Talk:Proteasome

older entries

Although the proteasome article does include information regarding the ubiquitin proteasome system, it is important to recognize that the proteasome is only the final component of the ubiquitin proteasome system. The ubiquitin proteasome system is extremely extensive and has a high relevance to many areas of biomedical science e.g. cancer. Therefore I believe it is justified for this article exist in it's own right, but in a much more extensive form than at present.

The above paragraph was copied from the article The Ubiquitin Proteasome System which was merged with this Proeasome article. --Splette ^Talk 10:22, 19 October 2006 (UTC)

Bortezomib

Pharmacological information should relate primarily to bortezomib, the proteasome inhibitor used for multiple myeloma. JFW | T@lk 12:32, 1 November 2006 (UTC)

Pathway diagram

Motivated by the impressive diagrams of WikipedianProlific I'd like to have a go, too and draw one for the ubiquitin-proteasome-pathway. What steps do you think we should include (maybe starting from ubiquitination...) and do you know any good reviews about the topic? --Splette :) ^Talk 23:31, 2 November 2006 (UTC)

Great idea - could be useful in the ubiquitin article also. There's overview with a very schematic diagram in this paper on the role of the proteasome in autoimmune disease, and a thorough but slightly unorganized review with diagrams in this paper - IMO the structural schematics with the alpha/beta/etc subunits in the second paper would be particularly nice. Opabinia regalis 07:31, 13 November 2006 (UTC)

Consider for GA

I think that this article is about ready for GA nomination... what do you all think? – ClockworkSoul 15:00, 2 December 2006 (UTC)

I've got a bit of text left to add on the immunoproteasome and its products as MHC ligands, and Splette is planning to create a diagram or two soon, so I'd rather wait just a bit. On that general subject, though, have you heard from ShaiM recently at all? I think it would be great for the project if cell nucleus went to FAC, but since he did the balance of the work on that article, I'd hate to nominate it without him. Opabinia regalis 00:57, 3 December 2006 (UTC)

Lower level? Schematic diagram?

Ummm, my initial impression is that the article is wonderfully complete; but it could be daunting for a typical lay-reader, who might benefit from a rough sketch of the structure and function early on. Maybe you agree? If I were a novice reader (not too far off ;), I think I might have an easier time reading more like this:

The proteasome is a barrel-like structure whose core consists of four stacked rings of seven protein subunits each (reference schematic diagram here). The proteins of the inner two rings (denoted as the β subunits) can act as "protein scissors", cutting a protein into short unfolded peptides, typically only 7-11 residues long; the "blades" of these scissors are found only on the inside of the barrel, however. The proteins of the outer rings (called the α subunits) control access to the inside of the barrel, forming a very narrow gateway (≈1.1 nm across) through which only unfolded proteins may pass. Thus, the proteasome identifies proteins tagged for destruction, unfolds them and threads them into the barrel, where they are chopped into small pieces.

The proteasome is one of the main mechanisms responsible for degrading cellular proteins. Inhibition or clogging of the proteasome causes unwanted proteins to accumulate in the cell, and can lead to cell death. In general, the proteasome chops indiscriminately; however, in a few cases, the proteasome makes only specific cleavages that help a protein reach its mature form. In higher organisms, many of the resulting peptides are sent to the cell surface, where they report on the proteins being synthesized within the cell; in particular, this allows the intracellular production of foreign viral proteins to be detected extracellularly, provoking the immune system to flag that whole cell for destruction.

Ubiquitin is the tag that marks proteins for destruction by the proteasome or, more properly, a long chain of ubiquitin molecules attached to a lysine of the ill-fated protein (reference another schematic diagram here)...

This is just a sketch and, since I'm going from memory, I'm not even sure whether it's accurate! It's just meant to give you an idea of the level that I think might be more comfortable for many non-expert readers. If you all think it'd be helpful, I'd be happy to make a 2D (subunits=circles) or 3D (subunits=spheres) schematic Figure of the 20S proteasome and the poly-Ub tag.

