Samantha Vos, Virginia Wesleyan University

Week 1

 

This week I developed my project proposal with Dr. Olorunseum Ogunwobi. We decided to develop a visualization of the cell lineage plasticity process using either VMD or Paraview. To do this, I will find either the same or extremely similar miRNA, mRNA, and oncogenes that Dr. Ogunwobi suggested I use for the research. I began to search for these components in databanks that had files compatible with VMD or Paraview. So far it has been difficult to find these molecules that have compatible files. PBD is a great databank for proteins, but since I’m dealing with DNA, I need to find a databank that provides compatible files for genetic components. I’ve been reading Dr. Ogunwobi’s previous publications to learn more about this phenomenon’s purpose and process. This project will be focused on combining this specific biological process with the coding to produce a visualization that can be used to educate people.

We had class this week, where we learned about the definitions, history, and functionality of VR, AR, and MR. We also had a self-paced lab where we learned more about Paraview. There are also lectures to learn about VMD, so I will utilize both of these next week. I have been to input proteins into VMD and Paraview so I can learn to upload files and manipulate molecules in this software.

These are pictures of the protein 4LSD, a protein I used to test the functionality of Paraview and VMD.

Week 3

This week I focused on finding compatible files for mRNA. As far as I know, there is a very specific file type that can hold DNA and RNA and upload them onto VMD. However, I have absolutely scoured the internet and have yet to find files that were compatible. Due to this complication, my project has been adjusted. I will be taking the FNDC3 protein and mutating it by changing different amino acids in different positions to change the protein’s functionality or structure. I will be using mutations that have been found in prostate cells and that have a correlation with cancer proliferation. I will then be comparing the mutations to their original protein and demonstrating how the mutations affect the prostate cells. I have already found 9 mutations that lead to cancer in prostate cells, and next week I will be mutating the original FNDC3 protein in VMD with the amino acid adjustments.

 

Week 4

This week I focused on trying to find the binding or active site of FNDC3 so that I can make mutations to its sequence. The 9 mutations that I had previously found were not compatible with the VMD software, so I will be working on finding new mutations in FNDC3. I created a mutation in VMD and labeled the mutated amino acid for my midterm presentation on Friday. Everyone’s presentations looked amazing and very well developed. It was fascinating to learn about other people’s projects and how they have overcome obstacles they’ve encountered. I am working on developing an interactive video with my mutations so that the viewer can move and examine the mutations. I will be looking for more mutations and watching lots of videos next week to learn how to do this.

Week 5

This week I found 8 mutations that work with my protein. I applied these mutations using the mutate residue feature on VMD, and saved all of their visualization states. I also made visualization states of the originals with the same position highlighted so that it would easier to compare them to the mutations. I also figured out how to have multiple visualization states in one window, so now I can create my larger, final visualization state to use for my interactive video. Next week I will be working on my interactive video and sending it to the other participants in the program to test its efficiency and capabilities. I will also be working on creating a survey for them to fill out so I can get some feedback as to how to better my video and perfect it before the end of the program. I have learned so much throughout this program and I am excited to keep learning throughout these final weeks.

Week 6

This week I experienced some difficulty in recording my video. I struggled with trying to figure out how to create an interactive video, and I learned that I do not have the proper computer for ray tracing, so I cannot create an interactive video on my computer. I worked on my paper this week to make sure it was designed exactly how I pictured it, made small changes, and found more literary sources for my paper. I decided to work on styling my representations of my mutations to make sure that when I did make my presentation, it looked perfect. Here are some pictures of my mutations. Next week I will be recording a video and sending it out for data collection,

 

Week 7

I recorded my video successfully, which was an absolute relief. I now have to collect data and analyze it. I will be working on my survey for my presentation and finishing up my paper. I have faced many challenges during this project, and I am happy that I can finally say I have completed it. I am proud of my work, and I am excited to have other people test it. I used many different features of VMD to create my visualization, like mutate residue, sequence viewer, representations, and atom labeling. I enjoyed working on this projects completion, and now I will be working on a power point presentation to sum up my project at the VR-REU Symposium 2023. I am very excited to present my work!

Week 8

This week I finished collecting data from my survey and analyzed it, finally adding it to my paper. I also presented my work in the VR-REU Symposium 2023, and I really enjoyed teaching others about my project and the intricacies of protein structure. My fellow students all had wonderful presentations, and I was truly impressed by all of the work they had done. I think it was a successful presentation, and afterwards we got together and had lunch as a final group celebration of our work. On Friday, we came together one last time to finish our papers, submit them, and put all of our data files into Github. I submitted my paper to the ISS conference, and I really hope it gets accepted. I felt happy for completing the program, but also a small sense of sadness at its ending. I truly had a great experience, I learned a lot about coding and the computers science world. I believe this experience has helped me grow, and I will never forget my classmates, Dr. Ogunwobi, or Dr. Wole.

Final Paper:
Samantha Vos, Oyewole Oyekoya, and Olorunseun Ogunwobi. 2023. Visualization of Point Mutations in Fibronectin Type-III Domain-Containing Protein 3 in Prostate Cancer. In Companion Proceedings of the 2023 Conference on Interactive Surfaces and Spaces (ISS Companion ’23). Association for Computing Machinery, New York, NY, USA, 10–13. https://doi.org/10.1145/3626485.3626531 – pdf