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Molecules – A Work of Art

    By Harry T. Rahn

    My work relationship with Dr. Benore began as the Supplemental Instruction (SI) Leader for Intro to Cell Biology and Molecular Biology. I worked with her for two semesters, and during that time, we had many conversations on student success and the politics in higher education. 

    As the pandemic hit, searching for laboratory experience became hard. I was a biology major nearing the end of my senior year, and I was looking for ways to improve my hands-on skills. Not taking this lightly, I sought out faculty members who I knew would be able to help. Fortunately, my previous experience as an SI leader with Dr. Benore revealed that she needed student researchers working on 3-dimensional protein research. This opened the door for the chance to use my love for art and passion for communicating science to students.

    In the following summer and fall semesters of 2019, I taught myself how to use PyMOL, a software used for rendering 3-dimensional proteins on a computer. However, in the summer of 2020, I was unable to acquire an academic license for PyMOL due to some changes in the company’s licensing agreements. I then set out on the search for something new.

    I eventually found myself in contact with Maria Zarandieta, a sales representative from Schrodinger (the developer of PyMol and another modelling software called Maestro). Later that summer, I met with Maria over a Zoom call to discuss my work with Dr. Benore. She forwarded my request to their software development team, and I was able to get a free-use license for Maestro for 6 months. During the next 4 months, I taught myself to use this new 3-D modelling software. As I became more accustomed to Maestro, I was invited to multiple Schrodinger teaching conferences. I later found out that the product was being test piloted for programs designed to allow students to learn and become certified in molecular modeling. 

    As Dr. Benore and I moved forward and conducted a literature review, we discussed what was absent within the literature: “riboflavin changes when under acidic conditions.” I sought out papers to find out what information was available discussing what happens to the rings within riboflavin molecules under various pH levels. I was unsuccessful in finding any concrete information, though  I did find some papers on flavin mononucleotide (FMN). I then created a catalog referencing these proteins under various pH levels. We were able to extrapolate the comparison to riboflavin that, under the right conditions, the rings within the molecule would experience folding similar to a butterfly’s wings while in flight. 

    In the fall of 2020, I presented a poster discussing my findings and the comparative structural analysis of riboflavin to FMN. At the end of the year, Schrodinger finished the development phase of Maestro, opening it up to all molecular modeling with a free-use educational license. 

    That following winter of 2021, I received an email from BioMolViz, a group of biochemistry professors supported by the National Science Foundation with the goal of creating an open-source biomolecular visualization assessment repository. I furthered my exploration into 3D molecular protein modeling by working alongside these esteemed faculty members from all around the world. From my perspective as a student, I always felt like an asset, and never felt inadequate while working with BioMolViz. 

    I worked with BioMolViz over the next two years, and our mission was to create assessments focusing on improving student visual literacy of 3-D molecules. At the end of my first year working with the BioMolViz team, I became certified in backward assessment design. To think that these assessments, which I helped co-edit and co-author, would be seen by students from around the world is a truly amazing feeling. 

    The intersection of science, art, and literacy is a fascinating journey. As for right now, I work with the BioMolViz team to help maintain the repository. None of this would have been possible without Dr. Marilee Benore. She saw potential in me and skills I didn’t even know I had. Being given this opportunity solidified my career goals and vision of my future. This work I’ve done over the last two years is driven by a personal goal of self-reflection and academic improvement. I want to help give back to the educational community to help students strive for academic success.