium between these states. Boghog (talk) 10:17, 1 March 2015 (UTC)
Just noticed Opabinia regalis's comment that allostery isn't always inhibition and I agree. Hence it might make more sense to merge "Dynamics" and "Allosteric modulation" sections and keep the merged section under "Mechanism". Boghog (talk) 10:38, 1 March 2015 (UTC)
I also think that the current emphasis in the dynamics section is completely backwards. The emphasis currently is on what enzymes say about dynamics whereas the emphasis should be more on what dynamics says about enzymes. In addition, several of the sources in this section are primary. Restricting the sources to secondary may help in establishing a better overview and significance of dynamics to enzymes. For example, PMID: 20822947 and: 23988159 both unequivocally state conformational fluctuations in enzymes are needed for the binding of substrate, attaining the transition state, and to release product. 19355979 presents evidence that internal protein dynamics are responsible for allosteric regulation. Boghog (talk) 20:45, 1 March 2015 (UTC)
I agree that allostery is a more natural fit with dynamics than with inhibition. I trimmed the current dynamics section awhile back but didn't significantly change the text, which was clearly written in the context of the dispute in the field about whether internal protein dynamics can couple to/drive/modulate/etc. the chemical step of catalysis. (Relevance to binding, product release, and regulation is obviously not disputed.) The substance of the catalysis argument is several orders of magnitude too technical for an article at this level. I think a couple of (ideally open-access) recent reviews should do it for the level of detail that's reasonable here. Opabinia regalis (talk) 07:08, 2 March 2015 (UTC)
Just another suggestion for consideration - We could even put dynamics in the structure section given that the structure section. T.Shafee(Evo﹠Evo)talk 00:03, 7 March 2015 (UTC)
I also agree Opabinia that you would be the ideal editor to wok on the dynamics section. IMHO, dynamics provides a link (although clearly not the only link) between structure and mechanism (i.e., structure → dynamics → induced fit / mechanism of catalysis / allosteric regulation). One the one hand, discussing dynamics along with structure makes sense because dynamics is a consequence of structure. On the other hand, this organization makes it more difficult to state why dynamics is important. Perhaps the structure section should end with a brief statement that enzymes are not static and leave the dynamics section where it is so that its significance to mechanism and allosteric regulation can be made clear. In a general article on enzymes aimed at a wide audience, I think the emphasis should be on what dynamics says about enzymes, not the reverse. Boghog (talk) 10:05, 7 March 2015 (UTC)
Not ideal at all! It's one of those 'can't see the forest because I'm busy looking at the bark on this one particular tree' things :) I made some relatively small edits to the dynamics and allostery sections to try to communicate the importance of these features without getting too bogged down in details. I noticed we've written ourselves into a corner a bit here in discussing induced fit but not conformational selection, which is the more dominant view in recent literature (though of course it's really both, in some sense) and I'm not sure the general reader will really benefit from introducing the distinction. Maybe I'll overhaul protein dynamics eventually, which is really the right place for these issues. Opabinia regalis (talk) 07:02, 9 March 2015 (UTC)
Your new dynamics section is much tighter and logically presented. Since the structure section also touches on allosteric sites and cofactors, I'll add a short sentence on dynamics so that it is complete. T.Shafee(Evo﹠Evo)talk 11:16, 9 March 2015 (UTC)

Images[edit]

I'm glad that you like the images so far. Please feel free to suggest any changes to them and I'll update. I love the improved clarity of the methotrexate image. I hope no-one is offended if I update a few of the other figures that have already been changed. I'm still planning on editing:

  • Lead image (much the same, ribbon image, but same colour scheme and style as others)
  • Inhibitors (similar layout to the induced fit figure)
  • Involvement in disease (may look for good example of genetic mutation causing obvious change)
  • Reaction coordinate energies (minor changes to tiny writing and maybe colour)
  • Saturation curve (maybe remove? Too much detail for this article)

T.Shafee(Evo﹠Evo)talk 11:26, 1 March 2015 (UTC)

I don't mind if you replace the lead image. The current image is probably the best that can be rendered with PyMOL. These images look great if larger, but I agree the perspective is more difficult to see when thumbnail sized. If you have another program that can produce more distinct rendering outlines, by all means, please go ahead. BTW, what program are you using to create protein graphics? They look gorgeous. Boghog (talk) 12:09, 1 March 2015 (UTC)
I think this sounds great! One comment on the new images: File:Enzyme_structure.png looks like the patch on the protein is purple but the box labeled "binding site" is blue. I use f.lux and I thought it was just me, but it still looks different with the app turned off. Is that on purpose? The box and protein look consistent for the catalytic site.
Saturation curve: I agree the current image doesn't add much. But since we do go through the main MM constants maybe a "cartoonier" version would work better. Opabinia regalis (talk) 07:18, 2 March 2015 (UTC)
@Opabinia regalis - Thanks for letting me know about the purple issue. PyMol calls the colour 'slate blue' and I'm colourblind so I have to trust the colour names! Have updated the structure image in 'marine blue'. Will have to do the induced fit tomorrow.
@Boghog - Glad you like the figures. I actually am using PyMol. I've picked up a couple of typed command tricks that the GUI doesn't show:
show surface,          
set ray_trace_mode, 1   # adds the outline (nb, tends to clash with 'fancy helices')
set antialias, 2        # higher rendering quality and thinner outline
bg_colour white         # outline is complementary colour of background
ray
T.Shafee(Evo﹠Evo)talk 09:49, 2 March 2015 (UTC)

Your use of color in images is very effective' would not have guessed that! Not sure offhand if this is current, but pymol does have some weird choices of color names. FWIW, the induced fit image is consistently light purple in both the cartoon and the structure.