I'll look the article over later again today and see if I have any other ideas/suggestions; this was just a cursory look. Willow 16:24, 6 December 2006 (UTC)

We've talked about a schematic for the 20S particle; Splette originally was planning on creating something similar, but I think he's been rather busy lately, if you'd like to do one. I tried just coloring the subunits in one of the proteasome structures by α or β ring, but I think a schematic would be much easier to look at.

I think you're probably right that the lead jumps into specifics too soon and could use more explanation... 'protein scissors' might be going a little too far; we do link protease, after all. I did a little bit of a rewrite; take a look... I don't think it's an improvement from a writing standpoint, but maybe it's less intimidating? Opabinia regalis 02:46, 7 December 2006 (UTC)

OK, I'll try to make a decent schematic sometime today. Do you have any special preferences for colors or layout? My initial thought is to represent the proteasome by 3D spheres located at the centroid of each subunit, perhaps using the same colors as you do in the ribbon diagram? A cutaway diagram might be cool, too, say, by removing two subunits from each ring so that the reader could look inside and see the catalytic threonines — they're found in the crystal structure, I hope, not too floppy/disordered? Oooh! cooler yet, how about modeling in a hapless polypeptide in the throes of its destruction? I'll fool around and try to make a diagram that's instructive, yet respectful of the moritura.

Re:the lead section, I'm still worried that it may confound even smart lay-people, or at least make for slow reading, since they'll have to look up what "sub-unit", "complex", "protease", etc. means. Here I feel an awful pang of conscience, since Laplace-Runge-Lenz vector is far worse for obscurity. :( — BTW, thanks very much for your excellent insights/comments over there; it's so helpful to have an extra five non-physicist/mathematician eyes look it over! :) — Still, although my own articles fall short, I would warmly encourage you to make the lead section even more accessible to those smart lay-people who may not know the terminology but wish to form a picture of the proteasome, what it's doing, and why. I sometimes think of a much-cherished aunt, but you could imagine writing for a fondly remembered history professor, a hip high-school physics teacher, a nice doctor, a savvy science reporter, or, say, a judge deciding a patent case involving proteasomes. Willow 12:16, 7 December 2006 (UTC)

I reorganized the structure paragraph a bit in the hopes of being a bit clearer. (though I think those who need to look up 'subunit' might have bigger problems... :) I think my original idea might have been the right way to go after all - the existing proteasome image is excellent, but it might give a clearer picture and cut down on the ancillary text if the alpha and beta rings were different colors. I think the cutaway idea is great. There are many structures of proteasomes complexed with inhibitors; I don't think there's one with a polypeptide - that would probably be difficult to cocrystallize - but since the original images were so nice, I didn't look too hard for new structures. Opabinia regalis 02:42, 9 December 2006 (UTC)

Rather than locating a scanner, I thought you might appreciate a Figure or three:

• Image:1G0U_subunits_sideview.png
• Image:1G0U_subunits_topview.png
• Image:1G0U_active_sites_cutaway3.png

They're described in more detail on their respective pages on the Commons. I had lots of fun making them — the proteasome is so beautiful!

Are these Figures kind of what you wanted? The third one is cute, but might need more refinement? I can fix them up however you'd like. Dream big, for magic abounds. ;) Willow 23:52, 12 December 2006 (UTC)

Excellent! You are once again awesome :) Added the first two to the structure section; what do you think?

The proteasome is a beautiful structure, isn't it? The third image is very cool - my first thought would be to make the CA atom spheres smaller, so they don't immediately catch the eye when you look at the image. Does MOLMOL allow depth cueing/fog? It might give a better sense of the 'cutaway-ness' of the middle section. Another idea - just kind of thinking 'out loud' - would be to replace the solid green spheres with a translucent green outline of the molecular surface of the alpha subunits, to illustrate the binding interactions, but that might not mesh well with the cutaway idea.

