Talk:Protein domain

Structural domain

I don't think the Structural_domain article adds anything new. In fact some of it is out of context (Designability and disease - new research) and the definition provided is the opinion of the author, and not the definition that has been adopted in structural biology (i.e. Richardson 1981). Even the external links are out of context - domain databases that deal with sequence-domains (recurring mobile sequence modules) - where are the structural domain databases like SCOP and CATH? My suggestion would be to redirect Structural_domain to Protein domains. RAG —Preceding unsigned comment added by 129.94.6.28 (talk • contribs) 18:25, March 21, 2007

I agree; the very term structural domain is very unhelpful - since it doesn't clearly refer to proteins. This article, however, is quite a good start; what is missing is a comprehensive list of protein-protein interaction domains... (that's a huge job, and may be too much for a particular article)

Gacggt 21:36, 29 March 2007 (UTC)

Definitely, they cover the same subject. A move of the article itself may be needed too though - Domain (protein) would probably be better as the current name is plural. Richard001 03:50, 18 April 2007 (UTC)

Done. But this article now needs a lot of work.Biophys 04:08, 12 July 2007 (UTC)

Headers and subheaders added

Because the text could be very hard for some readers, I think it was a very good thing to separate it into shorter paragraphs. Now readers can fast scroll to the section they want to read, instead of haveing to read it all. You might want to check if headers and subheaders really are appropriate to the text. I've might have done mistakes. Mortsggah 16:01, 7 April 2007 (UTC)

Assessment

The article is a good length and very well referenced. It just needs a little layout work to improve readability (for example the lead section is fairly long) and the referencing needs to be converted to inline throughout. The merge from the other article is the only other issue. Richard001 03:54, 18 April 2007 (UTC)

Someone invested a lot of effort here, but he/she wrote a lot of things that belong to other articles: primary->secondary->tertiary structure, description of protein folding and some other things. They should be removed or modified.Biophys 04:19, 12 July 2007 (UTC)

Spamming Wikipedia

Biologicalworld.com has spammed wikipedia like no tomorrow. He is a site of only a few pages and a LOT of adsense. Not much information is given except for "protocols" which are not referenced, and cannot be trusted from a site of that quality.

check: Links from Wikipedia

The following have been cleaned up:

• en.wikipedia.org/wiki/Plasmid
• en.wikipedia.org/wiki/Gel_electrophoresis
• en.wikipedia.org/wiki/Green_fluorescent_protein
• en.wikipedia.org/wiki/Homology_(biology)
• en.wikipedia.org/wiki/HeLa
• en.wikipedia.org/wiki/Protease
• en.wikipedia.org/wiki/Restriction_enzyme
• en.wikipedia.org/wiki/Petri_dish
• en.wikipedia.org/wiki/Structural_domain
• en.wikipedia.org/wiki/Trypsin
• en.wikipedia.org/wiki/Oligonucleotide
• en.wikipedia.org/wiki/Transmission_electron_microscope
• en.wikipedia.org/wiki/Agar_plate
• en.wikipedia.org/wiki/Calcium_phosphate
• en.wikipedia.org/wiki/Disulfide_bond
• en.wikipedia.org/wiki/Denaturation_(biochemistry)
• en.wikipedia.org/wiki/DNA_ligase
• en.wikipedia.org/wiki/Wild_type
• en.wikipedia.org/wiki/Tissue_culture
• en.wikipedia.org/wiki/Transmission_electron_microscopy
• en.wikipedia.org/wiki/Reporter_gene
• en.wikipedia.org/wiki/Northern_blot
• en.wikipedia.org/wiki/Protein_engineering
• en.wikipedia.org/wiki/Sticky_end/blunt_end
• en.wikipedia.org/wiki/Taq_polymerase
• en.wikipedia.org/wiki/Protein_domain
• en.wikipedia.org/wiki/Coomassie
• en.wikipedia.org/wiki/Native_state
• en.wikipedia.org/wiki/Chinese_Hamster_Ovary_cell
• en.wikipedia.org/wiki/Peptidase

and many more Sciencetalks (talk) —Preceding comment was added at 02:50, 4 January 2008 (UTC)

The following is a closed discussion of the proposal. Please do not modify it. Subsequent comments should be made in a new section on the talk page. No further edits should be made to this section.