(Off-topic: I've noticed that setting antialiasing to 5-10, turning shadows off, and rendering 3-5x the intended display size minimizes the artifacts from raytraced outlines with fancy helices, potentially at a cost of detail. This GPCR doesn't look too bad at infobox size.) Opabinia regalis (talk) 07:24, 3 March 2015 (UTC)

I really like the new thermodynamics and kinetics images - much clearer presentation. And since it looks like the FAR is wrapping up, I'll post here to thank Boghog for all those extra citations! Will try to deal with the dynamics section this weekend unless someone else wants to rewrite it. I am very familiar with the literature on this but that actually makes it harder to avoid producing a boring textwall :) Opabinia regalis (talk) 05:09, 5 March 2015 (UTC)
@Opabinia regalis: I've enjoyed working working on the article with both of you. Seems like you'd be the ideal candidate to work out what to do with the dynamics section and statements that are scattered through the article. T.Shafee(Evo﹠Evo)talk 11:47, 6 March 2015 (UTC)

The last image I'm going to tackle is the Involvement in disease section. Planning on using either phenylalanine hydroxylase or Gaucher's disease as the example. Will read papers tomorrow. As always, please let me know if you have any changes to any of the figures I'm putting up. Also, @Boghog: I hope that you don't mind that I edited your File:Methotrexate_vs_folate.svg a little. I've explained the alterations in the changelog. T.Shafee(Evo﹠Evo)talk 11:59, 6 March 2015 (UTC)

@Evolution and evolvability:. No problem with the edit of File:Methotrexate_vs_folate.svg. I agree that the color change makes sense. Boghog (talk) 09:11, 7 March 2015 (UTC)

@Evolution and evolvability: I got a bit distracted but just noticed your update to the metabolism section. There are a zillion drawings of the glycolysis pathway out there and I'm pretty sure File:Glycolysis_metabolic_pathway.svg is the best one I've ever seen. Fantastic work! Opabinia regalis (talk) 07:07, 15 March 2015 (UTC)

I agree. The new drawing is much more legible and easier to follow than the previous one. Excellent work! Boghog (talk) 08:49, 15 March 2015 (UTC)

Comments from Adrian[edit]

Thought I'd take a look while this article is getting a lot of attention, and made a bunch of small changes you can see in history. Got about halfway through... not sure whether I'll have time to finish in the near future. I haven't had time to read talk archives, so apologies if I re-hash any old points. A few comments follow... Those regarding the lead in particular are really just ideas, so please feel free to disagree:

Lead

  • "Enzymes are known to catalyze about 5,400 biochemical reactions." I see this has been updated since this passed FA. Per WP:ASOF, should this begin "As of 2013..."?
Resolved by Boghog. Adrian J. Hunter(talkcontribs) 02:39, 8 March 2015 (UTC)
  • "For example, the reaction catalyzed by orotidine 5'-phosphate decarboxylase will consume half of its substrate in 78 million years if no enzyme is present. When decarboxylase is added, the same process takes just 25 milliseconds." A striking example, but (1) seems like a lot of words for one concept in the lead, (2) seems overprecise - surely the rate when enzyme is present will depend on the amount of enzyme added, as well as temperature etc (3) seems odd to me to cite a primary study like this in the lead (4) this sort of clashes with the preceding sentence, as it is not strictly an example of an enzyme making a reaction occur millions of times faster. Would anyone else support moving this example to #Kinetics or elsewhere?
Resolved T.Shafee(Evo﹠Evo)talk 23:26, 7 March 2015 (UTC)
  • "Enzymes are also affected by features of their environment, such as temperature, pressure, and pH." Kinda humdrum... Suggest something along the lines of "An enzyme's activity decreases markedly outside a narrow range of temperature and pH." (I think pressure is less often relevant in biology.) Better yet, integrate with the bit about tertiary structure at the end of the preceding paragraph.
Fixed Boghog (talk) 14:49, 7 March 2015 (UTC)

Cofactors

  • "These tightly bound molecules are usually found in the active site and are involved in catalysis." Seems like the context has been lost here. The previous sentence refers to a zinc ion, which is not a molecule, and the previous paragraph explained that cofactors are not necessarily tightly bound. Is this sentence meant to refer specifically to metal ion cofactors?
Fixed Boghog (talk) 15:05, 7 March 2015 (UTC)

Thermodynamics

  • "Secondly the enzyme stabilises the transition state such that it requires less energy to achieve compared to the unanalysed reaction (ES‡)." Typo for "uncatalysed"?
Fixed Boghog (talk) 14:49, 7 March 2015 (UTC)
  • I'm probably showing my ignorance here, but the image depicts EP as lower energy than the products. Wouldn't that mean the products don't dissociate from the enzyme? Or is it that the combined energy of the dissociated products and enzyme is lower than EP, but the graph shows the energy of the products only?
YesY All good. Adrian J. Hunter(talkcontribs) 02:39, 8 March 2015 (UTC)
  • "Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive" a thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates." If anyone's feeling energetic, this is a vital concept that would be much clearer with an accompanying figure.