Also, you should render the final result twice as big with antialiasing and think about nominating it as a featured picture. They need more proteins! :) Opabinia regalis 01:48, 13 December 2006 (UTC)

MOLMOL does indeed have fog depth-cueing and I succeeded in shrinking the atoms down to a more decorous 3 Å. But looking at image #3 and its successors more closely, I noticed that some of the grey "loop" ribbons seemed disconnected, which I don't understand and can't seem to fix. :( So, I'm thinking of trying to re-make the Figure in PyMOL, with which I have only the vaguest experience. (Willow hears the beating of mighty wings as she rushes in. — "What can that be?" she wonders. "It sounds familiar." ;) Can you wait until tomorrow sometime? I'll do my best. :) Willow 23:23, 13 December 2006 (UTC)

No problem waiting, I'm not doing any real work tonight :) When you did the cutaway thing, did you just remove the extra subunits, or use a clipping plane? Maybe the disconnections are near or far clipping plane mispositioning errors? But you probably thought of that already anyway. Opabinia regalis 05:58, 14 December 2006 (UTC)

Proteasome category question

copied from User_talk:Serephine

Is it really an organelle? I don't think of it that way, and the closest text I had on hand gives it the next classification down - "molecular machine" - which is not really specific enough to get its own category. Opabinia regalis 03:31, 19 December 2006 (UTC)

I wasn't totally sure myself, however, I checked with a Google search ([1] [2] [3]) and found the scientific community to largely refer to it as an organelle in addition to machinery. I couldn't find anything disputing its inclusion as an organelle. Also, it is consistent with the definition of an organelle: In cell biology, an organelle is a discrete structure of a cell having specialized functions. -- Serephine ♠ talk - 03:43, 19 December 2006 (UTC)

I suppose they can be organelles :) It just sounds wrong to my mind though - like calling the spliceosome an organelle (nobody's tried to do that yet, have they?). Opabinia regalis 07:00, 19 December 2006 (UTC)

Heh heh you've caught me in a categorising mood so maybe I'll try ;) If it makes you feel any better, things like centrioles and ribosomes are included as organelles even though they have similarly non-membranous structures. -- Serephine ♠ talk - 07:21, 19 December 2006 (UTC)

Centrioles? Ugh. Organelles are membrane-bound, dammit :) Opabinia regalis 01:59, 20 December 2006 (UTC)

Featured article nomination

This review is transcluded from Wikipedia:Featured article candidates/Proteasome

The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article review. No further edits should be made to this page.

The article was promoted 20:17, 9 January 2007.

---

Proteasome

This A-class article was the Molecular and Cellular Biology collaboration from November. The current text was largely written by me, with helpful edits and image contributions from Splette and Willow. It's had an MCB peer review here and a less active main peer review here. Thanks for your comments and suggestions. Opabinia regalis 06:27, 3 January 2007 (UTC)

• Support. The article is comprehensive, well-referenced, and well-written. The editors have greatly improved the article since my comments on the peer review (where I volunteered to help with examples of prose needing improvement, then got caught up in other things and forgot to come back...sorry), especially the removal of an overuse of the passive voice. Even though some of the body of the article is still over my head, it is a complicated subject matter that I don't think could be simplified much more without turning into a whole dissertation on cellular and molecular biology. Instead, the article's lead section introduces the subject matter and conveys the main points in terms that are easily understandable to readers who want the "CliffsNotes" version of things. Nice job. Neil916 (Talk) 07:27, 3 January 2007 (UTC)
• Support. Congratulations to Opabinia et al. :) for taking a complex but very important topic and making it as accessible as it could probably ever be and an interesting read to boot. Fvasconcellos 14:56, 3 January 2007 (UTC)
• Comments

• The first paragraph in the "Unfolding and translocation" section is muddled. Could these steps be put in chronological order?

Tried to clarify. It's hard to be chronological, since it's not known whether deubiquitination (necessarily) precedes substrate unfolding, and there's still debate over which step(s) require ATP hydrolysis vs just binding. Opabinia regalis 03:14, 4 January 2007 (UTC)

• I don't understand this sentence ''The general mechanism for globular protein unfolding itself is not well characterized; however, it is not entirely independent of the amino acid sequence."

