Team:Freiburg/3D-Modeling

From 2008.igem.org

(Difference between revisions)

Latest revision as of 02:40, 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 [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"):

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

@@ 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", 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 [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>
-[[Image:Freiburg2008_Fab_on_Origami_animated.gif|left|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]]
-<br><br><br>
 <table>
 <tr>
 <td>
-[[Image:Freiburg08_DNA-NIP.png|thumb|left|380 px|'''Fig.2:'''DNA-Origami with NIP-molecules and anti-NIP-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]]
+</td>
+<td>
+</td>
+</tr>
+</table>
+<br>
+<table>
+<tr>
+<td>
+[[Image:Freiburg08_DNA-NIP.png|thumb|left|375 px|'''Fig.2:''' DNA-Origami with NIP-molecules and anti-NIP-fragment]]
 </td>
 <td>
-[[Image:Freiburg08_DNA-NIP5.png|thumb|left|380 px|'''Fig.3:'''Oligo-pattern with scale and two fragments (dimerization model)]]
+[[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)]]
 </td>
 </tr>
@@ Line 21: / Line 29: @@
 <tr>
 <td>
-[[Image:Freiburg08_DNA-NIP8.png|thumb|left|800 px|'''Fig.4:'''Oligo-pattern with scale and two T-Cell-receptors (dimerization model)]]
+[[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)]]
 </td>
 </tr>
@@ Line 29: / Line 37: @@
 <tr>
 <td>
-[[Image:Freiburg08_DNA-NIP3.png|thumb|left|800 px|'''Fig.5:'''Oligo-pattern with NIP-molecules and Fab-fragment, binding accessibility estimation model]]<br>
+[[Image:Freiburg08_DNA-NIP3.png|thumb|left|800 px|'''Fig.5:''' Oligo-pattern with NIP-molecules and Fab-fragment, binding accessibility estimation model]]<br>
 </td>
 </tr>
 </table>
 == Fusion Proteins ==
-The pictures below show models of the fusion proteins 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 [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>
 [[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>
+'''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:
+Cerulean-CFP: 2Q57<br>
+Venus-YFP: 1MYW<br>
+Engineered Lipocalin: 1n0s<br>
+B1-8 Fv-Fragment:1a6w<br>
 }}