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A fact from this article appeared on Wikipedia's Main Page in the "Did you know?" column on April 17, 2012. The text of the entry was: Did you know ... that the protein Concanavalin A (pictured) cuts itself in two and then reassembles in a circularly permuted order? |
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This article was adapted from
Spencer Bliven; Andreas Prlić (2012). "Circular permutation in proteins". PLOS Computational Biology. 8 (3): e1002445. doi:10.1371/JOURNAL.PCBI.1002445. ISSN 1553-734X. PMC 3320104. PMID 22496628. Wikidata Q5121672.((cite journal)) : CS1 maint: unflagged free DOI (link) after peer review (reviewer reports) under a CC BY 4.0 license (2012). |
Just a quick note that Spencer Bliven and I are working on a major extension of this article, which we will try to submit to the PLoS comp biol Topics section as discussed at WP:COMPBIO and WP:MCB. --Andreas (talk) 00:25, 29 September 2011 (UTC)
The new version of the article is emerging here. We are editing outside of wikipedia, so we can license the text under a dual license (CC-by and CC-by-sa), so this is compliant both with PloS and wikipedia requirements. --Andreas (talk) 05:40, 17 November 2011 (UTC)
We're waiting on PLoS to publish the article, due to the dual license. Expect the new version to replace the one here sometime Thursday 29 March. --Quantum7 05:22, 28 March 2012 (UTC)
The article has been published now at PLoS comp biol, see also the related editorial. --Andreas (talk) 22:54, 29 March 2012 (UTC)
The existing stub was completely rewritten as part of PLoS Computational Biology's new Topic Page feature. The article was drafted on the PLoS topic page wiki, then peer reviewed and published on PLoS Comp Biol under their CC-BY-2.5 license.
Finally, a note on licensing. Andreas Prlić was the major author of the preexisting stub article. However, to avoid any conflict between wikipedia's CC-BY-SA-3.0 license and the PLoS CC-BY-2.5 license, the article was completely rewritten.
We enjoyed working with PLoS on improving this article, and hope that the Topic Page track will lead to many more improvements to wikipedia's coverage of computational biology.
--Spencer Bliven Quantum7 22:59, 29 March 2012 (UTC)
The version of this article that was published at PLoS comp biol underwent an open peer review process. Here what was discussed at http://topicpages.ploscompbiol.org/wiki/Talk:Circular_permutation_in_proteins. --Andreas (talk) 23:15, 29 March 2012 (UTC)
Spencer, below you'll find Rob Russell's review. I am awaiting to hear from one other reviewer, shortly. Please await to hear from the other reviewer before implementing any changes to this page.
This page describes circularly permuted proteins and for the most part is a good starting point for this subject. However, I have several comments.
The first line reads "Circular permutation is a process during evolution <http://en.wikipedia.org/w/index.php?title=Evolution> that changes..." I think strictly speaking it isn't an evolutionary process, but a description of the relationship between proteins that sometimes is a clear evolutionary process (sometimes a post-translational one, which I get-it is also evolutionary in some sense; at other times they are engineered as the author points out). The first permutation (concanavalin A) is more of a functional modification. I think a better opener would be to speak of it as a relationship between proteins. in other words, "Circular permutation in proteins describes the situation where one protein is circularly permuted relative to another related protein." (and then ellaborate on the other points)
I would perhaps mention that the post-translational modification of concanavalin A is a cleavage and an unusual protein-ligation (there are, I presume, suitable cross-references here too).
Re: the Swaposin story, Russell has two Ls, and I would avoid the non-wikipedia subjectivity statements like "lighthearted" - I would just say nicknamed. These are the kinds of things that get flagged in Wikipedia - the stuff has to read like an encyclopedia and not an editorial.
Re: Programmatic detection. I think this English is a bit dubious and perhaps the section would be more appropriately headed "Detection of Circular Permuations" (or similar). This section could also do with some slightly longer introduction about why it is problematic to detect these using standard techniques like dynamic programming, etc. And one reference in this list is missing which I believe to be the first method to detect permutations: Michael Zuker, JMB 221:403-420, 1991 Suboptimal sequence alignment in molecular biology: Alignment with error analysis.
The figure showing Concanavalin A and Lectin is a little hard to understand - it might be easier to use a two color (N- and C- terminus) rather than a color ramp, but perhaps this won't help - worth trying perhaps.