Reworded. The unfolding mechanism of the proteasome has to work on any protein that might need degrading, but some substrates are 'better' than others. Opabinia regalis 03:14, 4 January 2007 (UTC)

• Many of the references lack PMIDs

Fixed. Ugh, that's boring. Opabinia regalis 03:14, 4 January 2007 (UTC)

If any refs still lack PMIDs or formatting, I'll gladly help—I love gnome work. Fvasconcellos 21:10, 4 January 2007 (UTC)

Thanks, I think I got them all - I really should start remembering to put them in in the first place. But if you really like this stuff, then you just might be my new favorite editor...no, we need you to keep making nice SVG chemical structures! Opabinia regalis 05:08, 5 January 2007 (UTC)

Yes, you did. Thank you! :) Don't worry, I'll not get sidetracked from my goal of universal vector graphics domination... I've not even joined the Project so as not to get in over my head! Fvasconcellos 15:58, 5 January 2007 (UTC)

However, overall extremely good. TimVickers 00:44, 4 January 2007 (UTC)

Thanks for the suggestions! (Also, excellent prose fixes.) Opabinia regalis 03:14, 4 January 2007 (UTC)

Support. All my concerns have been addressed. A very good article. TimVickers 04:23, 4 January 2007 (UTC)

• Question: what is the general opinion on putting external links above the references? The references section is over a screenful on my very high-res screen; most people must see a wall of text and become rather disinclined to scroll any further. I made this move once on this article and it was un-done not long after; it is that egregious a violation of the WP:MOS? Opabinia regalis 07:39, 4 January 2007 (UTC)
  • My inclination is that external links should *always* be last, since Wikified content is preferable to external content - we don't want to send readers outside of Wiki easily. If there is something really important in an External link, it's good to try to Wikify it. I try to stick to the exact WP:MOS for that reason - See also first, as that is Wikicontent. SandyGeorgia (Talk) 16:12, 4 January 2007 (UTC)
    • That "makes sense" from an editor's perspective, but in terms of usability, the external links are not very visible buried below screenfuls of references that no one in their right mind wants to read through. (Agree about see also above links, but there's no see alsos here.) Opabinia regalis 01:09, 5 January 2007 (UTC)
      • I guess I don't have a problem with External links being buried, as our priority should be to give Wikified content, with External links being a last resort. Just my two cents, SandyGeorgia (Talk) 01:20, 6 January 2007 (UTC)
        • I suppose the link in the TOC is enough. In this case the Nobel interviews are particularly interesting, IMO. Opabinia regalis 02:08, 6 January 2007 (UTC)
• Comment Does anyone think that the lead-in is maybe too long? I'm not used to seeing four long paragraphs of text before the table of contents. --Cyde Weys 17:34, 4 January 2007 (UTC)

Good point. Lead condensed to three paragraphs. TimVickers 17:46, 4 January 2007 (UTC)

Thanks Tim. I added back the definition of protease, since it's a good bet that some readers won't know the term. Opabinia regalis 01:09, 5 January 2007 (UTC)

