Talk:Green fluorescent protein

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Comments[edit]

GFP is also lurid fun fluorescent aquarium fish

transfectable FP of every color are findable online Blue Green Red are more affordable Yellow is newer — Preceding unsigned comment added by 129.101.7.57 (talkcontribs) 05:27, 7 October 2004

how come this page lacks scientific references? for a subject like GFP, one could find endless supplies of papers...— Preceding unsigned comment added by 142.150.56.131 (talkcontribs) 15:27, 8 July 2006

Since 69.123.68.35 keeps trying to add a Chalfie reference I decided to add a bit of history, including the specific contributions of the 4 main players in the development of GFP. I also fleshed out some detail on the specific mutants that led to EGFP. -AH — Preceding unsigned comment added by AndrewHires (talkcontribs) 00:28, 8 February 2007

GFP gene insertion[edit]

Does someone think he/she could discuss how insertion of GFP into a genome/gene/"gene encoding for a protein" works? --Cyberman (talk) 19:31, 24 June 2010 (UTC)

GFP Structure[edit]

GFP is not a unique structure in fact it has a very typical beta barrel structure seen frequently in membrane proteins such as OmpA. I have corrected that statement. Nick

Nick Hayward (talk) 14:34, 21 January 2008 (UTC)

Uses[edit]

In short, whats it used for? Like many scientific and historical articles on wikipedia, this one goes of at a tangent, without actually describing its importance. You know, scientists don't wear lab coats and drink coffee into the night just to discover a protein they do it for a reward, or its use in the science community. And that reward/use is....? Anyone care to help out?Tourskin 23:47, 17 February 2007 (UTC)

Agreed, need to flesh out WHY the protein is so important, and the diversity of it's uses. AndrewHires 21:54, 19 February 2007 (UTC)

Well actually you are wrong. Very often scientists do research on something purely because they are interested in it. Much research is mostly theoretical in the hopes that somehow it will be useful but with no understanding of what that use migh be. In short, often the purpose is merely to expand the body of knowledge we already have and to be able to take what we learn and apply it. I have only heard anecdotally that GFP was discovered because some scienist wanted to figure out why jelly fish glowed. He was given money for this because the scientific community often funds many projects that have biological significance because you never know where the next big discovery will be found and in theory evey piece of information will one day be useful. As for why GFP is important, it can be bound to many biomolecules and now that we know the genes that can encode for it we have investigated how proteins move, interact and degrade, due to the flourscent tag. Also it is used to deterimine when and where certain genes are expressed. On a personal note, I am interested if anyone knows of an industrial, non-biological use. Seems like it should have some applications there. 75.187.39.176 (talk) 16:44, 18 October 2008 (UTC)

I agree with Tourskin and Andrew, we need more structure and less random tangents for this section. I suggest to start with 'pure' GFP (labeling of cells, organelles, brainbow), then explain fluorescent tagging of other proteins (cellular and subcellular localization, timing), then GFP-based sensors (pH, Ca, etc.). Permission to rewrite? --Millencolin (talk) 21:14, 4 February 2009 (UTC)

Please be bold; if you screw up, the current digressions remain in the archive and may be mined for useful and encyclopedic information. - Eldereft (cont.) 19:18, 5 February 2009 (UTC)

Merge[edit]

mGFP should probably be merged as it is only a slight modification of GFP and it may be more informative to have the mGFP content in the main GFP page. It may be a bit confusing though, as m before GFP (or RFP or CFP, etc) more commonly refers to monomeric versions. Any other votes? 66.75.152.122 16:25, 7 May 2007 (UTC)

Looks like a good merge candidate to me. -- MarcoTolo 20:22, 10 May 2007 (UTC)
Merged! AndrewHires 01:36, 5 July 2007 (UTC)

A question[edit]

Is the gene itself fluorsecent, or is it only the protein product of the gene that is.

Meaning, if one were to light UV light on a concentration of plasmids containing this gene (but with no nutrient such as arabinose added and no bacteria or other organism), would it be fluorescent? (green?) —Preceding unsigned comment added by 62.107.66.155 (talkcontribs) 15:05, 10 May 2007 (UTC)

The protein (the green fluorescent protein) is the light-reactive product of the gfp gene. Thus, no, a plasmid containing the gfp gene would not, by itself, fluoresce in the green portion of the visible spectrum. -- MarcoTolo 20:20, 10 May 2007 (UTC)

Emmision and excitation spectra[edit]

A. victorias GFP is excited at 395 nm and 470 nm and emmits light at 509 nm (Maximums). Source: http://public-1.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm --David Munch 12:30, 10 June 2007 (UTC)

Primary references are preferred over webpages and the existing references already cover this aspect of GFP. AndrewHires 01:35, 5 July 2007 (UTC)

Non working link[edit]

The link "• Interactive Java applet demonstrating the chemistry behind the formation of the GFP fluorophore." does not work anymore. I wouldn't just remove it, since I dont have time to check up if the link has just changed to something else. --David Munch 20:27, 14 June 2007 (UTC)

