Talk:Zinc finger

Zinc atom vs. ion
Does a zinc finger bind to a zinc atom or zinc ion? I performed a brief Yahoo search that returned a significant number of hits suggesting it is a zinc ion rather than a zinc atom. Can someone familiar with this topic either confirm or refute this and make appropriate modifications to the article?--GregRM 20:57, 3 March 2006 (UTC)

You are right! Miguel Andrade 23:39, 7 March 2006 (UTC)

Charge of a zinc finger?
I remember learning that a zinc finger is mainly (I think) positive charges, so that is why it binds so tightly to DNA which is mostly (I think) negative charges due to the phosphates. I think a very simple visual explanation like this is good in helping people understand moreso than telling them the exact spots it binds. ~Ryan
 * You might be right. Maybe an additional schematic picture would be helpful -- Splette [[Image:Happyjoe.jpg]] Talk 04:26, 10 September 2006 (UTC)

Where are the beta strands?
The article says that there are beta strands in a zinc finger, but the picture doesn't show any.128.163.224.198 22:46, 9 September 2007 (UTC)
 * Hmm, the answer is yes and no. Typically the loops, that are shown in the picture would be the beta strands but this is not always the case. Have a look here. I just rechecked the structure that is shown in the picture. When I run DSSP, a secondary structure prediction method, I get beta strands for two of the zinc fingers but not the third, while the current picture shows the secondary structure as defined in the original PDB file. If I got some time, I might redo the figure. -- Splette :) How's my driving? 11:56, 12 September 2007 (UTC)
 * Ok, I added the sheets now. Hope it doesn't look too messy. -- Splette :) How's my driving? 16:29, 13 September 2007 (UTC)

Modular Assembly vs. Selection methods in zinc finger design
There are definitely some diverse opinions on this issue. I tried to add the most relevant reference expressing each side of the debate. But there are certainly others. The recent Genome research paper is certainly on point. As are the recent maize papers in Nature. Anyone else have an opinion? ScienceGeekling (talk) 12:37, 15 October 2009 (UTC)

There are some automated tools that can generate the journal citations based on only a pubmed id:. Definitely better than doing things manually! ScienceGeekling (talk) 15:05, 15 October 2009 (UTC)

Another user appears to disagree with my edits to this section since he or she has reverted all of the edits on two separate occasions. I've repeated the most obvious edits one at a time and gave my justification for each. I am more than happy to discuss each edit in this discussion section. I still feel several of the statements in the current modular assembly section need references to back them up or they could be taken as personal opinion rather than verifiable encyclopedic content. ScienceGeekling (talk) 13:55, 19 October 2009 (UTC)

My main concern with the previous version of the modular assembly section is that it is extremely one sided and only recognized the contributions of one group. The following claim: "In the early 1990's, Barbas and coworkers of The Scripps Research Institute developed and patented the first selection methods for modifying zinc finger specificity and assembling novel zinc finger domains into proteins for fusion for use in transcription factors, nucleases and other enzymatic fusion approaches." seems extremely difficult to justify given that three other groups published such systems prior to Barbas and coworkers. They may been the first group to file a patent, but this article is on a scientific topic and scientific publications are far more relevant. I'll add the four references when I have the time. ScienceGeekling (talk) 02:43, 22 October 2009 (UTC)

Added references for the four early phage display papers. The new material added to this section over the past several weeks indicates that the modular assembly and selection methods sections should probably be merged with the engineered zinc finger array section (or otherwise reorganized), but I won't tackle that until the content has stabilized. ScienceGeekling (talk) 14:46, 22 October 2009 (UTC)

Etymology
"The name "zinc finger" was originally coined to describe the hypothesized structure of the repeated unit in Xenopus laevis transcription factor IIIA."