• Support. Seems to meet all the criteria. Comments: {{Template:Protein topics}}? Years alone shouldn't be linked per WP:DATE, I found quite a few instances where Nobel Prize in Chemistry years were linked. Remove unnecessary bolding from the "Proteasome inhibitors" section, these words should be linked rather than bolded. From the lead: In eukaryotes, they are located in both the nucleus and the cytoplasm. - Remove both, same for many other instances of the word in the article. ...consists of a total of 19 individual proteins - Remove of a total. Add a see also section and link to the Molecular and Cellular Biology portal from it. ...regions,[34] are degraded - No need in a comma here. The Polish interwiki link should probably come earlier in the interwiki list. "Enzyme" is linked twice in the lead. . ..such as infection, heat shock, or oxidative damage, heat shock proteins are expressed - Move the word or. The quotation marks in the second paragraph of the lead make it sound a bit unencyclopedic. Michaelas10 (Talk) 09:44, 5 January 2007 (UTC)
  • Fixed some of these. I don't know what you mean about the protein topics template; could you explain? I added the portal link, but given that the protein topics template is there and most other related articles are linked in the text, I don't think there's much use in a see also section. I think the quotes in the lead are, if not exactly necessary, useful in introducing the terms that used somewhat metaphorically or as an analogy. Opabinia regalis 01:06, 6 January 2007 (UTC)
• Oppose Journal names should not be abbreviated. Abbreviation might be appropriate for a medical journal, but wikipedia is not one (WP:MOS: Do not assume that your reader is familiar with the acronym or abbreviation you are using.), and the non medical students should be able toe easily trace the journal.Circeus 18:39, 5 January 2007 (UTC)
  • Comment Several recent "scientific" FAs (acute myeloid leukemia, Tourette syndrome and cell nucleus to name a few) passed FAC with abbreviated journal names in References. I assume this would be easy enough to fix, but, as this could have significant ramifications (e.g. stipulate the use of full journal names in WP:MEDMOS?) I would, no offense, like to hear other editors' opinions. Fvasconcellos 19:14, 5 January 2007 (UTC)
    • I've found these abbreviated references to be consistently unhelpful, sometimes *actively* so, and systematically change them to longer names when I happen to copyedit medical articles. If it's the task that you find annoying, I can do it myself, and I would have opposed every single of these medical articles on the same ground. I certainly would favor a change in WP:MEDMOS if that is what is needed for this practice to change (I didn't even know such a style guide existed!). It's just another example of the jargonistic tendencies of the medical community to me. Of course, your request for comments is only relevant as far as those commenting are not familiar with the practice of abbreviating journal names.Circeus 19:46, 5 January 2007 (UTC)
      • As I mentioned above, I have no problem whatsoever in doing "grunt" work—it probably wouldn't take more than a few minutes. What I meant by requesting comments was to make sure no one would object to such a change. By the way, WP:MEDMOS is still a proposed guideline, so feel free to comment on its Talk page if you like. Fvasconcellos 20:10, 5 January 2007 (UTC)
    • You can change this if you want, but I don't think this is much of an issue, since authors and title is all you meed to find any article in PubMed and if it has a PMID it is even simpler. It certainly doesn't hurt though and it might help somebody under some circumstances I can't think of. TimVickers 22:53, 5 January 2007 (UTC)
  • I hope I don't sound reactionary in thinking this is an increase in text clutter with little practical benefit? I'm curous to know where/how you're searching if abbreviated journal names are an impediment. Because the abbreviations are standardized and unique, they're actually at least as good if not better than the full title if you just want to find the journal - a search for "chem phys" will get what you want, but "chemical physics" will pick up Chemical Physics, Journal of Chemical Physics, Chemical Physics Letters, etc. And the linked PMIDs largely obviate the need for searching for the citations anyway. Opabinia regalis 01:06, 6 January 2007 (UTC)
    • I disagree with Circeus here for the simple reason that Wiki provides a PMID template which links to the full information on journal-published research - there's no reason to take up space when full bibliographic info and an abstract is one click away, and when standard abbreviations are used. On the other hand, if the trend takes hold, I'll do the grunt work as well (sigh) - but it will certainly take more than a few minutes - it will take me weeks on everything I've written. If this is a strong objection, Circeus might approach Diberri about changing his script to give the full journal name, because doing them by hand will be a b. SandyGeorgia (Talk) 01:18, 6 January 2007 (UTC)
      • Did some more checking, and I don't believe it's possible for Diberri's script to return full journal names, since even PubMed doesn't cite them without clicking on a separate place - so, if we have to do this, it will all be done manually, and will be a lot of work. I also disagree with the argument about laypersons vs. medical jargon - I'm a layperson - all I need to know is how to find PubMed, or Medline if I want to order the full text of the article. I've never known the full names of the journals, or needed them. When I go to a medical library to request the full text of an article, the abbreviations are standard, and there's never been a problem locating the journal I'm asking for. I really don't consider this a valid objection. SandyGeorgia (Talk) 01:47, 6 January 2007 (UTC)
    • It can only be construed as "an increase in text clutter" by people who a) know that some/many journals have "standard" abbreviations. b) are used to seeing them. 90% of our readership don't. Circeus 13:18, 9 January 2007 (UTC)
  • Comment Circeus' suggested formatting of journal titles does not currently have consensus among editors in the sciences. See also followup here and here. Opabinia regalis 05:46, 9 January 2007 (UTC)

