User:Jarle Pahr/GFP

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Notes on GFP and related proteins:
Notes on GFP and related proteins:
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http://openwetware.org/wiki/GFP
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http://nic.ucsf.edu/dokuwiki/doku.php?id=fluorescent_proteins
http://bio-net.10840.n7.nabble.com/Bio-net-Fluorpro-f29586.html
http://bio-net.10840.n7.nabble.com/Bio-net-Fluorpro-f29586.html
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A Bilirubin-Inducible Fluorescent Protein from Eel Muscle: http://www.sciencedirect.com/science/article/pii/S0092867413006442
A Bilirubin-Inducible Fluorescent Protein from Eel Muscle: http://www.sciencedirect.com/science/article/pii/S0092867413006442
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=Stability=
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http://2008.igem.org/Team:KULeuven/Data/GFP
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Li 1998. Generation of Destabilized Green Fluorescent Protein as a Transcription Reporter. http://www.jbc.org/content/273/52/34970.full
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Andersen 1998. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/#B12
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http://nic.ucsf.edu/blog/?p=81
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Scruggs 2005. Development and Characterization of Green Fluorescent Protein Mutants with
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Altered Lifetimes. http://rebekka-wachter.com/Scruggs_05.pdf
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Destabilized green fluorescent protein detects rapid removal of transcription blocks after genotoxic exposure.  http://www.ncbi.nlm.nih.gov/pubmed/17824390
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Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. http://www.ncbi.nlm.nih.gov/pubmed/10802622
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Integrated non-invasive system for quantifying secreted human therapeutic hIL2. http://www.ncbi.nlm.nih.gov/pubmed/16933326
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Visualizing long-term memory formation in two neurons of the Drosophila brain.: http://www.ncbi.nlm.nih.gov/pubmed/22323813
=Structure and function=
=Structure and function=
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Shaner 2013. Nature Methods. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. http://www.nature.com/nmeth/journal/v10/n5/full/nmeth.2413.html
Engineering and characterization of a superfolder green fluorescent protein.: http://www.ncbi.nlm.nih.gov/pubmed/16369541
Engineering and characterization of a superfolder green fluorescent protein.: http://www.ncbi.nlm.nih.gov/pubmed/16369541
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Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein.: http://www.ncbi.nlm.nih.gov/pubmed/15558047
Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein.: http://www.ncbi.nlm.nih.gov/pubmed/15558047
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'''Biobricks:'''
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http://parts.igem.org/wiki/index.php/Part:BBa_E0040
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=Maturation=
=Maturation=

Current revision

Notes on GFP and related proteins:


http://openwetware.org/wiki/GFP

http://nic.ucsf.edu/dokuwiki/doku.php?id=fluorescent_proteins

http://bio-net.10840.n7.nabble.com/Bio-net-Fluorpro-f29586.html

http://www.protocol-online.org/biology-forums-2/GFP.html

http://greenfluorescentblog.wordpress.com/tag/gfp/

http://greenfluorescentblog.wordpress.com/tag/gfpmut3/

http://www.dmlim.net/vectors/z%20For%20CAIN/pGFPmut3-1.pdf

GFPmut3b: http://www.sciencedirect.com/science/article/pii/0378111995006850

http://microscopy.bitesizebio.com/articles/gfp/

http://microscopy.bitesizebio.com/articles/excited-emitting-light-an-introduction-to-fluorescent-microscopy/

http://userpages.umbc.edu/~jili/ench772/quantitative.html

  • Contains figure of a GFP sensor setup.

http://philosophicallydisturbed.wordpress.com/2011/01/17/the-source-of-the-glow/


UnaG:

A Bilirubin-Inducible Fluorescent Protein from Eel Muscle: http://www.sciencedirect.com/science/article/pii/S0092867413006442


Contents

Stability

http://2008.igem.org/Team:KULeuven/Data/GFP


Li 1998. Generation of Destabilized Green Fluorescent Protein as a Transcription Reporter. http://www.jbc.org/content/273/52/34970.full