This doesn't explain very much. Anybody know more details? DS (talk) 15:12, 14 March 2011 (UTC)
 * My uderstanding of this is that the original paper describing the zinc-binding repeats in TFIIIA included a sketch of how the sequence might fold around the coordinated zinc. This sketch looked a bit like a finger and thus the name was born.  I'll try to clarify the wording.  Getting the image would be even better, but getting the copyright holders permission is probably going to be difficult. ScienceGeekling (talk) 14:37, 24 March 2011 (UTC)
 * I believe you are correct. From a recent review of the discovery of zinc fingers (doi:10.1146/annurev-biochem-010909-095056): "In the autumn of 1982, Miller, a new graduate student, began studies on TFIIIA. This led to the discovery of a remarkable repeating motif within the protein, which was later, in laboratory jargon, called a zinc finger because it contained zinc (Zn) and gripped or grasped the DNA." The DNA binding loops formed from the coordination of histidines and cysteines by zinc resemble fingers. I've edited the wording to reflect this. P millerrhodes TalkContrib 18:58, 10 March 2013 (UTC)

Merge
Any opposition to merging the zinc finger protein article into this one? Vramasub (talk) 14:55, 21 January 2012 (UTC)
 * Makes perfect sense to me. ScienceGeekling (talk) 18:55, 25 January 2012 (UTC)

Recent removal of text and references
While I agree that the organization of the existing article could be improved, I feel that the recent drastic edit removed a great deal of useful information (along with 29 of the 33 references). The reasoning given for this edit does not seem logical as much of the information was moved to a relatively poorly maintained article that dealt with fusions of zinc finger DNA binding domains to other protein domains while much of the information that was removed dealt with alterations to the DNA binding domain to alter the DNA binding specificity. Engineered zinc finger arrays are often used in zinc finger fusions (a.k.a. zinc finger chimeras). But this doesn't mean engineered zinc finger arrays are always part of a zinc finger fusion.

If moving some of the details information to a more specialized (and appropriate) location would improve the article then that would be a good thing. But simply hacking out the majority of the content without any prior discussion is not very helpful. In my experience completely reverting all portions of good faith edits is not very productive and simply results in an edit war. But I also don't want to see useful information removed without a good reason so I'm restoring most of the removed text and references pending a proper discussion of how to better organize the article. ScienceGeekling (talk) 03:30, 13 June 2012 (UTC)

After discussing the issue with another editor, I have reorganized the engineered zinc finger protein/applications section so that the more specialized information is at the end of the section and the introduction is easier for a non-expert reader to understand. It still needs some work, but I think it is a definite improvement. Please feel free to further improve. ScienceGeekling (talk) 15:24, 25 June 2012 (UTC)

Unclear sentence
I find the following sentence in the lead very confusing: Unlike many other clearly defined supersecondary structures such as Greek keys or β hairpins, the secondary structures of proteins containing zinc fingers differ greatly from protein to protein and cannot be predicted simply from knowing that the fold involves a zinc finger. Correct me if I am wrong, but zinc fingers including the type of zinc finger can be easily be predicted based on primary sequence alone (i.e., each of the classes has a well defined and non-overlapping primary sequence motif as defined in Pfam). Wouldn't it be more accurate to state:

Unlike many other clearly defined supersecondary structures such as Greek keys or β hairpins, there are several classes of zinc fingers and each class possesses a unique three-dimensional architecture. Am I missing something? Boghog (talk) 03:34, 27 June 2012 (UTC)


 * No I think you're perfectly right, this version makes more sense Vramasub (talk) 06:17, 5 August 2012 (UTC)

Redundancy
Isn't the fact that the C2H2 is represented twice redundant? I was about to remove it, but wasn't quite sure whether it was redundant or not. I'd appreciate feedback on this. 1.238.19.133 (talk) 05:53, 1 July 2015 (UTC)


 * Thanks for asking. C2H2 is not redundant.  C2H2 or Cys2His2 stands for two cysteine + two histidine amino acid residues.  A total of four residues in the zinc finger are need to bind tightly to zinc (see for example Image:Zinc finger rendered.png). Boghog (talk) 06:43, 1 July 2015 (UTC)


 * I meant the fact that there are two infoboxes with C2H2 in it, at least from my browser. (Google Chrome Version 36) 1.238.19.133 (talk) 02:29, 6 July 2015 (UTC)

Suspected typo in first table.
In the first table showing the different structures and their key features it appears to me that each instance of "from" should read "form". I could be wrong, what do I know. JamesDono (talk) 23:51, 3 March 2020 (UTC)