Circular permutation is a process during evolution ... Concur with Robb Russell. Circular permutation is not just an evolutionary process, since it can be made in the laboratory by engineering, as the article shows later.
Circular permutation ... changes the order of amino acids ... A process that changes the order of the amino acid residues would be called simply as a permutation. Circular permutation is a particular kind of permutation, wherein the N- and C- termini of one protein is found joined together in another that is homologous.
Genetic mechanism of circular permutation One could add exon shuffling as another potential mechanism.
Among the motivations for engineering circular permutation One could mention not only the order in which it folds, but also its effect on folding kinetics (with reference to some of Howard K. Schachman's work).
"Programmatic" detection of circular permutation Concur with Robb Russell.
Spencer, the review process is complete. Please modify your pages, provide me with details about the modifications that you introduced either by e-mail, or on the discussion page of the revised version (Don't know exactly who this works..) , and send me the link to the revised version.
Thanks to Dr. Russell and Dr. Lee for their helpful reviews of our topic page. The manuscript has been significantly rewritten in response to their comments.
A full diff of the revisions made can be viewed at [1]
In addition to addressing the comments from the reviewers, the following sections were added or heavily modified. We would welcome any additional comments on these sections.
Spencer Bliven 18:29, 14 December 2011 (PST)
Andreas Prlić 18:38, 14 December 2011 (PST)
I hope this won't discourage what you are attempting to do here, I think you're onto a useful project:
As distinct from the norms in journals, Wikipedia discourages the use of primary sources, as their selection and interpretation is itself considered a form of original research, something which we avoid as a matter of policy. This article makes extensive use of such sources. There are possible ways to remedy this. For the references which were published long ago, there are frequently other published sources that review or at least cite them, discussing the same ideas. Alternatively, primary sources may be used, with caution, being careful not to put their ideas in "the voice of the encyclopedia". Instead, they are reported as inline-attributed statements, such as
Huang et al. reported on a dozen different green fluorescent proteins made by leaving out each of twelve secondary structure elements.[1]
Still, such statements should be used with restraint, particularly if the editors of the Wikipedia article have any connection which might impute their independence from the original work.
Pubmed's filtering capability is a useful tool in selecting secondary sources. After querying on your subject terms, simply click on "See reviews" to show only secondary sources. This is not fail-proof, but it is helpful. LeadSongDog come howl! 21:44, 31 March 2012 (UTC)
Excellent, very well-written article, imo. It could be rewritten at a more general level in a few areas. I have not read it fully to understand the primary research issue, but this should be carefully reported, if at all, to fully comply with Wikipedia's stated standards.
A great addition to Wikipedia. Thanks for everyone who wrote or reviewed. 68.107.141.42 (talk) 15:57, 17 April 2012 (UTC)
An older revision by User:Abyzov added the TOPOFIT algorithm to the algorithm list. User:U+003F promptly reverted the edit as self promotion. I think that in general, we should be forgiving of self promotion in expanding the algorithms list. For instance, the Structural alignment software contains many contributions by algorithm authors.
That said, I do not think TOPOFIT should be included in the list. The server fails to find even trivial circular permutations, such as 3P28.A vs 3AI5.A, which are 100% sequence identical and have nearly identical structures. While the paper[2] does claim to be topologically independent, it doesn't seem to work for me for circular permutations.
--Quantum7 23:37, 11 May 2012 (UTC)
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Reviewing |
Note to reviewers: This article was written as part of PLoS Computational Biology's new Topic Page feature. The article was drafted on the PLoS topic page wiki, then peer reviewed and published on PLoS Comp Biol. Whilst I've nominated this article in its own right, I'd also appreciate any feedback as to how these Topic Pages can be closer aligned with WP guidelines.
Reviewer: Sasata (talk · contribs) 05:49, 20 September 2012 (UTC)
I'll review this. Will need a few days to read carefully (and juggle other things). Sasata (talk) 05:49, 20 September 2012 (UTC)
Comments. Here's are some comments from a quick readthrough. I'll do a literature check and check compliance with criteria 2 and 3 soon. Sasata (talk) 17:23, 27 September 2012 (UTC)
Thanks again. I've had a first pass at dealing with your comments and suggestions. Let me know what you think. U+003F? 17:56, 3 October 2012 (UTC)