Talk:ATP synthase

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Oldest comments

I don't recall all of the history of these particles, but given that it's one of the few enzyme complexes large enough to be visualized by a microscope, I think it deserves some space here, and perhaps a little more than a redirect to proton pump (which, under normal physiological conditions, it is not). Dwmyers 17:12 Feb 9, 2003 (UTC)

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This is a wonderful reference with excellent discussions of the ATPase mechanism, and we need to incorporate some of this here: http://www.nobel.se/chemistry/educational/poster/1997/history.html Dwmyers 20:07 Feb 13, 2003 (UTC)

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ATP synthase is F-ATPase and there are articles under both headings they need to be condensed. If no one objects in either field I will do so and redirect on into the other.

Also there are several vary award grammatical structures that need fixing.

The worked of the Cell by Becker, Kleinsmith and Hardin has a good chapter on ATPases. I’ll up date this article from the information with in and fix the above problems soon if there are no objections. Jasoninkid April 16, 2006

Binding Change Mechanism section outdated

The last paragraph and the animated GIF are outdated. Subsequent experiments have found ATP release and ADP binding occur at the same time at different catalytic sites. Also Phosphate binding/release occurs at a different time than ATP/ADP binding release. I unfortunately do not have time to update this article myself, but here is the reference.

"Coupling of rotation and catalysis in F1-ATPase revealed by single-molecule imaging and manipulation" Kengo Adachi, Kazuhiro Oiwa, Takayuki Nishizaka, Shou Furuike, Hiroyuki Noji, Hiroyasu Itoh, Masasuke Yoshida, and Kazuhiko Kinosita Jr. Cell 130 (2007) 309-321. —Preceding unsigned comment added by 129.7.239.171 (talk) 00:45, 14 March 2010 (UTC)

types of ATP synthase

There should be some differentiation between F-type and A-type ATP synthases. Currently, only F-type ATPases are represented. Silasmellor (talk) 11:52, 27 April 2010 (UTC)

ATPase article

ATPase —Preceding unsigned comment added by 92.238.176.160 (talk) 00:28, 23 January 2011 (UTC)

Evolution of ATP synthase is completely speculative and unscientific

The section devoted to the evolution of ATP synthase does not cite one fact, nor one experiment, nor one hard empirical study of the ATP synthase. It is mere speculation and completely without scientific merit. The article is mere metaphysics and has no place in a scientific article. Take a hard look and notice how often the word "could" is used. The section should be deleted. — Preceding unsigned comment added by Kylefoley76 (talk • contribs) 18:12, 10 February 2011 (UTC)

File:ATPsynthase labelled.png Nominated for Deletion

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ATP synthase picture

In the ATP synthase picture the F1 unit of the protein extends only to the alpha and beta subunits. While for example in "biochemistry 5th edition" by berg, tymoczko and stryer it also includes the stalk, i.e. the gamma and epsilon subunits (page 509). So probably the figure needs to be reedited or another figure used which incorporates these change. Latrocinia (talk) 09:35, 28 June 2011 (UTC)

Picture

I'm not well educated on this subject. The animation on the page is great but I find myself wondering weather it is perfectly accurate at describing the timing of the process perhaps more could be written about it. Also I didn't understand what the animation was depicting without finding a graphic of the structure on another site. including such a picture on the page would make it much better. The most best I have come across is here http://www.ks.uiuc.edu/Research/f0atpase/. -Just some suggestions that I think would improve the page. 180.181.66.245 (talk) 12:11, 23 September 2011 (UTC)

Verification of statements concerning the nomenclature

Currently (2014) the article does not cite from where it got the names Fo and F1. A link should be added to confirm the statements given therein. 84.113.183.242 (talk) 13:13, 9 September 2014 (UTC)

F= Fraction, or Factor?

It is my understanding that the F in F1 and Fo stands for factor, not fraction. These preparations were called "coupling factors". However looking at the original literature "fraction" could be supported. There are phrases like "a mitochondrial fraction (Fo) which confers oligomycin sensitivity" but also "the factor(Fo) which confers oligomycin sensitivity" and "a preparation was obtained which was capable of conferring oligomycin sensitivity (Fo)". I believe "fraction" like "preparation" describes how it was obtained but "Factor" is what it is specifically named. Perhaps Racker's "Bioenegetics" book has the answer. Eaberry (talk) 06:53, 16 December 2014 (UTC)

Would it be reasonable to mention that of "fraction" and "factor", the latter is used more frequently? Jjexpat (talk) 05:42, 21 April 2016 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:ATP synthase/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 "high" as high school/SAT biology content. The article needs expansion (e.g. ATP synthase in different organisms) and references. - tameeria 23:05, 18 February 2007 (UTC)

Last edited at 23:05, 18 February 2007 (UTC). Substituted at 19:43, 1 May 2016 (UTC)

Expansion

I would like to expand on the structure and function of ATP synthase’s domains and subunits. Subunits have their own function that help for example, in F1 which is water soluble plays a major role in hydrolysis which was not stated in the article. I would also like to expand on the ATP synthase regulation and conformational change. Any feedback or suggestions would be greatly appreciated. Thank you. — Preceding unsigned comment added by BiochemEkaterina (talk • contribs) 22:09, 11 May 2017 (UTC)

