Experimenting with Nanome

HPC Support Staff and Pomona College student Ekeka Abazie reviews the research he’s conducted while using the Virtual Reality environment Nanome, focusing on how the program can visualize and render molecules.

Capture of me using Nanome on the Oculus Tethered Headset

I’ve made one poster presenting my summer computational chemistry research with the chemistry department that I will be presenting on Stover Walk at Pomona College as well as at the SACNAS conference in Honolulu, Hawaii. However, I’m also interested in presenting the work that I did with Nanome while at HPC for the Pomona College summer presentations at Stover Walk. After getting permission from Jorgensen, who is coordinating the poster presentation at Stover Walk, I am now hoping to present two posters—one based on my work with Nanome and another based on my SURP research.

         It was difficult at first to decide what I would present on my poster concerning Nanome. I originally wanted to use Nanome as a research tool with the main focus being on competitive inhibition of the enzyme complex, Succinate Dehydrogenase, of the Citric Acid Cycle. I had previously worked on a similar and more experimentally focused project with resources provided by the Biology department, but this was going to be a different examination that was based more on distances and modeling. After talking to Senior Shklyar [sic], I decided against this and opted for a poster that looked more at the capabilities of Nanome; in other words, focusing more on the VR software. However, after internalizing my conversation with Senior Shklyar even more, I’ve realized that the blog posts that I write concerning Nanome are sufficient to display my work on the project. We already have 3 posters that will be representing HPC, and there will definitely be other opportunities for me to demonstrate my love and commitment to my work at HPC. Nonetheless, I still learned a lot more about Nanome by getting into it with the intent to make a presentation, so I think that deserves some discourse.

  

Normal Glutamic Acid positioning (healthy patient)

I modeled the mutation of Sickle Cell Anemia using Nanome. Sickle Cell Anemia is caused by a single point mutation at the 6th codon of the β-globin gene which causes GAG which codes for Glutamic Acid to be changed into GUG which codes for Valine. I thought this was a cool undertaking, because for me at the time, it represented a valuable use of VR in education. I’m imagining a genetics class that allows students to mutate sections of DNA and see how that would affect an organism. Imagine a whole class in VR working on mutating DNA molecules, sounds like Ender’s Game to me which is super exciting.

Mutated Valine positioning (sick patient)

I also modeled the binding of Carbon monoxide to myoglobin which causes Carbon Monoxide poisoning. Carbon Monoxide causes reduction of the central metal ion of myoglobin upon binding to Fe2+ turning the complex into Carbonmonoxymyoglobin which can’t perform the normal respiratory functions of the standard oxymyoglobin complex and leads to respiratory difficulty and, possibly, death. Pretty cool health education application in my eyes. It is also worth mentioning the attention to detail in the visualization that Nanome provides for these molecules. It’s astounding.

Normal Oxymyoglobin Fe Complex

Lastly, I learned that Nanome could run a lot of functions which I didn’t expect, such as running a multitude of commands or accept different extensions and attachments to make it easier for the user. I find the addition of extensions and attachments to be the most promising because it seems the most boundary extending for what Nanome could be used for, similar to how games that accept mods can be used for so much more.

Aberrant Carbonmonoxymyoglobin Fe Complex

I also learned how to render unique modified molecules using Nanome. For example, I rendered a modified human Lactate Dehydrogenase where the first 20 amino acids of each chain had been replaced with the GFP (Green Fluorescence Protein) from Aequorea Victoria jellyfish. I wonder what else I thought Nanome couldn’t do that it actually can.

– By Ekeka Abazie

Author: Amin Nash

HPC Support - Blog Editor CGU Student - Master's in English '20