Andersen 1998. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/#B12


http://nic.ucsf.edu/blog/?p=81


Scruggs 2005. Development and Characterization of Green Fluorescent Protein Mutants with Altered Lifetimes. http://rebekka-wachter.com/Scruggs_05.pdf


Destabilized green fluorescent protein detects rapid removal of transcription blocks after genotoxic exposure. http://www.ncbi.nlm.nih.gov/pubmed/17824390

Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. http://www.ncbi.nlm.nih.gov/pubmed/10802622


Integrated non-invasive system for quantifying secreted human therapeutic hIL2. http://www.ncbi.nlm.nih.gov/pubmed/16933326

Visualizing long-term memory formation in two neurons of the Drosophila brain.: http://www.ncbi.nlm.nih.gov/pubmed/22323813

Structure and function

http://www.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm


Variants

Protein Description Excitation Emission Stability Robustness Maturation time Reference
Aequora GFP
GFPmut3
mCherry
EGFP
EYFP
Superfolder GFP


Shaner 2013. Nature Methods. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. http://www.nature.com/nmeth/journal/v10/n5/full/nmeth.2413.html

Engineering and characterization of a superfolder green fluorescent protein.: http://www.ncbi.nlm.nih.gov/pubmed/16369541


Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein.: http://www.ncbi.nlm.nih.gov/pubmed/15558047

Biobricks:

http://parts.igem.org/wiki/index.php/Part:BBa_E0040


Maturation

Bionumbers 106889. Maturation time of wildtype green fluorescent protein (GFP) . http://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&id=106889&ver=2

Lizuka 2011. Kinetic study of de novo chromophore maturation of fluorescent proteins. http://www.sciencedirect.com/science/article/pii/S0003269711002223


Applications

Lu et al. 2004. A high-throughput approach to promoter study using green fluorescent protein. http://www.ncbi.nlm.nih.gov/pubmed/15575693

  • GFP expression experiments in 96-well format.

Differential rates of gene expression monitored by green fluorescent protein: http://onlinelibrary.wiley.com/doi/10.1002/bit.10295/abstract


Trezzani et al. 2003. Monitoring of recombinant protein production using bioluminescence in a semiautomated fermentation process. http://www.ncbi.nlm.nih.gov/pubmed/12892506


Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria: http://jb.asm.org/content/183/23/6752

Chae et al. 2000. Framework for online optimization of recombinant protein expression in high-cell-density Escherichia coli cultures using GFP-fusion monitoring: http://www.ncbi.nlm.nih.gov/pubmed/10861407


Randers-Eichorn and Albano 1997. On-line green fluorescent protein sensor with LED excitation. http://www.ncbi.nlm.nih.gov/pubmed/18636601

Reviews

2011. Fluorescent proteins at a glance. Journal of Cell Science. http://jcs.biologists.org/content/124/2/157.full

Chong 2010. Fluorescent Proteins as a Visible Molecular Signal for Rapid Quantification of Bioprocesses: Potential and Challenges. Chinese Journal of Chemical Engineering. Volume 18, Issue 5, October 2010, Pages 863–869 http://www.sciencedirect.com/science/article/pii/S1004954109601403#

2009. Engineered fluorescent proteins: innovations and applications. Nature Methods. http://www.nature.com/nmeth/journal/v6/n10/abs/nmeth1009-713.html

2007. Advances in fluorescent protein technology. Journal of Cell Science. http://jcs.biologists.org/content/120/24/4247.abstract

Fluorescent proteins: maturation, photochemistry and photophysics. Curr Opin Struct Biol. 2006 Dec;16(6):714-21. Epub 2006 Oct 24. http://www.sciencedirect.com/science/article/pii/S0959440X06001734

