<p>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. </p>
<p>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. </p>
<h2style="margin-top: 10vh;">New Part Characterization</h2>
<p>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."</p>
