Talk:Biomolecular structure

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Sections other than prediction[edit]

This article is exclusively about structure prediction, not RNA structure in general. Interesting facts related to RNA structure, but not prediction specifically, include: Depending on the structure, a given RNA molecule will have regions of relatively high or low accessibility. For mRNA, highly accessible regions are more sensitive to RNA-interference (RNAi). Highly structured RNA slows and causes ribosomal pausing during translation (See Farabaugh, P. J. Programmed translational frameshifting. Microbiol. Rev. 60) (See Wen, J. D. et al. Following translation by single ribosomes one codon at a time.)

However, we already have a List of RNA structure prediction software, and we also have a section in the RNA article called Structure [[1]], which mention secondary structure.

So, I guess the question is, what do we want this article to be about? --Adamuu (talk) 17:06, 6 August 2009 (UTC)

Massive reorganization of biomolecular structure articles[edit]

This article was moved from RNA structure as a result of a proposal at WT:MCB. RNA structure now redirects to Nucleic acid structure instead.

A number of redirects have been changed to point here (most notably Primary structure, Secondary structure, Tertiary structure, and Quaternary structure). Editors may want to consider redirecting these wikilinks to point to the appropriate protein or nucleic acid whateverary structure article instead. Antony-22 (talk) 18:47, 10 April 2010 (UTC)

Expand request[edit]

PLEASE EXPAND ARTICLE: INCLUDE ACCUARATE DIAGRAMS — Preceding unsigned comment added by Ridem92 (talkcontribs) 17:32, 13 October 2010

Do you have any specific requests? This general sort of criticism isn't terribly helpful as it could be applied to any Wikipedia article.--Paul (talk) 12:28, 14 October 2010 (UTC)

Suggestions to improve clarity[edit]

main image until Nov 2016

I have two main problems with this article. The first is that its treatment of primary through quaternary structures is inconsistent and unclear. For starters, are all four levels of structure relevant to the same class of entities? If not, then which apply to which and why? As it currently reads, primary seems to apply to "biological molecules," while secondary applies to [at least some] biopolymers, tertiary applies to macromolecules, and finally quaternary applies to "protein molecules." Likewise, as it currently reads, primary applies within biochemistry, secondary within biochemistry and structural biology, tertiary within biochemistry and molecular biology, and quaternary once again within biochemistry. I suspect that this is just inconsistency deserving of some cleaning up, but I would not perform that cleaning up before knowing that it was indeed appropriate to do.

Secondly, the lead ought to do a better job of sketching out the similarities and differences between the four levels of structure. I'll focus these comments on the accompanying image (Protein_structure.png). It would appear that the image was included in order to convey the relationships between the four levels, but as for myself, I've had to puzzle several minutes over it before arriving at this (hypothesized!) interpretation:

"Along the bottom of the image are two sequences of amino acids. I guess each is a primary structure, and that's not too unclear.
"Now, judging from the colors of their respective text, and from those colors' similarity (but not identity) to the two main colors in the subimages labeled α-helix and β-sheet, even though those two subimages are spaced pretty far apart, they must constitute the part of the image being labeled "secondary structure." Ah... so the bluish sequence of amino acids must be the primary structure of the α-helix. OK, I'm beginning to get it.
"But then there's a pair of green-blue-purple things. Are they identical? Hmmm... they look identical. What do they mean? And are the two in the same subimage or not? Based on how they align with respect to the labels "tertiary structure" and "quaternary structure" I guess not. Wait, I guess the blue and pink bits in each are continuations, respectively, of the α-helix and β-sheet, which isn't itself pink but purple (Oh, I guess that's an artifact of a decision to use something like the Phong reflection model to render the image). So I suppose that would mean that the green is (for our current purposes) simply miscellaneous other stuff providing the context for illustrating the tertiary structure.
"Well, by now I'm pretty confident that color is being used consistently within this metaphor. And by that logic, the red stuff would be additional miscellaneous other stuff introduced as context to illustrate the quaternary structure. And that would mean that the lefthand green-blue-purple thing is not part of the tertiary-structure subimage, but instead joins the red gunk to constitute the quaternary-structure subimage."

Look, just because I was able to work all of that out doesn't mean that it's a good idea to require readers to slog through it on their own. If the above interpretation is correct, then the figure suffers a few design flaws. It requires one to march upstream against the natural top-to-bottom, left-to-right habit. It has some misleading placements and spacing that tend to obscure which bits of the image belong conceptually in a single cluster. It could unify the presentation of each level of structure by placing each atop a subtly chosen matte to create cohesion. My hunch is that the image was not produced specifically for this article, but for some other not-quite-similar application, and was merely put into service here without any tuning. Understandable but unfortunate.