If you want to see the reference, click on the link. It is that simple. TimVickers 16:34, 9 January 2007 (UTC)

• Support with a nitpik - book sources need page numbers, pls separate and plug those in, along with an ISBN for the book. (^ a b c d Lodish, H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Cell Biology', 5th, New York: WH Freeman.) SandyGeorgia (Talk) 01:25, 6 January 2007 (UTC)
  • ISBN added, thanks. Honestly, while I admire your consistent push for better referencing, requiring page numbers on generic textbook references raises my academic heckles. Citations to standard, uncontroversial textbook material are provided for the reader to have a general reference - I never (well, I try not to) cite a textbook for anything that isn't thoroughly well-established material that could be found in any decent text on the subject (I use the Lodish text because that's the one I have on hand, but another one would do just as well). In cases where there are dozens of citations to many disparate portions of the same text, I can see the utility, but here I don't see the point in repeating the same citation four times just to say "p66", "p68", etc. I added the (very short) page range covering the general introduction to proteolysis and the proteasome. What do you think? Opabinia regalis 02:08, 6 January 2007 (UTC)
    • I think that's a fine solution (which I couldn't have known beforehand, since I didn't know the actual pages - sorry to suggest individual page nos when they turn out to be in such a close bracket - but since I wasn't objecting anyway ... ). SandyGeorgia (Talk) 03:30, 6 January 2007 (UTC)
      • Sorry, that was more of a general rant, mostly written before I looked up the page numbers :) I'll get off the soapbox now. Opabinia regalis 03:34, 6 January 2007 (UTC)
        • No need :-) Best, SandyGeorgia (Talk) 03:37, 6 January 2007 (UTC)
• Comments. Not quite there, but nearly. Let's look at the lead.
  • "as well as" (opening sentence) is a marked form of "and". Why is it unexpected that some bacteria should be in the list?
    • See the evolution section - current thinking is that the proteasome proper evolved from hslVU after the divergence of archaea and bacteria, in the archaeal lineage that led to eukaryogenesis. Then lateral gene transfer occurred in those bacteria that possess a proteasome. So it is surprising that bacteria have a 20S proteasome, especially since they don't express ubiquitin itself.
  • "of about 7–8 amino acids long"—better "of seven to eight amino acids long"; but I'm still unsure of the meaning. Should "long" be "length"? Does an acid have length?
    • The lead reorganization lost the wikilink to amino acid, which should answer that question. Wrote the numbers out, but some hedge is needed, since the products' length varies depending on the organism and state of the cell.
  • "Each ring is in turn composed of seven individual proteins"—Is "in turn" necessary?
  • "are made from seven β subunits"—"of", to avoid the sense that only part of the subunits contributes?
  • "was acknowledged in the awarding of the 2004 Nobel Prize"—Remove "ing".

It's very good, but I think you might ask the League of Copy-editors to do a quick once-over when everything else is fixed. Fresh eyes required, and it won't take them long. Tony 11:28, 6 January 2007 (UTC)

Last three minor things fixed, couple of later wording failures fixed; I'll give the copyeditors a ring. Opabinia regalis 03:59, 7 January 2007 (UTC)

The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article review. No further edits should be made to this page.