Fixed link - thanks for the heads-up. -- MarcoTolo 20:34, 14 June 2007 (UTC)

Post translational modification of GFP to make it work[edit]

As I understand it, residues of the alpha helix react inside the beta barrel to form the fluorophore, so that the final, fluorescent, protein is chemically modified from the original string of amino acids. Any info about this? 141.5.194.4 12:36, 26 June 2007 (UTC)

You are correct. The exact side-chain composition induces particular cyclizations to occur. The exact chromophores that are created is gone into in some detail in the Green Fluorescent Protein review by Tsien. Also, papers by Remington on crystallography of various mutants would be a good place to go for greater depth on this issue. AndrewHires 07:17, 4 July 2007 (UTC)

Errors in history section[edit]

GFP and aequorin are totally different proteins (hence the different names). Aequorin is an ion-sensitive indicator, and GFP is (mainly) used to tag individual proteins. There is some GFP history here, and also some good information on the differences between the two proteins and different methods of fluorescent marking in "Molecular Biology of the Cell" (Alberts et al, 4th Ed, 2002). -203.171.67.232 09:38, 10 September 2007 (UTC)

GFP and Aequorin were not implied to be the same protein, but perhaps the distinction should have been more clear. Modified it. That link is bad, correct link added to External links. I think credit is properly given to all major contributors according to the various reviews, so removed the disputed marking. If someone has additional specific concerns re: history, happy to discuss or add the tag back. AndrewHires 23:54, 17 September 2007 (UTC)

Species[edit]

For all technical purposes the species should be noted as A. aequorea as noted by Osamu Shimomura who is widely credited with discovering GFP. He notes in Green Fluorescent Protein: Properties, Applications, and Protocols, Second Edition Ch 1 that they are in his opinion the same species. Furthermore he says that A. forskalea is also the same species. --Budlight 02:18, 26 October 2007 (UTC)


Spamming Wikipedia[edit]

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

Sciencetalks (talk) —Preceding comment was added at 02:48, 4 January 2008 (UTC)

Given that it has already been made clear earlier in the article that a number of GFP-expressing organisms have been produced, the entire content of the notes section of this article serves no purpose other than to draw attention to the work of one group of researchers. Perhaps this should also be considered to be spam. —Preceding unsigned comment added by 128.32.173.32 (talk) 23:28, 25 March 2008 (UTC)

My Personal Attempt to Spam WP[edit]

My dilemma is my conflict of interest in being involved with the company referenced, but as the information seems relevant I'll take the liberty to boldly edit. I'm adding a comment in the "GFP in fine art" section to mention that my company produces a GFP fine art piece. Let me know if you think this is appropriate. At some point I hope to get a photograph of one of our GFP crystals in the page to demonstrate what sub-surface laser engraved fine art looks like. —Preceding unsigned comment added by 63.249.110.34 (talk) 03:59, 27 November 2008 (UTC)

Some amount of explanation of the reversion would have been educational. —63.249.110.34 (talk) 04:27, 4 December 2008 (UTC)

References to add[edit]

Here is some references for the new section on GFP in Nature. I don't have time to fiddle with the formatting right now, if someone wants to insert them in the appropriate manner, it'd be much appreciated.

The serine 65 residue of the GFP chromophore is responsible for the dual peaked excitation spectra of wild type GFP. It is conserved in all three GFP isoforms originally cloned by Prasher. ^ Prasher D, Eckenrode V, Ward W, Prendergast F, Cormier M (1992). "Primary structure of the Aequorea victoria green-fluorescent protein". Gene 111 (2): 229–33. doi:10.1016/0378-1119(92)90691-H. PMID 1347277.

Nearly all mutations of this residue consolidate the excitation spectra to a single peak at either 395nm or 480nm. Since a single mutation can make dramatically enhance the 480nm excitation peak,

Heim R, Cubitt AB, Tsien RY. 1995. Nature 373:663–64 Delagrave S, Hawtin RE, Silva CM, Yang MM, Youvan DC. 1995. Bio- Technology 13:151–14 Cormack BP, Valdivia RH, Falkow S.1996. Gene 173:33–38

Further discussion in ^ a b Tsien R (1998). "The green fluorescent protein" (PDF). Annu Rev Biochem 67: 509–44. doi:10.1146/annurev.biochem.67.1.509. PMID 9759496, http://tsienlab.ucsd.edu/Publications/Tsien%201998%20Annu.%20Rev.%20Biochem%20-%20GFP.pdf.