Even if we can't generate a more easily interpreted image, if somebody who actually knows this stuff would kindly confirm my understanding, then I'd be willing to rework the text to walk nonbiologist readers through the example.—PaulTanenbaum (talk) 16:40, 23 February 2016 (UTC)

Everything you say is completely right. I cleaned up some of the inconsistencies across the different sections; this article was merged from separate articles, which is why the descriptions were inconsistent. Of course, the article could use more work. And yes, that image isn't the greatest. Antony–22 (talkcontribs) 01:54, 12 April 2016 (UTC)
Agreed. Improving the image used in the lead has been on my todo list for a while, so this may spur me into action on it finally. It's good to know that it's not just me that finds it unclear. T.Shafee(Evo﹠Evo)talk 05:37, 12 April 2016 (UTC)
protein structure lead figure as of Nov 2016
RNA structure lead figure as of Nov 2016
@PaulTanenbaum: I've now implemented a set of images across the protein structure and RNA structure pages ({{protein structure}} and {{RNA structure}}). Hopefully they are a bit clearer than the original file:protein structure.png image. I'll update the captions on each page that the image appears on to explain the highlighted features. T.Shafee(Evo&Evo)talk 05:06, 8 November 2016 (UTC)

Many thanks to both @Antony-22: and @Evolution and evolvability: these figures are much, much clearer now. And that additional clarity has allowed me to take a swipe at expanding the lead a bit to make it gentler for non-specialists. I'd appreciate any comments, corrections, etc. on what this non-specialist has done there.—PaulTanenbaum (talk) 16:43, 11 November 2016 (UTC)

@Evolution and evolvability: Okay, I have some very specific comments on the nucleic acid figure since that happens to be my area of expertise.  :-)
First, in general, the relevant articles are all of the form "Nucleic acid X structure", which means that they encompass both DNA and RNA structure. This needs to be reflected in the figure.
Second, we have to be careful about the distinction between secondary and tertiary structure, since it's somewhat different than protein structure. For nucleic acids, secondary structure encompasses only the pattern of basepairing and the resulting topology, without regard to the overall geometry of the resulting complex. For example, take a look at the figures in the article Holliday junction. The top figure shows only secondary structure, since it shows which bases are paired without showing their 3D structures. The two figures below it show two possible tertiary structures. There is a similar situation with the two figures in the article Pseudoknot. Right now the images in the secondary structure section of the figure are actually showing tertiary structures, not secondary structures. They should be revised to look like the top figures of the two articles I mentioned.
Third, the different types of double helix are actually a consequence of tertiary structure: A-, B-, and Z- double helixes all have the same base pairings, meaning that they have identical secondary structures, but external factors cause them to have different 3D structures. We have a separate article on Nucleic acid double helix, which could perhaps be linked from a diagram of the three helix forms at the right side of the tertiary structure section.
Fourth, it would be nice to have an image of a Nucleosome in the quaternary structure section, since that's a good example of DNA quaternary structure.
Thanks again for putting these together; hopefully these suggestions are helpful. Antony–22 (talkcontribs) 02:32, 17 November 2016 (UTC)
@Antony-22: Thank you so much for the recommendations. It's always great to get I'll aim to get onto the corrections and improvements this weekend. There seems to be a bit of variation in how secondary structure in DNA is discussed (e.g. Box 1 of "DNA secondary structures: stability and function of G-quadruplex structures". Nature reviews. Genetics. 13 (11): 770–780. 17 November 2016. ISSN 1471-0056. doi:10.1038/nrg3296. ). Do you think it's best to do a single, combined RNA+DNA diagram or separate side-by-side DNA and RNA ones? I'm leaning towards separate, since the examples would be different for DNA (helices, holiday junction, nucleosome). Conversely, for helices, my understanding is that B-form is dominant for DNA, and A-form dominant for RNA but both can form both. Any opinions? T.Shafee(Evo&Evo)talk 09:29, 17 November 2016 (UTC)
@Evolution and evolvability: Thanks for taking this up, I know that was a lot of commentary. The thing is, there aren't separate articles on DNA and RNA structure. I don't think it would make sense to separate them, since nearly all types of structure are relevant to both. It doesn't make sense to have two figures that link to the same set of articles, so I think it's best to use a single figure and more-or-less devote the left side to RNA and the right to DNA.
FYI, here's a reference for the base-pair definition of secondary structure: [2] "The secondary structure of a nucleic acid strand is simply a list of base pairs between Watson–Crick complements...; it may be described as a graph with connections between paired bases on a polymer backbone."' In protein structure it's a similar concept, since both alpha-helices and beta sheets are the direct result of a specific pattern of hydrogen bonds that suggest a specific local structure, but it's possible different authors or subfields are more or less strict about making the distinction. Antony–22 (talkcontribs) 17:49, 17 November 2016 (UTC)

Assessment comment[edit]

The comment(s) below were originally left at Talk:Biomolecular structure/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.

Rated "top" as highschool/SAT biology content; consistent with protein structure. - tameeria 02:35, 29 April 2007 (UTC)

Last edited at 01:48, 1 January 2012 (UTC). Substituted at 09:42, 29 April 2016 (UTC)

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