Talk:Binding site

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This article was the subject of a Wiki Education Foundation-supported course assignment, between 28 August 2018 and 21 December 2018. Further details are available on the course page. Peer reviewers: Chintal01.

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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): Liucatherinek.

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untitled

I am a third year student studying Genetics and Biochemistry. The binding site of a protein is site that interacts non-covalently with other molecules. Meaning it interacts not by sharing electrons, but by differences in charges between molecules, so that really depends what you mean by physical. — Preceding unsigned comment added by ChrisDumigan (talk • contribs) 23:45, 11 September 2014 (UTC)[reply]

I came to Wikipedia to get a description for binding site. What I found made no sense to me, so I have done some other research, and editied this page. I have stripped out information that seemed more related to DNA. I would love if a bio-chemist out there could fix this page. I can't verify that DNA and RNA have binding sites. It seems to me that binding sites are unique to protein, and DNA and RNA are not proteins.David Henderson 15:48, 8 December 2005 (UTC)[reply]

Surely if there exists "DNA binding sites", then binding sites cannot be unique to proteins. Nucleic acids also have binding sites. Shushanto (talk) 10:51, 21 July 2011 (UTC)[reply]

More explanation needed from an Expert

Is the binding site a physical region?

More explanation needed on "competition". The link is an irrelevant one (I am guessing the intended link is competition (biology)). Even the relevant link does not mention "competition" in the context of chemical bonds. Similar explanation needed on "equilibrium".

Maybe we need a biochemist with access to some textbooks and papers. That might be useful. Shushanto (talk) 10:49, 21 July 2011 (UTC)[reply]

_________________________________________ Hi Shushanto! I am currently working on this page. I have addressed some of your concerns about specificying whether or not the binding site is a physical region. I also agree with your concern about the topic of competition and am already planning to add a section about regulatory binding sites. I am still figuring out what to write in regards to the topic of equilibrium. Please let me know if you would like to discuss any of these aspects further! I'd gladly discuss with you to develop a thorough and accessible article here on Wikipedia! Liucatherinek (talk) 02:18, 25 October 2018 (UTC)[reply]

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Recent edits

@Liucatherinek: Which of my edits were not factually correct? Concerning your edits:

Ligands bind to induce a conformation change. Misleading. Only some ligands induce a conformational change. Neutral or silent agonists are notable exceptions.
Bonds formed at the binding site are transient and non-covalent Misleading. Most but not all ligands bind reversibly. Reversible covalent inhibitors are notable exceptions.
Since binding sites are comprised of amino acids, optimal conditions for functional binding sites are normally at physiological pH or at the pH of the protein compartment in which the site is located. This statement makes no sense. I think you are confusing enzymes with receptors. Even enzymes are not necessarily optimized for maximal catalytic activity at physiological pH. Other factors such as specificity of binding may be more important. Boghog (talk) 21:48, 14 December 2018 (UTC)[reply]

Re: Recent Edits

@Boghog Hi! Thank you for sharing with me your concerns and revisions! Regarding the two misleading sentences, I appreciate your input! Could you please add the appropriate citations to these changes? Also, regarding your third concern about pH, I believe that pH does in fact play a role since the composition of proteins are amino acids, which can easily be denatured due to pH sensitivity. You are right, specificity is important but the environment of the binding site is also important! Please let me know what you think and if I have misunderstood you in any way! I hope to be able to find some common ground with you. Last but not least, I believe there may have been an overstatement in the characterization of ligands and binding sites in the intro. I agree that ligands bind to binding sites with high specificity, however, ligands may not always bind to binding sites with high affinity. That is why there is such a value as K_d which calculates the affinity of a ligand and its binding site. For example, hexokinase and glucokinase both bind to glucose. Hexokinase has a low K_d or high affinity for glucose so it can move glucose into glycolysis to form ATP. However if there are very high levels of glucose and hexokinase has been inhibited by its product Glucose 6 Phosphate, glucokinase, which has a high K_d or low affinity, can begin to convert glucose to glycogen for long term energy storage in the liver. Therefore it makes sense why not all ligands bind with high affinity because there are certain roles that are necessary for proper physiological regulation that can only be done by low affinity molecules. Again, please let me know if you have any concerns about my thoughts! Liucatherinek (talk) 22:08, 14 December 2018 (UTC)[reply]

Hi Liucatherinek. Thanks for your very positive response! Your point on affinity vs. specificity is well taken. Higher affinity is usually associated with higher specificity and vice verse but there are exceptions as you point out. Of course I need to supply sources to back up my statements. While there are numerous sources to back up the individual statements, I am having troubling locating sources that back up these statements in the context of binding sites. I am still working on this. Overall I think we are largely in agreement. We just need to find appropriate sources. Boghog (talk) 22:54, 14 December 2018 (UTC)[reply]

I have added a few citations to the lead. I hope these are sufficient. On a seperate issue, the function section I think needs to be split into two parts: (1) driving forces for ligands binding (hydrophobic effect, hydrogen bonding, etc.) and (2) what function do binding sites have (ligand binding triggers a conformational change that leads to down stream effects). Concerning driving forces, it should be mentioned that the stability of the protein is sacrificed in order to create a binding site (exposing hydrophobic surfaces to solvent, unfulfilled hydrogen bonds) and this loss of stability is recaptured on binding a complementary ligand. Conerning function, part of the energy of ligand binding is used to drive the conformational change in the protein. Boghog (talk) 20:01, 15 December 2018 (UTC)[reply]

"Binding sites, antibody" listed at Redirects for discussion

An editor has identified a potential problem with the redirect Binding sites, antibody and has thus listed it for discussion. This discussion will occur at Wikipedia:Redirects for discussion/Log/2022 February 1#Binding sites, antibody until a consensus is reached, and readers of this page are welcome to contribute to the discussion. Steel1943 (talk) 06:51, 1 February 2022 (UTC)[reply]

Binding site as physical location something is bound TO

@Liucatherinek: Nice article! I wonder if the current first sentence in the lead could be changed at its end to: "...that allows or requires another molecule to bind to it with specificity.[1]", in order to indicate that it is the 'other molecule' that is being bound TO the site, rather than just some binding occurring?
And what exactly IS 'binding' in this regard? I assume it has to do with intermolecular forces, but wouldn't hurt to mention that? UnderEducatedGeezer (talk) 01:00, 23 June 2022 (UTC)[reply]