Team:Freiburg/3D-Modeling

From 2008.igem.org

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== DNA-Origami ==
== DNA-Origami ==
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Planning the input pattern on the DNA-Origami surface, we generated various 3D-models of the huge molecule using "Nano-Engineer"  (a  free program in its beta-version), Pymol and SwissPdbViewer (both freeware). Some of those models are shown here to give you an impression of the molecules we have engineered this year.<br>
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Planning the input pattern on the DNA-Origami surface, we generated various 3D-models of the huge molecule using [http://www.nanoengineer-1.com/content/ NanoEngineer], [http://pymol.sourceforge.net/ Pymol] and [http://spdbv.vital-it.ch/ SwissPdbViewer] (both freeware). Some of those models are shown here to give you an impression of the molecules we have engineered this year.<br>
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[[Image:Freiburg2008_Fab_on_Origami_animated.gif|800 px]]
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'''Fig.1:'''Some of the oligo nucleotides that shape the single-strand template fused to NIP-molecules and an anti-NIP-Fab-Fragment<br><br><br>
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[[Image:Freiburg08_DNA-NIP.png|thumb|400 px|'''Fig.2:'''DNA-Origami with NIP-molecules and anti-NIP-fragment_______]] [[Image:Freiburg08_DNA-NIP5.png|400 px|'''Fig.3:'''Oligo-pattern with scale and two fragments (dimerization model)]]<br>
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[[Image:Freiburg2008_Fab_on_Origami_animated.gif|left|thumb|800 px|'''Fig.1:''' Some of the oligonucleotides that shape the single-stranded template fused to NIP-molecules and an anti-NIP-Fv-Fragment]]
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[[Image:Freiburg08_DNA-NIP3.png|800 px]]<br>
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'''Fig.4:'''Oligo-pattern with NIP-molecules and Fab-fragment, binding accessibility estimation model<br><br><br>
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[[Image:Freiburg08_DNA-NIP.png|thumb|left|375 px|'''Fig.2:''' DNA-Origami with NIP-molecules and anti-NIP-fragment]]
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[[Image:Freiburg08_DNA-NIP5.png|thumb|left|375 px|'''Fig.3:''' Oligo-pattern with scale and two fragments (distance estimation model, distances given in &Aring;ngstrom)]]
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[[Image:Freiburg08_DNA-NIP8.png|thumb|left|780 px|'''Fig.4:''' Oligo-pattern with scale and two T-Cell-receptors (distance estimation model, distances given in &Aring;ngstrom)]]
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[[Image:Freiburg08_DNA-NIP3.png|thumb|left|800 px|'''Fig.5:''' Oligo-pattern with NIP-molecules and Fab-fragment, binding accessibility estimation model]]<br>
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== Fusion Proteins ==
== Fusion Proteins ==
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The pictures below show models of the fusion proteins our composite parts Bba_K157032 and Bba_K157033 code for (generated with "SwissPdbViewer"):<br>
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The pictures below show models of the fusion proteins of our composite parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K157032 Bba_K157032] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K157033 Bba_K157033] code for (generated with "SwissPdbViewer"):<br>
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[[Image:Team-Freiburg2008_Lipo_alpha_nCFP.png|400 px]][[Image:Team-Freiburg2008_Lipo_alpha_link_cCFP.png|400 px]]
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[[Image:Team-Freiburg2008_Lipo_alpha_nCFP.png|400 px]][[Image:Team-Freiburg2008_Lipo_alpha_link_cCFP.png|400 px]]<br>
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'''Fig.5: Red:''' LipocalinFluA, '''Grey:''' "Transmembrane region (BCR, no structural data; symbolized by helix), '''Blue:''' '''left:''' Split-Cerulean (CFP), N-terminal fragment; '''right:''' Split-Cerulean (CFP), C-terminal fragment<br>
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'''Fig.6: Red:''' LipocalinFluA, '''Grey:''' "Transmembrane region (BCR, no structural data; symbolized by helix), '''Blue:''' '''left:''' Split-Cerulean (CFP), N-terminal fragment; '''right:''' Split-Cerulean (CFP), C-terminal fragment<br>
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Following pdb-files have been used to generate the models:
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Cerulean-CFP: 2Q57<br>
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Venus-YFP: 1MYW<br>
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Engineered Lipocalin: 1n0s<br>
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B1-8 Fv-Fragment:1a6w<br>
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Latest revision as of 02:40, 30 October 2008


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_3D-modeling



DNA-Origami

Planning the input pattern on the DNA-Origami surface, we generated various 3D-models of the huge molecule using [http://www.nanoengineer-1.com/content/ NanoEngineer], [http://pymol.sourceforge.net/ Pymol] and [http://spdbv.vital-it.ch/ SwissPdbViewer] (both freeware). Some of those models are shown here to give you an impression of the molecules we have engineered this year.

Fig.1: Some of the oligonucleotides that shape the single-stranded template fused to NIP-molecules and an anti-NIP-Fv-Fragment


Fig.2: DNA-Origami with NIP-molecules and anti-NIP-fragment
Fig.3: Oligo-pattern with scale and two fragments (distance estimation model, distances given in Ångstrom)
Fig.4: Oligo-pattern with scale and two T-Cell-receptors (distance estimation model, distances given in Ångstrom)


Fig.5: Oligo-pattern with NIP-molecules and Fab-fragment, binding accessibility estimation model

Fusion Proteins

The pictures below show models of the fusion proteins of our composite parts [http://partsregistry.org/wiki/index.php?title=Part:BBa_K157032 Bba_K157032] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K157033 Bba_K157033] code for (generated with "SwissPdbViewer"):
Team-Freiburg2008 Lipo alpha nCFP.pngTeam-Freiburg2008 Lipo alpha link cCFP.png
Fig.6: Red: LipocalinFluA, Grey: "Transmembrane region (BCR, no structural data; symbolized by helix), Blue: left: Split-Cerulean (CFP), N-terminal fragment; right: Split-Cerulean (CFP), C-terminal fragment
Following pdb-files have been used to generate the models: Cerulean-CFP: 2Q57
Venus-YFP: 1MYW
Engineered Lipocalin: 1n0s
B1-8 Fv-Fragment:1a6w

Freiburg08 FT3.png

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