History section

Hi, I am trying to better this page on the content and the structure and I would like to offer to move quoted below information to a new section named, History Names of ATP Synthase. I might be wrong, but it seems under section - Structure we would usually expand on the structure of the content and not on how the names are came about? Thank you. Your feedback is very much appreciated. "The nomenclature of the enzyme has a long history. The F1 fraction derives its name from the term "Fraction 1" and FO (written as a subscript letter "o", not "zero") derives its name from being the binding fraction for oligomycin, a type of naturally-derived antibiotic that is able to inhibit the FO unit of ATP synthase.[1][2] These functional regions consist of different protein subunits — refer to tables." — Preceding unsigned comment added by BiochemEkaterina (talk • contribs) 13:25, 26 May 2017 (UTC)

Since the subunits are discussed throughout the article, I have moved this section to the beginning of the article. Boghog (talk) 09:04, 17 June 2017 (UTC)

Graphics

@BiochemEkaterina: Thank you for your contributions. Concerning the two figures that you have added:

• File:Fo subunit of ATPase C1. Picture Created in PyMol .png, The caption points to ATP5J (P18859), but there are no structures of this protein in the PDB (see PDBe P18859 search.
• File:Fo_complex_subunit_F6.png

I would really help if you would indicate from which PDB structures (four character PDB IDs) these were derived from so that proper citations can be added. Also please take a look at How do I get a white background?. In PyMOL, it is a good idea to turn off depth cueing and fog. In addition these figures should be ray traced and cropped. Thanks. Boghog (talk) 09:14, 17 June 2017 (UTC)

 Fixed I found the second structure which is based on PDB: 1VZS​​ and updated the caption and figure accordingly. Boghog (talk) 10:01, 17 June 2017 (UTC)

 Fixed I also found the first structure which is based on PDB: 5ARA​ and have updated the caption and figure accordingly. Boghog (talk) 11:01, 17 June 2017 (UTC)

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ATP formation Gibbs free energy

ATP hydrolysis is energetically favourable and, to the best of my understanding, the formation of ATP is not. The standard Gibbs energy of ATP hydrolysis was finally found to be -31.55±1.27 kJ mol^-1. DO correct me if I'm mistaken in this regard please. Revanchist317 (talk) 12:56, 9 October 2020 (UTC) https://pubmed.ncbi.nlm.nih.gov/28282626/

proton pump equation conventions

I'm not a subject expert - the very kind of person for whom Wikipedia is written.

I have studied chemistry to below degree level and so am familiar with chemical equations.

I was mystified by the subscripted "out" and "in" used in the equation in the lead:

ADP + P_i + 3H⁺_out ⇌ ATP + H₂O + 3H⁺_in

I followed up a suspicion when I read, in the "Binding model" section, as far as "...with ATP hydrolysis driving proton pumping across the membrane." "Proton pump" was a term I knew by without much understanding, so I did a web search for "Proton pump" which led me back to Wikipedia article "Proton pump". (I have since created a link from the text "Proton pumping" in this article to the article "Proton pump".)

I am making the guess that the subscripted "out" and "in" mentioned above, correspond, respectively, with the subscripted "[on one side of a biological membrane]" and "[on the other side of the membrane]" found in the equation lead of the proton pump article:

H⁺
_{[on one side of a biological membrane]} + energy ⇌ H⁺
_{[on the other side of the membrane]}

- and presumably (from section "Structure and function" in the current article) the membrane we would be talking about here would be the inner mitochondrial membrane (in eukaryotes) and the thylakoid membrane (in photosynthesising organisms) or the plasma membrane in bacteria; so the "H⁺_out" and "H⁺_in" would refer to H⁺ respectively outside of and inside the mitochondrion, thylakoid or bacterium.

If this is the case, then I would suggest that an explanation that spells all this out would be helpful for anyone like myself who goes to Wikipedia for education on such topics and perhaps the place for it would be in the "Structure and function" section.

Since all the above is only guesswork, I have not made any changes, but - assuming it is correct -

(1) it did occur to me that a simple way of making the linkage slightly more obvious, right in the lead, would be to make a wikilink between the "out" and the "in" in the formula and the article "proton pump". however, I cannot recall having ever seen, in Wikipedia, a wikilink from an element of an equation, so I don't know if this would be considered within normal Wikipedia practice;

(2) Here is a suggested additional paragraph at the end of the "Structure and function" section

"The equation above:

ADP + P_i + 3H⁺_out ⇌ ATP + H₂O + 3H⁺_in

shows the movement of H⁺ ions (protons) through the membrane from outside to inside of the the organelle which powers the energy consuming reaction adding inorganic phosphate to ADP to produce the ATP product."

Alternatively something similar, but without repeat of the equation, could be added after the paragraph in the lead immediately under the equation, but perhaps some work needs to be done to combine it with that existing paragraph to avoid duplication of explanation.

Hedles (talk) 11:49, 18 November 2020 (UTC)

DNA code

May I put the DNA code of ATP synthase or at least a portion of it? BloxyColaSweet (talk) 21:30, 16 March 2023 (UTC)