Talk:Protein–protein interaction

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 28 August 2018 and 14 December 2018. Further details are available on the course page. Student editor(s): 1974manish.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 02:47, 18 January 2022 (UTC)

Wiki Education Foundation-supported course assignment

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Jukakim.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 07:21, 17 January 2022 (UTC)

How does Protein-protein interaction work?

This article is called "Protein-protein interaction", but it is mostly about how they are detected. Does anybody know more about the molecular concepts of the interactions (like leucine zipper, etc.)? —Preceding unsigned comment added by 134.102.101.48 (talk) 12:10, 18 August 2009 (UTC)

Merge.

I am against merging this article with the one on Protein-protein docking. Protein docking is a bioinformatics method. Protein-protein interactions are an observable. But this article needs expansion.--Miguel Andrade 15:15, 24 January 2006 (UTC)

You are correct about not merging. However, Protein-protein interaction methods include also protein docking modeling, Molecular Dynamics of several kinds , as well as several theoretical analysis methods that have now been included in this entry. Nu 23:57, 26 May 2009 (UTC)Talk

Bci2:Talk

Scope.

I think this article should be made more general. Currently it is focussed on mapping of protein-protein interaction networks. Protein-protein interaction are also important in structural biochemistry. For example, I believe the physico-chemical mechanisms (ie intermolecular forces) would be of interest here. Hendrik Fuß 09:34, 6 May 2007 (UTC)

Agreed. Such changes have been incorporated .

Bci2 May 26, 2009,Nu 00:17, 27 May 2009 (UTC)

Sugiyama.

I dont think Sugiyama (layout algorithm) is force-directed. Can anyone check and edit? —Preceding unsigned comment added by 65.207.2.2 (talk • contribs) 2007-08-13T17:01:46

X-ray crystallography and NMR.

In my opinion this part still lacks information on X-ray crystallography and NMR, which are techniques to study protein-protein interactions. I'm not sure if you could call it detection methods, because they are more useful to study the details of the interaction. Perhaps a link to these subject is enough? Cheers, Sandra —Preceding unsigned comment added by 132.229.113.29 (talk • contribs) 2007-10-05t13:33:14z

Agreed: NMR techniques have been specifically included. Bci2Nu 00:18, 27 May 2009 (UTC)BCi2, 2009 Bci2

External links.

I wish to share with the users a link for a free access valid 7 days of a protein interaction knowledgebase kindly advise me on the same —Preceding unsigned comment added by Jkbioinfo (talk • contribs) 2007-11-05t12:12:28z

Post the link here, and if the editors of this article think it's useful they can add it. -- Jeandré, 2007-11-11t10:07z

Protein Microarrays

I believe Protein Microarrays are a way to identify protein-protein interactions and should be added to the list.--ZareliMan (talk) 23:03, 22 June 2008 (UTC)

I agree that protein array like nucleic acid programmable protein array (NAPPA) technology should be added to the method list of protein-protein interaction. This method has the advantage of bypassing protein purification procedure which is time consuming and expensive and large number of protein can be identified in the single reaction.1974manish (talk) 14:40, 29 November 2018 (UTC)

differentiation

In my opinion there should be differentiation between methods that enable studying specific interactions (like with antibodies where its target must be determined) and methods for searching unknown/potential protein interactions. —Preceding unsigned comment added by 153.19.202.101 (talk) 17:11, 22 June 2010 (UTC)

Gold standard? direct protein-protein interactions

The article says: Co-immunoprecipitation is considered to be the gold standard assay for protein–protein interactions... Yet later in the paragraph it says A note of caution also is that immunoprecipitation experiments reveal direct and indirect interactions. Thus, positive results may indicate that two proteins interact directly or may interact via one or more bridging molecules. So while it might be reliable for detecting interactions, it doesn't reliably indicate a direct interaction. Perhaps the article could be clearer on how to identify direct protein-protein interactions. pgr94 (talk) 09:32, 25 July 2010 (UTC)

Therapeutics

Molcules that disrupt protein-protein interactions have therapeutic applications. It would be good to add a new section to this article on the subject. Here are a couple of papers that looks like they would provide a good starting point although they are a little old.

