Team:Freiburg/3D-Modeling

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== DNA-Origami ==
== DNA-Origami ==
Planning the input pattern on the DNA-Origami surface, we generated various 3D-models of the huge molecule using "Nano-Engineer", 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>
Planning the input pattern on the DNA-Origami surface, we generated various 3D-models of the huge molecule using "Nano-Engineer", 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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[[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]]
[[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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The pictures below show models of the fusion proteins of our composite parts Bba_K157032 and Bba_K157033 code for (generated with "SwissPdbViewer"):<br>
The pictures below show models of the fusion proteins of our composite parts Bba_K157032 and Bba_K157033 code for (generated with "SwissPdbViewer"):<br>
[[Image:Team-Freiburg2008_Lipo_alpha_nCFP.png|400 px]][[Image:Team-Freiburg2008_Lipo_alpha_link_cCFP.png|400 px]]<br>
[[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>
Following pdb-files have been used to generate the models:
Following pdb-files have been used to generate the models:
Cerulean-CFP: 2Q57<br>
Cerulean-CFP: 2Q57<br>

Revision as of 01:29, 30 October 2008


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DNA-Origami

Planning the input pattern on the DNA-Origami surface, we generated various 3D-models of the huge molecule using "Nano-Engineer", 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.

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 (dimerization model)
Fig.4: Oligo-pattern with scale and two T-Cell-receptors (dimerization model)


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 Bba_K157032 and 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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