Team:Freiburg/3D-Modeling

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Revision as of 01:52, 30 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-Fv-Fragment

Fig.2: DNA-Origami with NIP-molecules and anti-NIP-fragment

Fig.3: Oligo-pattern with scale and two fragments

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.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

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-[[Image:Freiburg08_DNA-NIP.png|thumb|left|380 px|'''Fig.2:''' DNA-Origami with NIP-molecules and anti-NIP-fragment]]
+[[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|380 px|'''Fig.3:''' Oligo-pattern with scale and two fragments ]]
+[[Image:Freiburg08_DNA-NIP5.png|thumb|left|375 px|'''Fig.3:''' Oligo-pattern with scale and two fragments ]]
 </td>
 </tr>