Freiburg07/sandbox

From 2007.igem.org

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[[Image:DHFR_Calmodulin_Ca_sensor.png|thumb|398px| DHFR Calmodulin Ca2+ sensor]]
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== Reporter / Executor Part ==
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Pelletier JN, Arndt KM, Pluckthun A, Michnick SW. "An in vivo library-versus-library selection of optimized protein-protein interactions." Nat Biotechnol. 1999 Jul;17(7):683-90.
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split DHFR
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Pelletier JN, Arndt KM, Plückthun A, Michnick SW. "An in vivo library-versus-library selection of optimized protein-protein interactions." Nat Biotechnol. 1999 Jul;17(7):683-90.
Pelletier JN, Campbell-Valois FX, Michnick SW. "Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments." Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12141-6. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=9770453&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum pubmed]
Pelletier JN, Campbell-Valois FX, Michnick SW. "Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments." Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12141-6. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=9770453&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum pubmed]
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split lactamase
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Hecky J, Müller KM "Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase" Biochemistry. 2005 Sep 27;44(38):12640-54.
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Galarneau A, Primeau M, Trudeau LE, Michnick SW "Abstract Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions." Nat Biotechnol. 2002 Jun;20(6):619-22.
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CFP - YFP
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Venus YFP
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Nagai T, Ibata K, Park ES, Kubota M, Mikoshiba K, Miyawaki A. "A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications." Nat Biotechnol. 2002 Jan;20(1):87-90.
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Cerulean CFP
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Rizzo MA, Springer GH, Granada B, Piston DW "An improved cyan fluorescent protein variant useful for FRET.
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Nat Biotechnol. 2004 Apr;22(4):445-9."
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Kremers GJ, Goedhart J, van Munster EB, Gadella TW Jr "Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Forster radius." Biochemistry. 2006 May 30;45(21):6570-80.
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Piston DW, Kremers GJ "Fluorescent protein FRET: the good, the bad and the ugly." Trends Biochem Sci. 2007 Sep;32(9):407-14.
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Malo GD, Pouwels LJ, Wang M, Weichsel A, Montfort WR, Rizzo MA, Piston DW, Wachter RM "X-ray structure of Cerulean GFP: a tryptophan-based chromophore useful for fluorescence lifetime imaging." Biochemistry. 2007 Sep 4;46(35):9865-73
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Koushik SV, Chen H, Thaler C, Puhl HL 3rd, Vogel SS "Cerulean, Venus, and VenusY67C FRET reference standards." Biophys J. 2006 Dec 15;91(12):L99-L101
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== Ca2+ sensor Calmodulin ==
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[[Image:DHFR_Calmodulin_Ca_sensor.png|thumb|398px| DHFR Calmodulin Ca2+ sensor. Image adapted from Truong et al. 2001]]
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Calmodulin Sensor
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Pham E, Chiang J, Li I, Shum W, Truong K "A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space." Structure. 2007 May;15(5):515-23.
Truong K, Sawano A, Miyawaki A, Ikura M. "Calcium indicators based on calmodulin-fluorescent protein fusions."
Truong K, Sawano A, Miyawaki A, Ikura M. "Calcium indicators based on calmodulin-fluorescent protein fusions."
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Truong K, Sawano A, Mizuno H, Hama H, Tong KI, Mal TK, Miyawaki A, Ikura M. "FRET-based in vivo Ca2+ imaging by a new calmodulin-GFP fusion molecule." Nat Struct Biol. 2001 Dec;8(12):1069-73.
Truong K, Sawano A, Mizuno H, Hama H, Tong KI, Mal TK, Miyawaki A, Ikura M. "FRET-based in vivo Ca2+ imaging by a new calmodulin-GFP fusion molecule." Nat Struct Biol. 2001 Dec;8(12):1069-73.
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Reviews on calmodulin:
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Grabarek Z "Structural basis for diversity of the EF-hand calcium-binding proteins." J Mol Biol. 2006 Jun 9;359(3):509-25.
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Soderling TR, Stull JT "Structure and regulation of calcium/calmodulin-dependent protein kinases." Chem Rev. 2001 Aug;101(8):2341-52<br>
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[[Image:Test.ppt]]
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<br>
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== light sensor PhyA - Fhy1 ==
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[[Image:PhyA_Fhy1_cycle.png|thumb|398px| PhyA - Fhy1 Interaction and light cycle]]
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Hiltbrunner A, Tscheuschler A, Viczian A, Kunkel T, Kircher S, Schäfer E. "FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor." Plant Cell Physiol. 2006 Aug;47(8):1023-34.
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Hiltbrunner A, Viczian A, Bury E, Tscheuschler A, Kircher S, Toth R, Honsberger A, Nagy F, Fankhauser C, Schäfer E "Nuclear accumulation of the phytochrome A photoreceptor requires FHY1." Curr Biol. 2005 Dec 6;15(23):2125-30.
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Gambetta GA, Lagarias JC "Genetic engineering of phytochrome biosynthesis in bacteria." Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10566-71.<br>
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<div style="float:right">
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{|
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|-
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| class="taxo-image" | [[Image:aktivtest.jpg|thumb|398px|'''Picture:''' DHFR-Calmodulin-Construct, active state]]
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|}</div>
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<div style="float:left">
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{|
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|-
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| class="taxo-image" | [[Image:inaktivtest.jpg|thumb|398px|'''Picture:''' DHFR-Calmodulin-Construct, inactive state]]
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|}</div>
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[https://2007.igem.org/Freiburg BACK]