Ubiquitin proteasome pathway

Should "ubiquitin proteasome pathway" be hyphenated (i.e., ubiquitin-proteasome pathway)? A quick Google search suggests so; I have also frequently seen it hyphenated in Portuguese. Fvasconcellos 15:04, 3 January 2007 (UTC)

Missed this yesterday, but I think you're right. Also made ubiquitin-proteasome system et al. as redirects. Opabinia regalis 01:32, 5 January 2007 (UTC)

Thank you. Fvasconcellos 17:39, 5 January 2007 (UTC)

Alfred Goldberg

Does anybody know something about him? He discovered it... — Preceding unsigned comment added by 98.216.105.235 (talk) 03:13, 11 August 2011 (UTC)

Types of Ubiquitin Chains

I added a little information on how there are different types of ubiquitin chains, and that only a subset of these chains will target proteins to the proteasome Maximus155 (talk) 00:43, 3 February 2013 (UTC)

E3 Ubiquitin Ligases

A newer review article talks a lot about the E3 ligases. Not sure if its needs its own page or a least add some of the names mentioned in the article. The article can be found at http://www.ncbi.nlm.nih.gov/pubmed?term=the%20ubiquitin-proteasome%20system%3A%20central%20modifier%20of%20plant%20signalling BreCaitlin (talk) 01:36, 4 February 2013 (UTC)

Types of Proteasomes

I'm fairly new to using wikipedia, and until this article, I have not uploaded any images. However, there is a great image in a review article: http://www.ncbi.nlm.nih.gov/pubmed/23029643 that details the several types of proteasomes that exist. Although I realize that there is the potential for a copyright infringement, I uploaded the photo to Commons Wikipedia and inserted it into the article under "Role in the Immune System." Unfortunately, I did not know what copyright tag to use on the photo and so I put it as "fairuse" (which I know is not allowed). I did this hoping that someone would be able to clarify the issue and put the correct tag on it and/or delete it. However, since I found the article online (NCBI) and it is available to the public, I was assuming the copyright permission for redistribution was also allowed. Would someone be willing to respond and tell me what the criteria are for images in scholarly articles?

Also, if it turns out the image I did use is in violation of copyright law and must be removed, I still think that adding an image to show the several types of proteasomes and their components would be ideal. Therefore, maybe someone would be willing to create a diagram or cartoon of this? Thanks! MChapman5 (talk) 02:02, 4 February 2013 (UTC)

• Thanks for the bold editing! From my understanding, though, use of published content from journal articles in wikipedia articles isn't covered under Fair Use. It may be available through PubMed but the image copyright is likely held by the article's publisher (in this case, Walter de Gruyter). That being said, creating a new image describing the same kind of material should clear any copyright issues. §everal⇒|Times 03:02, 4 February 2013 (UTC)

Recently Discovered Function of Immunoproteasome

There is new research [4] that shows that the immunoproteasome has another function outside of processing proteins for MHC I. It demonstrates that the immunoproteasome also helps to prevent apoptosis during IFN-induced oxidative stress. I want to include this information in this article, but I am not sure whether it should be included in the Apoptosis or Response to Cellular Stress section. Gpruett2 (talk) 04:38, 4 February 2013 (UTC)

• Sounds to me like it would work well in the Apoptosis section. §everal⇒|Times 17:23, 4 February 2013 (UTC)

S26 Proteasome Distinction

There are several references made the S26 Proteasome, but none of them out right say that they are only found in Eukaryotes. I would like to add this in one place based upon the following reference As I am a new Wikipedian I would like some feedback from more senior members. — Preceding unsigned comment added by Hakkinen2013 (talk • contribs) 17:32, 4 February 2013 (UTC)

• That reference looks like a good, recent review, though I can't access the paper so I don't know how clearly it states that the 26S proteasome is restricted to eukaryotes. I say, add it anyway. Here is the ref code if it helps - just remove the nowiki tags: <ref>{{cite journal|last=Tanaka|first=K|coauthors=Mizushima, T; Saeki, Y|title=The proteasome: molecular machinery and pathophysiological roles.|journal=Biological chemistry|date=2012 Apr|volume=393|issue=4|pages=217-34|pmid=23029643}}</ref> §everal⇒|Times 19:32, 4 February 2013 (UTC)

