Team:TU Darmstadt/Project/Simulation

From 2012.igem.org

(Difference between revisions)
(Simulation)
 
(8 intermediate revisions not shown)
Line 28: Line 28:
    <li><a href="/Team:TU_Darmstadt/Safety" title="Safety">Safety</a></li>
    <li><a href="/Team:TU_Darmstadt/Safety" title="Safety">Safety</a></li>
    <li><a href="/Team:TU_Darmstadt/Downloads" title="Downloads">Downloads</a></li></ul></li>
    <li><a href="/Team:TU_Darmstadt/Downloads" title="Downloads">Downloads</a></li></ul></li>
-
<li><a href="/Team:TU_Darmstadt/Human_Practice" title="Human Practice">Human Practice</a><ul>
+
<li><a href="/Team:TU_Darmstadt/Human_Practice" title="Human Practice">Human Practice</a></li>   
-
    <li><a href="/Team:TU_Darmstadt/Human_Practice/Panel_Discussion " title="Panel Discussion">Panel Discussion</a></li>
+
-
    <li><a href="/Team:TU_Darmstadt/Human_Practice/Symposia" title="Symposia">Symposia</a></li>
+
-
    <li><a href="/Team:TU_Darmstadt/Human_Practice/Classes" title="Classes">Classes</a></li></ul></li>   
+
<li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Sponsors</a><ul>
<li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Sponsors</a><ul>
    <li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Overview</a></li>
    <li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Overview</a></li>
Line 43: Line 40:
== Simulation ==
== Simulation ==
-
An other major contribution to our project is the simulation part. This part involves the generation of molecular dynamic data including visualisation, biochemical networks and enzymatic activity determination with additional consideration of solvents.
+
An other major contribution to our [https://2012.igem.org/Team:TU_Darmstadt/Project project] is the simulation part.
-
Numerical simulations are nowadays an indispensable (essential) part of modern engineering. The idea behind iGEM to design a biological machine implies, that biology becomes step by step an engineering science the synthetic biology. With the insistence of theoretical models and computational methods we can analyze the evolution of single enzyme molecules by simulation of their dynamics and substrate specificity's. We than use this information to build a whole new metabolic network of our synthetic biological machine.
+
Numerical simulations are nowadays an indispensable (essential) part of modern engineering. The idea behind [https://2012.igem.org/ iGEM] to design a biological machine implies, that biology becomes step by step an engineering science the synthetic biology. With the insistence of theoretical models and computational methods we can analyze the evolution of single enzyme molecules by simulation of their dynamics and substrate specificity's.
 +
[[File:OET.gif|1CEX with OET|right| Simulated Fs. Cutinase with OET in its active site]]
-
Within single-molecule simulations we focus on analyzing the enzymes of the degradation group. Therefore, we use reduced models (elastic network models ENM's) of these enzymes to quantify the mechanical dynamics. According to this we increase the complexity with force field based molecular dynamics simulations.
+
Within single-molecule simulations we focus on analyzing the enzymes of the [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation degradation group]. Therefore, we use reduced models (elastic network models ENM's) of these enzymes to quantify the mechanical dynamics. According to this we increase the complexity with force field based molecular dynamics simulations.
For the sequence analysis we quantify evolutionary relations of the amino acid sequence of the proteins used in our project. Therefore we utilize a spectrum of methods obtained from information science.
For the sequence analysis we quantify evolutionary relations of the amino acid sequence of the proteins used in our project. Therefore we utilize a spectrum of methods obtained from information science.
Line 53: Line 51:
We use force-field based docking simulations for detailed analysis of the interaction with substrate (Polyethylenterphtalat; short: PET) and enzyme. Moreover we analyze possible influence of the degradation process caused by additives of PET such as plasticizer.
We use force-field based docking simulations for detailed analysis of the interaction with substrate (Polyethylenterphtalat; short: PET) and enzyme. Moreover we analyze possible influence of the degradation process caused by additives of PET such as plasticizer.
-
To get a better understanding of all implemented Biobrick functions of our synthetic biological machine our group will illustrate these processes with graphical simulations by Autodesk Molecular Maya.
+
To get a better understanding of all implemented Biobrick functions of our synthetic biological machine our group will try to illustrate these processes with graphical simulations by Autodesk Molecular Maya. The results are featured in the [https://2012.igem.org/Team:TU_Darmstadt/Modeling modeling section].
-
[[File:sj.gif]]
+
We successfully showed, utilizing docking simulations, that plasticizer didn´t effect the active site of our degradation proteins. Moreover, we build high-quality homology models of nearly all our proteins. Furthermore, we quantified mechanical properties of AroY, pNB-Esterase 13 and TphA2. Due to the information theoretical analysis, we identified evolutionary important residues from the Fs. Cutinase as well as the pNB-Esterase 13. Unfortunately, our simulation project with Autodesk Molecular Maya crashed every time we worked on it. Nevertheless, we performed short Molecular Dynamics simulations of our sophisticated degradation construct.

Latest revision as of 01:38, 27 September 2012

Simulation

An other major contribution to our project is the simulation part.

Numerical simulations are nowadays an indispensable (essential) part of modern engineering. The idea behind iGEM to design a biological machine implies, that biology becomes step by step an engineering science the synthetic biology. With the insistence of theoretical models and computational methods we can analyze the evolution of single enzyme molecules by simulation of their dynamics and substrate specificity's.

Within single-molecule simulations we focus on analyzing the enzymes of the degradation group. Therefore, we use reduced models (elastic network models ENM's) of these enzymes to quantify the mechanical dynamics. According to this we increase the complexity with force field based molecular dynamics simulations.

For the sequence analysis we quantify evolutionary relations of the amino acid sequence of the proteins used in our project. Therefore we utilize a spectrum of methods obtained from information science.

We use force-field based docking simulations for detailed analysis of the interaction with substrate (Polyethylenterphtalat; short: PET) and enzyme. Moreover we analyze possible influence of the degradation process caused by additives of PET such as plasticizer.

To get a better understanding of all implemented Biobrick functions of our synthetic biological machine our group will try to illustrate these processes with graphical simulations by Autodesk Molecular Maya. The results are featured in the modeling section.

We successfully showed, utilizing docking simulations, that plasticizer didn´t effect the active site of our degradation proteins. Moreover, we build high-quality homology models of nearly all our proteins. Furthermore, we quantified mechanical properties of AroY, pNB-Esterase 13 and TphA2. Due to the information theoretical analysis, we identified evolutionary important residues from the Fs. Cutinase as well as the pNB-Esterase 13. Unfortunately, our simulation project with Autodesk Molecular Maya crashed every time we worked on it. Nevertheless, we performed short Molecular Dynamics simulations of our sophisticated degradation construct.