Hello there! I am Carmen, and this was my second and last week working with Dr. Igor Yorobyov, Dr. Slava Bekker, and Ph.D. Candidate John Dawson at the University of California, Davis School of Medicine, in the Department of Physiology and Membrane Biology.
At the beginning of the week, we finished our work with valinomicin. Dr. Igor guided us through the analysis of the drug by looking at graphs that were generated by the same program used to visualize them Visual Molecular Dynamics or VMD. The graphs were hard to understand, but our mentors were helpful and explained them to us.
After working with valinomycin, we worked with an ion channel called hERG, a subunit of a potassium ion channel found in the heart. This ion channel can conduct electricity, which is what our task for the last couple of days consisted of. We first created a simulation of the channel. We went step-by-step on how to clean our desired image. Many things are interacting with each other during these processes inside of the cells, for example, water molecules. Water molecules are important to consider since they can interact inside of the ion channel. After isolating the relevant water molecules, we began to look at the potassium ions that interact with the ion channel. Since the potassium ions are charged molecules and move through the channel, this creates an electric current. Dr. Igor challenged us to calculate the resistance and current of the system. Communication is key to solving problems, and after we joined our knowledge in electric circuits, we were able to get an answer which was close to the answer of our mentors. John Dawson explained how we could use graphs to see which potassium ions can create the current, and with that information, our math would have been more exact. The picture below is the simulation of the ions channel hERG.
We finalized this section of the internship by learning how we could create these simulations using a website called CHARMM-GUI, which is a program that generates membranes or proteins for these simulations.
I have learned so much about molecular dynamics and its applications in the pharmaceutical field for these past two weeks that I can not wait to work with Dr. Collen Clancy and Ph.D. candidate Gonzalo Hernandez for the last week of my internship.
I am sad that my internship is almost over, however, I have learned so many things about proteins and their importance that I look forward to learning more about them in the future. I have learned about the versatility of science, and I want to explore the field of physics since chemistry and physics can be great complements to each other.
This week I started to read the required text for AP Spanish Language and Literature. This class is not offered at my high school, however, I want to explore more of the literature of my own country, Mexico, so that I can continue to learn about the struggles of the past and how they are impacting the present.
I am also interested in exploring the literature of other Hispanic countries, and I am looking forward to reading work from Gabriel García Márquez, a Colombian author.
I hope everyone is staying safe and healthy!
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