The speculations are from a lecture at Janelia Farm. Here is a video of his nobel lecture where he touches on similar points.

http://nobelprize.org/mediaplayer/index.php?id=1070

The population collapse at Friday Harbor is mentioned in this article by Miyawaki in Cell doi:10.1016/j.cell.2008.11.025 AndrewHires (talk) 16:34, 17 December 2008 (UTC)

Patent holding on GFP derivatives[edit]

Can someone include which GFP derivatives are subjected to patent rights? Is there any kind of protection on the green and blue naturally occurring GFPs? Is the recombinant GFP (but still with the original amino acidic sequence) expressed in bacterial systems a registered invention?
I think that the GFP model could be a relatively simple and highly informative reference to help understand how far patent rights can reach and be applied to products derived from natural sources. Heathmoor (talk) 17:47, 21 September 2010 (UTC)

ultraviolet blue light[edit]

forgive my ignorance, but what the hell is "ultraviolet blue light"? it's in the article's first sentence, and the link to the UV page doesn't mention it, and I don't understand how something uv-coloured can be blue-coloured at the same time. 174.6.72.195 (talk) 22:07, 26 April 2012 (UTC)

The article originally stated "blue light" and was changed in this edit to "ultraviolet blue light". I think what is meant here is "blue, violet, or ultraviolet light". In other words, light with a wavelength less than 475 nm. I am not sure best how to phrase this, "blue, violet, or ultraviolet light" is a bit awkward. Thoughts? Boghog (talk) 22:34, 26 April 2012 (UTC)
hmm. "when exposed to light in the blue to ultraviolet spectrum"? "when exposed to light in the blue to ultraviolet range"? 174.6.72.195 (talk) 01:18, 27 April 2012 (UTC)
I like your second suggestion and have edited the article accordingly. Boghog (talk) 05:52, 27 April 2012 (UTC)

Useful review[edit]

Here's a review I found that has a whole lot of useful info. (available for free on PMC too) I don't have the time to go through it in detail and make use of it but I felt it will be a good resource for those interested in florescent proteins so that they can improve this and other articles.


Day, R. N.; Davidson, M. W. (2009). "The fluorescent protein palette: Tools for cellular imaging". Chemical Society Reviews. Royal Society of Chemistry. 38 (10): 2887–2921. doi:10.1039/b901966a. PMC 2910338Freely accessible. PMID 19771335. 


Cheerio. Staticd (talk) 09:16, 10 January 2013 (UTC)

GFP icecream[edit]

Perhaps this is worth a mention?

dairyreporter.com Buzz-tardis (talk) 07:35, 13 April 2014 (UTC)

Image of chromophore[edit]

Please could someone put an image of the structure of 4-(p-hydroxybenzylidene)imidazolidin-5-one in the structure section? Testem (talk) 12:32, 14 November 2014 (UTC)

Suggestion for Dynamics seciton[edit]

Incoherent neutron scattering reveals dynamics from different parts of a protein based on the location of hydrogen in the system. Here we see on the left how a scattering experiment sees hydrogenated GFP in D2O (heavy water), and on the right, how the same experiment would see deuterated GFP in H2O (water).

As discussed below in the Applications section, GFP can be inserted onto many genes and used to track large scale domain motions and time dependent co-localizations in proteins by means of FRET.

Ease of expression has also enabled GFP to act as a prototype for studies of protein and hydration water dynamics using neutron scattering[1] This technique focuses on motions faster than ~1 nanosecond, and by expressing the protein in a perdeuterated state one can isolate the motions of hydration water from those of the protein. In fact, it is from the coherent scattering from perdeuterated GFP that has shown collective motions of adjacent chains in the beta barrel at ~1 THz.[2] These motions are thought to be sensitive to local rigidity within proteins, revealing beta structures to be generically more rigid than alpha or disordered proteins.[3][4]

— Preceding unsigned comment added by Jon33dn (talkcontribs) 23:46, 20 February 2015 (UTC)

References

  1. ^ Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, et al. (2012). "Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP". Biophys. J. 103 (7): 1566–75. doi:10.1016/j.bpj.2012.08.046. PMC 3471459Freely accessible. PMID 23062349. 
  2. ^ Nickels JD, Perticaroli S, O'Neill H, Zhang Q, Ehlers G, Sokolov AP (2013). "Coherent neutron scattering and collective dynamics in the protein, GFP". Biophys. J. 105 (9): 2182–7. doi:10.1016/j.bpj.2013.09.029. PMC 3824694Freely accessible. PMID 24209864. 
  3. ^ Perticaroli S, Nickels JD, Ehlers G, O'Neill H, Zhang Q, Sokolov AP (2013). "Secondary structure and rigidity in model proteins". Soft Matter. 9 (40): 9548. doi:10.1039/C3SM50807B. 
  4. ^ Perticaroli S, Nickels JD, Ehlers G, Sokolov AP (2014). "Rigidity, secondary structure, and the universality of the boson peak in proteins". Biophys. J. 106 (12): 2667–74. doi:10.1016/j.bpj.2014.05.009. PMID 24940784. 

Re-write[edit]

I've started to improve the writing on this article a bit. I've gotten rid of the worst bits (factually and stylistically) for now, intending to do the rest asap. Large sections, particularly in the fluorescence microscopy section, drone on an on without real structure, with very poorly written and confusing sentences. A high-importance article should be a lot better than this. Watch this space. Fgf10 (talk) 18:09, 17 July 2016 (UTC)