Collaborations | iGEM Project Cargo

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Our Friends in Many Places.

By Jason Hu and Madison Hypes

Team University of California, Santa Cruz

Team UC Davis has had a long and productive collaboration with UC Santa Cruz for several years now. Previously in 2020, they helped us prepare for our presentation at Nevada Union High School. They provided their notes, experience and feedback from their education outreach efforts. Through them we were able to accelerate our preparation for meeting the students. We continued to use their advice and sought to connect with more students again this year at the Davis Senior High School. Visit our “Education Outreach” for more information on how it went! Team Santa Cruz were gracious enough to provide us with fantastic material on how invaluable E. coli is as a chassis organism in the lab for DNA and protein amplification. They also explained exactly how work in the lab actually functioned through collaboration and wet/dry lab work pipelines.

Santa Cruz also was able to assist us with our disease spread modeling. Project Cargo wanted to demonstrate the mathematical significance of vaccination on the rate at which we achieve herd immunity. We were having difficulties exactly modeling a standard SIR disease spread system to also include the effect of vaccination on how soon we achieve herd immunity.

Team Stanford

Team UC Davis has also had great history with Team Stanford. Previously they had experience with bioinformatics and teaching and were able to provide us content to share with both Nevada Union High School and Saddleback Community College. That was one of Team UC Davis’s first times having a project that was primarily bioinformatics and we were very grateful to have their help in sharing how exciting that applications of computational biology can be for modeling and predictions.

Project Cargo utilized heavily wet and dry lab methods this year and as such we were better equipped to assist Team Stanford for their own computational needs. Through the efforts of Madison Hypes on Team UC Davis, we were able to run a docking simulation of their desired ligands 6',7'-Dihydroxybergamottin and Bergapten with their CYP6B proteins. We were able to calculate the binding energy of their ligand and produce 3D models with ChimeraX and SwissDock/SwissModel.

+Proteins CYP6B4 and CYP6B17 from the Eastern tiger swallowtail butterfly showed monooxygenase activity as an adaptation to metabolise plant toxins found in their diet. I assisted Stanford in testing the binding affinity of their desired enzyme to each of their Furanocoumarins. Since the structure of CYP6B4 and CYP6B17 had never been characterized by x-ray-crystallography, I first made homology models using SWISS-MODEL. Models were made with Human Microsomal P450 2A6 (PDB 1Z11) as the template. Homology models were then processed through SWISS-DOCK with both ligands to find the Gibbs free energy of the complex. The most favorable complexes were then imaged in ChimeraX to create 3D movies.

Results: CYP6B4 and Bergapten: Cluster 0 and Element 0. At -2950.86 FullFitness (kcal/mol) and -7.18 ΔG (kcal/mol).

CYP6B4 and 6',7'-Dihydroxybergamottin: Cluster 6 element 1. At -2943.98 FullFitness (kcal/mol) and -8.49 ΔG (kcal/mol).

CYP6B17 and Bergapten: Cluster 0 element 0. At -2895.39 FullFitness (kcal/mol) and -7.41ΔG (kcal/mol).

CYP6B17 and 6',7'-Dihydroxybergamottin: Cluster 0 element 0. At -2895.42 FullFitness (kcal/mol) and -9.09 ΔG (kcal/mol).

The files to the 3D movies for these guys are in that email I sent to Stanford and you, Jason.

Team Stanford also conducted a survey to assess the prominence of grapefruits in the diets of survey takers to better assess the impact of their modified yeast on improving the ability to avoid dangerous drug-food interactions. With the aid of Abigail Humphries, whose work is primarily to ensure ethical practices in data collection, we were able to help edit Team Stanford’s survey to better inform participants of the details of their project, improve answer options, and follow proper ethical practice.