Team:TU Darmstadt/Project/Simulation

From 2012.igem.org

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.

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.

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 didnĀ“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.