• Arkin MR, Wells JA (2004). "Small-molecule inhibitors of protein-protein interactions: progressing towards the dream". Nat Rev Drug Discov. 3 (4): 301–17. doi:10.1038/nrd1343. PMID 15060526. {{cite journal}}: Unknown parameter |month= ignored (help)
• Arkin M (2005). "Protein-protein interactions and cancer: small molecules going in for the kill". Curr Opin Chem Biol. 9 (3): 317–24. doi:10.1016/j.cbpa.2005.03.001. PMID 15939335. {{cite journal}}: Unknown parameter |month= ignored (help)

Any volunteers?Alexbateman (talk) 11:08, 8 August 2010 (UTC)

Assessment

This article was rated as a WP:Good Article. Looking at WP:Assessment suggested this was too high as the article still has a number of issues to be dealt with. There is some substantial content particularly around PPI discovery techniques, but there are important areas missing so I think that a C-class is reasonable. Alexbateman (talk) 11:21, 8 August 2010 (UTC)

It seems this article was promoted to GA in May 2009 without being nominated and reviewed (see diff). Given that, I think your summary demotion of the article was appropriate. However please note that a more formal good article reassessment must be completed before demoting articles which have legitimately attained GA status. Emw (talk) 13:44, 8 August 2010 (UTC)

Thanks for pointing out the correct procedure! WP:Assessment is a new area for me. Alexbateman (talk) 12:55, 9 August 2010 (UTC)

Merge proposal

I would suggest that the Multiprotein complex article be merged into this article. The current content of the two articles is not completely overlapping, but in my opinion they are the really the same thing from two different perspectives. Alexbateman (talk) 10:40, 22 August 2012 (UTC)

Alex, I am not in favor of merging at this point but I completely agree that redundancies should be removed or reduced. There are distinct properties of complexes that have little to do with PPIs, most importantly the fact that PPIs are often not known within a complex. Neither article is very well developed so there needs to be more information on both. I suggest to bring up the merger proposal again once there is more data. Peteruetz (talk) 18:35, 11 July 2013 (UTC)

Editing

I'm editing this topic and I read all suggestions that have been already made. In fact, there are some missing contents... So I'm thinking about: - change a little bit the introduction and include some consequences that emerge of aberrant protein-protein interactions; - introduce "classes of protein-protein interactions" (homo-oligomers and hetero-oligomers); - introduce "structural domains involved in protein-protein interactions" (SH2, SH3, PDZ, LIM, etc.); - introduce "characterization of protein-protein interfaces"; - introduce "factors that regulate protein-protein association"; - complete the techniques to study protein-protein interactions; - add a topic on "protein-protein networks" that includes the sections "visualization of networks" and "database collections" and additional information; - add a final section about the importance of study protein-protein interactions (drug targets). --JulianaCF (talk) 19:56, 19 December 2013 (UTC)

Hi. These all sound like good suggestions to me. Thanks for contributing! Alexbateman (talk) 20:47, 6 January 2014 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Protein–protein interaction/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Changed rating to "high" as this is an overview of protein-protein interaction. The article needs to be expanded to include sections on common interaction domains, biological significance, e.g. homo- and heterodimer formation of transcription factors etc. - tameeria 22:27, 18 February 2007 (UTC)

Last edited at 01:47, 1 January 2012 (UTC). Substituted at 03:29, 30 April 2016 (UTC)

Nucleic acid programmable protein array (NAPPA) technology

Protein-protein interaction Wikipedia Critique for protein-protein interaction for writing class, Fall 2018. The article I choose to work on is a good article, but I found recent methods for identifying protein-protein interaction are missing. The information mentioned in this article is clear and cover all the related field. The method section only covers the conventional method, but we can include a new and effective method like nucleic acid programmable protein array (NAPPA) technology and we can add the image, advantage, and limitation of this method. The information of the article is taken from a large number source and most of the source article are from the peer-reviewed article like advance molecular and cellular biology, Plos, Nature. In this article, a new method like protein array(NAPPA technology) is only included in subheading other protein methods, but I think it should be included as a main method along with other methods.1974manish (talk) 14:39, 29 November 2018 (UTC)

Phase transitions

I would like to write a section on how protein-protein interactions play a major role in the physical state of a solution of proteins. Namely, the miscibility of some proteins is concentration dependent, resulting in phase separation for certain concentrations. I'll rustle up a few review papers on this subject and start, unless anyone has any major concerns.

Cheers Malnu (talk) Malnu (talk) 14:17, 12 February 2024 (UTC)

Membrane transport: source

Hello. I saw on this article that it required a source to state that proteins can be carried by other proteins, such as when one from the cytoplasm is translocated into the nucleus.

"A protein may be carrying another protein (for example, from cytoplasm to nucleus or vice versa in the case of the nuclear pore importins).^{[citation needed]}"

Both Albert et al's book (Molecular Biology of The Cell, 7th edition) and Lodish et al's book (Molecular Cell Biology, 8th edition) talk about it in their 12th chapter "Intracellular Organization and Protein Sorting" and section 6 "Transport In and Out of the Nucleus" of chapter 13 "Moving Proteins into Membranes and Organelles", respectively.

I suggest that the required citation is either removed or that one of these sources is added. Itawewhr (talk) 20:34, 6 March 2024 (UTC)