Contribution
Useful contributions for future iGEM teams.
Useful contributions for future iGEM teams.
We have created a VCell BioModel that simulates our entire gene circuit. This model includes all components for the LuxR-LuxI gene regulatory system, an extremely common system in synthetic biology that does not yet have a VCell model. With a few modifications, our model can be used to model different types of genetic circuits involving the LuxR-LuxI gene regulatory system.
The models are hosted on VCell servers and are shared publicly in the “Uncurated” folder. They are completely free to use and modify for anyone with VCell.
Our most up-to-date model is named "PFAS Detectorv3_dgl". This model is free for anyone to tinker with and use, along with our prototype models (names found in Engineering)
Our team used seven reverse screening databases to identify proteins that interacted with PFAS Chemicals. These were the reverse screening databases used for this research: SuperPred (1), Pharmapper(2), Swissprot(3), SwissTargetPredict(4), TargetNet (5), SEA (6), and Stitch (7). Our team divided into groups and created a database consisting of a list of proteins that interact with PFAS with the highest probability of interaction and the function of the protein which allowed us to form the basis for the molecular modeling we would do in the future with platforms like V-Cell and OpenMM (Insilico part of research). Our database can been seen here.
These reverse screening databases were crucial in allowing our team to get a sense of what proteins interacted with a desired molecule. By using a SMILE string input of a molecule, the databases gave us three key pieces of information for further research: Name of protein, probability of interaction, and function of protein. With these given information, teams will be able to research deeply in wha roles the proteins partake in, where they are located, and more. For contribution, these reverse screening databases can be a great way for teams to identify a specific target proteins related to their desired molecule in their iGEM research.
The links to the reverse screening databases are down below
OpenMM was a great success because it allowed us to understand the potential effects of PFOA on LuxR, and how that compares to its natural ligand such as AHL. This helped us understand our gene insert better, and see any flaws that may have been missed. We used OpenMM to model our ligand and protein, to observe changes in structure since they were first docked. We had the ability to set our own parameters such as temperature, pressure, and forcefields . In the end, OpenMM was a valuable tool, particularly given our limited time in the lab, which enabled us to better our project. We strongly recommend that other iGEM teams make use of OpenMM for simulating their experiments in advance. This is especially helpful when there is not enough time in the lab, to have lots of trials and errors. We hope documentation of what we did with OpenMM can be of help to other teams that wish to use OpenMM.
We used our designed gene insert (reference Design page) to create a new composite part for the IGem registry: BBa_K5029000. In addition, we added clarifying information on the page for the prmA promotor (BBa_K2911000). We also added a proposed biological mechanism of effect of PFAS on the prmA promotor: “The proposed mechanism of activation of prmA from PFAS is as follows: PFAS results in a reduction in catalase efficacy by targeting PPAR-Alpha and other peroxisomal proteins. This causes H2O2 accumulation in the cell, which activates the FIS transcriptional regulator or the cAMP Receptor Protein, up-regulating the pRMA promoter region."