2003. Biotechnological applications of green fluorescent protein. http://www.ncbi.nlm.nih.gov/pubmed/12768245

Zimmer 2002. Green fluorescent protein (GFP): applications, structure, and related photophysical behavior. http://www.ncbi.nlm.nih.gov/pubmed/11890756

Understanding, improving and using green fluorescent proteins. Trends Biochem Sci. 1995 Nov;20(11):448-55. http://www.ncbi.nlm.nih.gov/pubmed/8578587

Bibliography

Dual Labeling with Green Fluorescent Proteins for Confocal Microscopy. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC91838/


2002. Chem Rev. Green Fluorescent Protein (GFP): Applications, Structure, and Related Photophysical Behavior. 102, 759−781. http://pubs.acs.org/doi/pdf/10.1021/cr010142r

2001.Seeing the wood through the trees: a review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence. Anal Biochem. 2001 Apr 15;291(2):175-97. http://www.ncbi.nlm.nih.gov/pubmed/11401292.

1998. Albano et al. Green fluorescent protein as a real time quantitative reporter of heterologous protein production. http://www.ncbi.nlm.nih.gov/pubmed/9548792

1998. The Green Fluorescent Protein. Annu. Rev. Biochem. 1998. 67:509–44. http://www.annualreviews.org/doi/pdf/10.1146/annurev.biochem.67.1.509

1997. Chromophore formation in green fluorescent protein. Biochemistry. 1997 Jun 3;36(22):6786-91. http://www.ncbi.nlm.nih.gov/pubmed/9184161.

"One potential limitation of GFP as a reporter for gene expression is its relatively slow rate of fluorescence acquisition in vivo limiting its use to experiments exceeding the hour time scale. The slow rate of fluorescence acquisition is reported to be due to the oxidation step in chromophore formation (Figure 1), which has been estimated to occur with a time constant of 2-4 h in vivo. (Heim et al., 1994)"


1997. Applications of the green fluorescent protein in cell biology and biotechnology. Nature Biotechnology 15, 961 - 964 (1997) doi:10.1038/nbt1097-961. http://www.nature.com/nbt/journal/v15/n10/abs/nbt1097-961.html

1996. Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Current Biology Volume 6, Issue 2, February 1996, Pages 178–182. http://www.sciencedirect.com/science/article/pii/S0960982202004505



Crystal Structure of the Aequorea victoria Green Fluorescent Protein. Science 6 September 1996: Vol. 273 no. 5280 pp. 1392-1395. http://www.sciencemag.org/content/273/5280/1392.short (BP;DR)

Albano et al. 1996. Quantitative measurement of green fluorescent protein expression http://link.springer.com/article/10.1007%2FBF00180401


1995. GREEN FLUORESCENT PROTEIN. Photochemistry and Photobiology Volume 62, Issue 4, pages 651–656, October 1995 http://onlinelibrary.wiley.com/doi/10.1111/j.1751-1097.1995.tb08712.x/abstract


Heim, Cubitt, Tsien 1995. Improved green fluorescence. http://www.nature.com/nature/journal/v373/n6516/abs/373663b0.html

Heim et al. 1994. Wavelength mutations and posttranslational autoxidation of green fluorescent protein. http://www.pnas.org/content/91/26/12501.short Science 11 February 1994: Vol. 263 no. 5148 pp. 802-805

1994. Green fluorescent protein as a marker for gene expression. http://www.sciencemag.org/content/263/5148/802.short

Inouye and Tsuji 1994. Aequorea green fluorescent protein. Expression of the gene and fluorescence characteristics of the recombinant protein.. http://www.ncbi.nlm.nih.gov/pubmed/8137953


Using GFP to see the light. Technical focus, Trends in Genetics Volume 11, Issue 8, Pages 295-334 (August 1995) http://www.sciencedirect.com/science/article/pii/S0168952500890903

1992. Primary structure of the Aequorea victoria green-fluorescent protein. Gene, 111(2), 229-233 (1992). http://www.ncbi.nlm.nih.gov/pubmed/1347277

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