Team:Freiburg/3D-Modeling

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Revision as of 22:05, 29 October 2008

_3D-modeling

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-Fab-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"):

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
Following pdb-files have been used to generate the models: Cerulean-CFP: 2Q57
Venus-YFP: 1MYW
Engineered Lipocalin: 1n0s
B1-8 Fv-Fragment:1a6w

@@ Line 37: / Line 37: @@
 [[Image:Team-Freiburg2008_Lipo_alpha_nCFP.png|400 px]][[Image:Team-Freiburg2008_Lipo_alpha_link_cCFP.png|400 px]]<br>
 '''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>
+Following pdb-files have been used to generate the models:
+Cerulean-CFP: 2Q57<br>
+Venus-YFP: 1MYW<br>
+Engineered Lipocalin: 1n0s<br>
+B1-8 Fv-Fragment:1a6w<br>
 }}