The result of the proposal was 'move. Anthony Appleyard (talk) 18:33, 3 April 2008 (UTC)

Protein domains vs Protein domain

Shouldn't this article be located at the non-plural Protein domain? The introductory paragraph even says "protein domain" and not "protein domains"... I'll be bold and move this. Jobjörn (talk) 09:18, 3 April 2008 (UTC)

Requested move

I couldn't move it, so I'm requesting a move. (See also the above section.) Jobjörn (talk) 09:22, 3 April 2008 (UTC)

The above discussion is preserved as an archive of the proposal. Please do not modify it. Subsequent comments should be made in a new section on this talk page. No further edits should be made to this section.

Content fork to protein structure

The primary structure (string of amino acids) of a protein ultimately encodes its uniquely folded 3D conformation.[19] The most important factor governing the folding of a protein into 3D structure is the distribution of polar and non-polar side chains.[20] Folding is driven by the burial of hydrophobic side chains into the interior of the molecule so to avoid contact with the aqueous environment. Generally proteins have a core of hydrophobic residues surrounded by a shell of hydrophilic residues. Since the peptide bonds themselves are polar they are neutralised by hydrogen bonding with each other when in the hydrophobic environment. This gives rise to regions of the polypeptide that form regular 3D structural patterns called secondary structure. There are two main types of secondary structure: α-helices and β-sheets.

Some simple combinations of secondary structure elements have been found to frequently occur in protein structure and are referred to as supersecondary structure or motifs. For example, the β-hairpin motif consists of two adjacent antiparallel β-strands joined by a small loop. It is present in most antiparallel β structures both as an isolated ribbon and as part of more complex β-sheets. Another common super-secondary structure is the β-α-β motif, which is frequently used to connect two parallel β-strands. The central α-helix connects the C-termini of the first strand to the N-termini of the second strand, packing its side chains against the β-sheet and therefore shielding the hydrophobic residues of the β-strands from the surface.

Biophys (talk) 14:00, 1 July 2010 (UTC)

Merge in Conserved domains

I would like to propose that the stub article Conserved domains be merged into this article. It is clear that both articles are about the same concept of a protein domain. One could argue that an article about conerved domain could talk about regions of proteins conserved in sequence. But from the title conservation could mean sequence or structural conservation. I would struggle to write to different articles under these titles and I think I know this area well. Alexbateman (talk) 14:56, 27 August 2010 (UTC)

• Agree about merging. May I ask however what is the difference between "Domains" and "Families" in PFAM? Some of the "Families" can be also found in different combinations in different proteins.Biophys (talk) 16:40, 27 August 2010 (UTC)

Merged. Biophys (talk) 23:36, 27 August 2010 (UTC)

SCOP, SMART, Pfam

Isn't it a bit peculiar to have a wide discussion of CATH, but hardly any mention of these resources? 82.134.28.194 (talk) 10:01, 16 June 2011 (UTC)

- Not when the principal author of the article used to be part of the CATH team! More seriously it's probably worth discussing the difference in approaches taken by SMART/Pfam and SCOP/CATH but it's beyond the scope of an introductory article to discuss the many, rather subtle differences between, e.g., SCOP and CATH. For consistency it's preferable to stick with one I think. The interested can be referred to the three articles now published comparing domain and classification differences between the two (Hadley & Jones, Structure 7:1099-1112 (1999) is a good start) 194.80.106.134 (talk) 12:35, 21 October 2011 (UTC)

The article should briefly discuss all relevant methods. If there is too much detail on CATH specifically, some of it can be split off, perhaps to the CATH article itself. Antony–22 (^talk⁄_contribs) 21:00, 22 October 2011 (UTC)

"Very long" tag

What are issues that are motivated into unnecessarily tagging this article as "very long"? --George Ho (talk) 19:14, 11 May 2012 (UTC)

I agree, I don't really see a problem with the article's length. It might benefit from some more imagery (I think protein domains lend themselves well to visualization anyway) but in terms of length, detail and navigability I have no complaints. --Milotoor (talk) 20:02, 14 June 2013 (UTC)