Difference between revisions of "Team:TU Darmstadt/Contribution"
Jankalkowski (Talk | contribs) |
|||
| Line 91: | Line 91: | ||
<div class="TFcontainer"> | <div class="TFcontainer"> | ||
<div class="containertext"> | <div class="containertext"> | ||
| − | We examined the <b>properties of the erythromycin esterase type II EreB</b>, that already shows <a href=” https://2020.igem.org/Team:TU_Darmstadt/Project/Pharmaceutical_Degradation#Degradationofsubstances” target="_blank">promiscuous activity towards azithromycin</a>, with macromolecular computational modeling approaches using the Rosetta and GROMACS applications. The crystal structure of EreB is not yet solved e. g. by analysis techniques like X-ray diffraction or Cryo-EM. Therefore, we applied a <a href=” https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#EreB_CM” target="_blank"><b>homology modeling approach</b></a> on the EreB sequence using Rosetta’s comparative modeling tool RosettaCM. When blasting the protein sequence against the PDB we found a succinoglycan biosynthesis protein possessing high structural similarity in its active site to EreB. We were able to find a <b>candidate for EreB crystal structure</b> after generating 20 000 structures and validated its structural stability by <a href=” https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#EreB_MD” target="_blank">molecular dynamics simulation (MD)</a>. In a <b>100 ns simulation</b> we were able to prove <b>structural stability</b> especially in EreB’s active site by principal component (PCA), Root-mean-square deviation (RMSD), small root-mean-square fluctuation (RMSF) and radii of gyration (Rg) analysis. To prove structural stability of the <b><a href=” https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#fus” target="_blank">fusion protein</a> of EreB with <i>B. Subtilis</i> extracellular matrix protein TasA</b> that we want to utilize for enzyme immobilization we predicted the fusion protein’s structure by comparative modeling and observed structural stability by MD simulation, that was again analyzed by PCA, RMSD, RMSF and Rg. In conclusion, we were able to generate a 3D structure candidate for EreB and validate our method of protein immobilization with TasA. | + | We examined the <b>properties of the erythromycin esterase type II EreB</b> (<a href="http://parts.igem.org/Part:BBa_K1159000" target="_blank">BBa_K1159000</a>), that already shows <a href=” https://2020.igem.org/Team:TU_Darmstadt/Project/Pharmaceutical_Degradation#Degradationofsubstances” target="_blank">promiscuous activity towards azithromycin</a>, with macromolecular computational modeling approaches using the Rosetta and GROMACS applications. The crystal structure of EreB is not yet solved e. g. by analysis techniques like X-ray diffraction or Cryo-EM. Therefore, we applied a <a href=” https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#EreB_CM” target="_blank"><b>homology modeling approach</b></a> on the EreB sequence using Rosetta’s comparative modeling tool RosettaCM. When blasting the protein sequence against the PDB we found a succinoglycan biosynthesis protein possessing high structural similarity in its active site to EreB. We were able to find a <b>candidate for EreB crystal structure</b> after generating 20 000 structures and validated its structural stability by <a href=” https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#EreB_MD” target="_blank">molecular dynamics simulation (MD)</a>. In a <b>100 ns simulation</b> we were able to prove <b>structural stability</b> especially in EreB’s active site by principal component (PCA), Root-mean-square deviation (RMSD), small root-mean-square fluctuation (RMSF) and radii of gyration (Rg) analysis. To prove structural stability of the <b><a href=” https://2020.igem.org/Team:TU_Darmstadt/Model/Enzyme_Modeling#fus” target="_blank">fusion protein</a> of EreB with <i>B. Subtilis</i> extracellular matrix protein TasA</b> (<a href="http://parts.igem.org/Part:BBa_K3429013" target="_blank">BBa_K3429013</a>) that we want to utilize for enzyme immobilization we predicted the fusion protein’s structure by comparative modeling and observed structural stability by MD simulation, that was again analyzed by PCA, RMSD, RMSF and Rg. In conclusion, we were able to generate a 3D structure candidate for EreB and validate our method of protein immobilization with TasA. |
</div> | </div> | ||
Revision as of 12:43, 23 October 2020
As in every iGEM year contributions to the iGEM community are a big part of every project. Due to Covid-19 we were not able to test any of our designed parts in the lab. Nevertheless, we provided basic parts together with literature and information for future teams to characterize.
In addition, we provide the iGEM community with several other contributions ranging from How-Tos, a self-designed flow chamber to our partnership page which gives insights into wastewater treatment with laccases for new teams.
In addition, we provide the iGEM community with several other contributions ranging from How-Tos, a self-designed flow chamber to our partnership page which gives insights into wastewater treatment with laccases for new teams.
Flow Chamber
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
The Oxiteers
Our “Oxiteers”-partnership with the iGEM Teams Stuttgart and Kaiserslautern is
aimed towards making it easier for future iGEM teams to tackle the issue of wastewater treatment.
Since this topic has become quite popular over the course of the years, e.g. iGEM Bielefeld in 2012 or iGEM Stockholm in 2018,
and our teams are working on fighting the diclofenac pollution in German wastewater this season, we decided to team up.
Therefore, we compared our projects, alongside with our workflows,
and came up with a subpage filled with experts regarding wastewater (treatment) and literature on this topic. Here you can find our joint wikipage.
EreB
We examined the properties of the erythromycin esterase type II EreB (BBa_K1159000), that already shows promiscuous activity towards azithromycin, with macromolecular computational modeling approaches using the Rosetta and GROMACS applications. The crystal structure of EreB is not yet solved e. g. by analysis techniques like X-ray diffraction or Cryo-EM. Therefore, we applied a homology modeling approach on the EreB sequence using Rosetta’s comparative modeling tool RosettaCM. When blasting the protein sequence against the PDB we found a succinoglycan biosynthesis protein possessing high structural similarity in its active site to EreB. We were able to find a candidate for EreB crystal structure after generating 20 000 structures and validated its structural stability by molecular dynamics simulation (MD). In a 100 ns simulation we were able to prove structural stability especially in EreB’s active site by principal component (PCA), Root-mean-square deviation (RMSD), small root-mean-square fluctuation (RMSF) and radii of gyration (Rg) analysis. To prove structural stability of the fusion protein of EreB with B. Subtilis extracellular matrix protein TasA (BBa_K3429013) that we want to utilize for enzyme immobilization we predicted the fusion protein’s structure by comparative modeling and observed structural stability by MD simulation, that was again analyzed by PCA, RMSD, RMSF and Rg. In conclusion, we were able to generate a 3D structure candidate for EreB and validate our method of protein immobilization with TasA.
Recombinases
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.
At vero eos et Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
At vero eos et Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
How to B-TOX
We made a manual for employees of wastewater treatment plants (WWTP), in which we give instructions on how to handle our product “B-TOX“.
In there, not only the risks of GMOs are described, but also a safety protocol and the application of “B-TOX” in the WWTP are to be found.
For further information please click here.
How to Rosetta
The Rosetta Commons Software developed by Baker Lab is a powerful computational toolbox for the modeling and analysis of protein structures. It shines with the broad applicability and variability of its applications. The Problem most people face with the software is that it isn’t very forgiving towards beginners and not particulary convenient to use in general. We ourselves faced a lot of difficulties with our modeling and are hoping to make the lives of future iGEMers just a little bit easier by providing a Guide to the applications that we used for our project and adding in our own tipps and tricks.
How to Podcast - A guide for the iGEM community
This year we created a podcast about biotechnology. There are many aspects to be considered turning an idea into a final podcast. This is why we decided to give the iGEM community an overview about everything they need to think about during the creation process and what we ourselves have learned. For further information please click here.