Latest revision as of 10:45, 23 October 2007

Reporter / Executor Part

split DHFR

Pelletier JN, Arndt KM, Plückthun A, Michnick SW. "An in vivo library-versus-library selection of optimized protein-protein interactions." Nat Biotechnol. 1999 Jul;17(7):683-90.

Pelletier JN, Campbell-Valois FX, Michnick SW. "Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments." Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12141-6. pubmed


split lactamase

Hecky J, Müller KM "Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase" Biochemistry. 2005 Sep 27;44(38):12640-54.

Galarneau A, Primeau M, Trudeau LE, Michnick SW "Abstract Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions." Nat Biotechnol. 2002 Jun;20(6):619-22.


CFP - YFP

Venus YFP Nagai T, Ibata K, Park ES, Kubota M, Mikoshiba K, Miyawaki A. "A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications." Nat Biotechnol. 2002 Jan;20(1):87-90.

Cerulean CFP Rizzo MA, Springer GH, Granada B, Piston DW "An improved cyan fluorescent protein variant useful for FRET. Nat Biotechnol. 2004 Apr;22(4):445-9."

Kremers GJ, Goedhart J, van Munster EB, Gadella TW Jr "Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Forster radius." Biochemistry. 2006 May 30;45(21):6570-80.

Piston DW, Kremers GJ "Fluorescent protein FRET: the good, the bad and the ugly." Trends Biochem Sci. 2007 Sep;32(9):407-14.

Malo GD, Pouwels LJ, Wang M, Weichsel A, Montfort WR, Rizzo MA, Piston DW, Wachter RM "X-ray structure of Cerulean GFP: a tryptophan-based chromophore useful for fluorescence lifetime imaging." Biochemistry. 2007 Sep 4;46(35):9865-73

Koushik SV, Chen H, Thaler C, Puhl HL 3rd, Vogel SS "Cerulean, Venus, and VenusY67C FRET reference standards." Biophys J. 2006 Dec 15;91(12):L99-L101



Ca2+ sensor Calmodulin

DHFR Calmodulin Ca2+ sensor. Image adapted from Truong et al. 2001

Calmodulin Sensor

Pham E, Chiang J, Li I, Shum W, Truong K "A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space." Structure. 2007 May;15(5):515-23.

Truong K, Sawano A, Miyawaki A, Ikura M. "Calcium indicators based on calmodulin-fluorescent protein fusions." Methods Mol Biol. 2007;352:71-82.

Truong K, Sawano A, Mizuno H, Hama H, Tong KI, Mal TK, Miyawaki A, Ikura M. "FRET-based in vivo Ca2+ imaging by a new calmodulin-GFP fusion molecule." Nat Struct Biol. 2001 Dec;8(12):1069-73.

Reviews on calmodulin: Grabarek Z "Structural basis for diversity of the EF-hand calcium-binding proteins." J Mol Biol. 2006 Jun 9;359(3):509-25.

Soderling TR, Stull JT "Structure and regulation of calcium/calmodulin-dependent protein kinases." Chem Rev. 2001 Aug;101(8):2341-52

File:Test.ppt



light sensor PhyA - Fhy1

PhyA - Fhy1 Interaction and light cycle


Hiltbrunner A, Tscheuschler A, Viczian A, Kunkel T, Kircher S, Schäfer E. "FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor." Plant Cell Physiol. 2006 Aug;47(8):1023-34.

Hiltbrunner A, Viczian A, Bury E, Tscheuschler A, Kircher S, Toth R, Honsberger A, Nagy F, Fankhauser C, Schäfer E "Nuclear accumulation of the phytochrome A photoreceptor requires FHY1." Curr Biol. 2005 Dec 6;15(23):2125-30.

Gambetta GA, Lagarias JC "Genetic engineering of phytochrome biosynthesis in bacteria." Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10566-71.

Picture: DHFR-Calmodulin-Construct, active state
Picture: DHFR-Calmodulin-Construct, inactive state

BACK

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