Modelling
Creating 3D Structure Files
A Guide for Future iGEM teams
Molecular Dynamics Analysis
Characterising Assemblase
Enzyme Kinetics
Verifying Substrate Channelling Design
Creating 3D Structure Files
A Guide for Future iGEM teams
Our team recounts the process of creating a model of our Assemblase system in a step-by-step fashion that aims to inform future iGEM teams how the process can be replicated to recreate their own protein systems. While some steps may be common knowledge to some iGEM participants we tried to build a holistic approach to the task of protein modelling that incorporates a variety of freely available software and web-tools. Indeed, in a simplified sense we oultine how a synthetic biologist can search for modelled parts, predict the structure of new parts, cut and paste parts together as well as assess the quality and make refinements on newly constructed parts. From our investigation, we believe that developing a better understanding of these in-silico tools will become of increasing importance to a Synthetic Biologist as the tools continue to be developed.
Molecular Dynamics Analysis
Characterising Assemblase
Our team ran multiple Molecular Dynamic (MD) simulations on our Assemblase system that co-localises pathway B as well as the generic scaffold part of Assemblase. The MD analysis performed on our system gave us three measures. Firstly, the scaffold part’s flexibility was observed from the MD simulation and supplemented with Normal Mode analysis to validate our decision to attach larger enzymes to our structure. Secondly, the distance between the active sites of the enzymes in our system was measured to be utilised by a Diffusion and Kinetic model developed by a previous iGEM team. Finally, the size dimensions of our Assemblase system were measured and used to inform the appropriate pore size that would hypothetically be used for a cross-flow filtration recovery of our system in an in-vitro bioreactor. We hope by presenting a well-documented account of our highly versatile MD analysis, we can inspire future iGEM teams to adopt and apply our methodology to their own projects.
Enzyme Kinetics
Verifying Co-Localisation Design
Our team implemented a Diffusion and Enzyme Kinetics model developed by the previous UNSW iGEM team. We altered the model to account for the enzyme kinetic parameters relevant to our Assemblase system, specifically the Assemblase system that co-localises pathway B. We hypothesised that, similar to last year's team, reducing the distance between consecutive enzymes in our reaction pathway would increase the reaction yield of the system and hence by extension would validate our project's protein scaffold design.