Adrian J. Hunter(talkcontribs) 12:42, 7 March 2015 (UTC)

Thanks for your insightful comments. In response:
  • WP:ASOF refers to information that will date quickly. The total number number of known types of enzyme catalyzed biochemical reactions has not changed that quickly (from ~4,000 ~5,000 in 9 years) and is probably slowly approaching an asymptotic limit. I may be missing something, but in the source, I cannot not locate where the 5,400 reaction number came from. The source does mention 5048 EC classes. A level 4 EC class node represents not a single reaction, but a group of closely related reactions. In this edit, I changed the text to include the phrase "greater than" so that the text will be more resistant to becoming dated. I also replaced "reaction" with "reaction types" for accuracy.
  • While the orotidine 5'-phosphate decarboxylase example may be overly detailed for the lead, this astonishingly large acceleration rate does help capture the readers attention. It is also an important property of enzymes and therefore should be included in the lead. Perhaps the language could be simplified a bit. While the cited source is primary, it is a classic paper published in a high quality journal that has been cited over 600 times. We could replace the primary source with this review: 17889251 which has the advantage of stating this is the most effective enzyme known (the rate enhancement of 1017 is 100 quadrillion which is indeed many many many million ;-). So I agree that this is not a typical example. Perhaps we should replace "For example" with "An extreme example".
  • Including your suggested text change in this edit. However I did not move its location. A change in conditions may also affect specificity (second paragraph), the main affect is on reaction rate (third paragraph). Hence this statement belong in the third paragraph.
  • Specified in this edit that cofactors may be ions or molecules for consistency with rest of section. The article seems to be consistent that cofactors are always tightly bound while coenzymes may be either weakly or strongly bound.
(Actually the article classifies coenzymes as a type of cofactor, in the first paragraph of #Cofactor. I believe different biochem textbooks define "cofactor" in different ways. All is well, though. Adrian J. Hunter(talkcontribs) 02:39, 8 March 2015 (UTC))
  • At first glance, the lower energy of the EP complex compared to dissociated E+P does seem counter intuitive but it is real and has functional significance. As product concentrations are usually low, much of the product will dissociate from the enzyme (see Le Chatelier's principle) allowing more substrate to bind. As product concentrations increase, a higher fraction of the enzyme is bound to product leading to product inhibition which limits the amount of additional product formed. This negative feedback loop helps maintain homeostasis. Boghog (talk) 14:49, 7 March 2015 (UTC)
Quick comments - on the first point, yes, the number of "reactions" was the number of EC classes, as it was in the old FA version - but it looks like I typo'd the update. Thanks for checking, Boghog!
On the ODCase data, adding a recent review discussing this isn't a bad idea (ideally full-text OA if there's one available, though the one you point out looks good), but I think the original paper should be cited for this kind of thing. This sentence has gone back and forth between the lead and the kinetics section, but I think it's effective as an up-front "wow" number. It's also a clunky fit with kinetics because ODCase is still a pretty slow enzyme in an absolute sense, which kind of undermines the wow factor. The top performers on sheer reaction rate are the diffusion-limited ones. Opabinia regalis (talk) 20:36, 7 March 2015 (UTC)
Also on the ODCase data, I've made an attempt at simplifying it by not talking in terms of T½s, but just comparative rates. Any number of uncatalysed T½s of the uncatalysed reaction measured in millions of years, happens to take roughly the same number of milliseconds when catalysed. T.Shafee(Evo﹠Evo)talk 23:26, 7 March 2015 (UTC)
Awesome, thanks all for the responses! I'm happy with all the changes. I followed Boghog's suggestion to note that OMP decarboxylase is an extreme example. Overall, I think the lead especially sounds more professional and flows much better now. Adrian J. Hunter(talkcontribs) 02:39, 8 March 2015 (UTC)

Front page[edit]

I've recently nominated the reviewed enzyme article to be featured on the front page since it's gone though so many changes since 2006. I've no idea if a page can be front-paged twice but it seemed appropriate to me. T.Shafee(Evo﹠Evo)talk 01:23, 8 March 2015 (UTC)

Too bad this is a one-and-done thing, but there's a surprising number of FAs that haven't been on the main page! IMO putting a successful FAR back in the main page queue might help convince people to fix their articles, but the whole FA system is such a delicate house of cards I'm hesitant to suggest changing anything. Opabinia regalis (talk) 07:02, 9 March 2015 (UTC)
Also, even if it's not on the main page, this article gets over 70k views a month which is good enough to be in the top 4,000 articles on the site. Not bad! Opabinia regalis (talk) 08:37, 9 March 2015 (UTC)