Team:Freiburg/3D-Modeling

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Revision as of 23:59, 28 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 oligo nucleotides that shape the single-strand 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 NIP-molecules and Fab-fragment, binding accessibility estimation model

Fusion Proteins

The pictures below show models of the fusion proteins 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

@@ Line 5: / Line 5: @@
 <br><br>
 == DNA-Origami ==
-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>
+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>
-[[Image:Freiburg2008_Fab_on_Origami_animated.gif|800 px]]
+[[Image:Freiburg2008_Fab_on_Origami_animated.gif|thumb|800 px|'''Fig.1:'''Some of the oligo nucleotides that shape the single-strand template fused to NIP-molecules and an anti-NIP-Fab-Fragment]]
-'''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>
+<br><br><br>
 <table>
 <tr>
 <td>
-[[Image:Freiburg08_DNA-NIP.png|thumb|left|370 px|'''Fig.2:'''DNA-Origami with NIP-molecules and anti-NIP-fragment_______]]
+[[Image:Freiburg08_DNA-NIP.png|thumb|left|380 px|'''Fig.2:'''DNA-Origami with NIP-molecules and anti-NIP-fragment_______]]
 </td>
 <td>
-[[Image:Freiburg08_DNA-NIP5.png|thumb|left|370 px|'''Fig.3:'''Oligo-pattern with scale and two fragments (dimerization model)]]
+[[Image:Freiburg08_DNA-NIP5.png|thumb|left|380 px|'''Fig.3:'''Oligo-pattern with scale and two fragments (dimerization model)]]
 </td>
 </tr>