References

Uses of Ubiquitin

I propose that a section be added to explain some of the laboratory uses of ubiquitin. For example, ubiquitin can be used to create an N-terminal fusion with your Protein of Interest (N-Ub-POI-C). This fusion protein could be transformed/transfected into a cell for expression (plasmid: 5'-promoter-Shine/Dalgarno-(1)-Ubiquitin-ORF-3'). This would be done because an N-terminal ubiquitin fusion can augment yield of your protein of interest ("Butt et al. 1989. "Ubiquitin fusion augments the yield of cloned gene products in Escherichia coli." Proc. Natl. Acad. Sci. USA. 86(8):2540-2544.)

The ubiquitin can then be cleaved from your protein of interest by any of a number of ubiquitin C-terminal hydrolases (Catherine A. Gilchrist, Douglas A. Gray and Rohan T. Baker. 1997. "A Ubiquitin-specific Protease That Efficiently Cleaves the Ubiquitin-Proline Bond." Journal of Biological Chemistry. 272(51):32280-5.)

97.77.53.176 (talk) 02:47, 7 May 2013 (UTC)

• That sounds fine, though I think the page on ubiquitin may be a better place for that material. §everal⇒|Times 15:30, 7 May 2013 (UTC)

Possible FAR

1. Lead section is too short, doesn't nearly summarize key points of its contents;
2. Chapter "Overview", second paragraph with no citation;
3. Aaron Ciechanover, Avram Hershko and Irwin Rose receive 2004 Nobel Prize in Chemistry, but after mention it at "overview", it shouldn't immediately repeat at next chapter;
4. Chapter "19S regulatory particle", second paragraph needs more citation; also with a lot sections need clear there sources, something like "Many bacteria also possess other homologs of the proteasome and an associated ATPase, most notably ClpP and ClpX. This redundancy explains why the HslUV system is not essential.""Lactacystin covalently modifies the amino-terminal threonine of catalytic β subunits of the proteasome, particularly the β5 subunit responsible for the proteasome's chymotrypsin-like activity. This discovery helped to establish the proteasome as a mechanistically novel class of protease: an amino-terminal threonine protease."--Jarodalien (talk) 14:13, 17 January 2016 (UTC)

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Sulfolobus

Proteasome in Sulfolobus:

• Evolutionary Insight: New Connection Discovered Between Primordial Organisms and Complex Life; on: SciTechDaily; August 28, 2020; source: Lancaster University
• Gabriel Tarrason Risa, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, Dimitra Papatziamou, Delyan R. Mutavchiev, Catherine Fan, Leticia Meneguello, Andre Arashiro Pulschen, Gautam Dey, Siân Culley, Mairi Kilkenny, Diorge P. Souza, Luca Pellegrini, Robertus A. M. de Bruin, Ricardo Henriques, Ambrosius P. Snijders, Andela Šaric, Ann-Christin Lindås, Nicholas P. Robinson, Buzz Baum: “The proteasome controls ESCRT-III–mediated cell division in an archaeon”; In: Science; 7 August 2020; doi:10.1126/science.aaz2532

Is it worth to add to the article? --Ernsts (talk) 16:05, 28 August 2020 (UTC)

WP:URFA/2020

I am reviewing this article as part of WP:URFA/2020, an initiative to review older featured articles to ensure that they still meet the featured article criteria. I have some concerns that this article does not meet the criteria anymore, which I outline below:

• There are many uncited statements, and whole paragraphs without citations.
• The "Clinical significance" section, particularily the last paragraph, uses a lot of sources from the early 2000s that need to be updated with more current medical literature. This will ensure that the information here is accurate and include the most recent discoveries of the protein.
• "Role in the immune system" could also be updated with more current literature, as the most recent source is from 2010.
• Other sections could also do with a review to see if the medical literature still supports the statements in the article.

Is anyone willing to undertake upgrading this article? I struggle with science topics so I can only help with jargon concerns at the end of the process. Z1720 (talk) 17:25, 17 July 2023 (UTC)