My Grayson

Students in our Biochemistry elective studied proteins and protein folding, and for their final project, each of Ms. Connolly-Sporing’s three biochemists chose a membrane-bound organelle to study. “I was excited to see that Morgan (’24), Rena (’25), and Nerya (’25) each took a very different path into the intricate world of transmembrane proteins, examining their structures, functions, and potential applications in various fields, from adaptive energy production to human health and immunology,” shares Ms. Connolly-Sporing. The students used PyMol, an open-source bioinformatics software program to study the structure of their chosen proteins. In addition to its use for molecular visualization, PyMol also allowed students to analyze the complex structures of these amino acids and perform various structural operations. One of the benefits of Grayson’s small class sizes is the in-depth discussion and collaborative support that both students and faculty share. Ms. Connolly-Sporing continued, “Each of us learned a lot about the specific proteins we analyzed and the paths they took through their work.”

Morgan chose to research a protein responsible for the down-regulation of T-cell immune response for her project. Through her research, she identified amino acid residues that were missing in the Protein Data Bank (PDB). While this may not be unusual since residues are not always captured, the PDB is the only repository of information about the 3D structures of proteins. Morgan is working with Ms. Connolly-Sporing on submitting her findings to this worldwide archive.

Biochemistry students working in PyMol to visualize the molecular structure of their chosen proteins.

Through this challenging and fast-paced elective, Ms. Connolly-Sporing was continually impressed by her class: “These students are simultaneously so serious and driven, but also creative, fun-loving teens who took their work to the next level by collaborating on a peer-reviewed journal to showcase their research projects. They’ve really set the bar high for future biochemistry classes!”

“I was expecting a standard report from each of them with their findings and was blown away when they asked me to write an introduction to the peer-reviewed journal that they planned to publish as their final work”  — Annie Connolly-Sporing, Grayson Science Teacher

As these young scientists were already familiar with reading scientific research, the idea to publish a scientific journal seemed like a natural extension of their work. Nerya took the lead in collaborating with Morgan and Rena to present their findings in the format of a peer-reviewed journal. “We had a few interesting style guide discussions on how  to present and format our findings, down to the smallest detail, like if we would use in-text or footnote citations,” shared Nerya. Rena recalled how they developed the name of their journal, proTein: “Most scientific journals have clear, one-word titles, like ‘Nature’ or ‘Science.’ We liked connecting our work on proteins to our love of science and the fact that we are very proudly pro-teen!” 

This shows a plant photosystem’s Lhca1 structure from 7DKZ studied by Rena. The stromal and lumenal side regions in blue contain more hydrophilic amino acids, while the green middle section are more hydrophobic.

Here is a  3D rendering of PD-1 (1NPU) generated in PyMol and included in Morgan’s investigations of the structure of a transmembrane protein responsible for the down-regulation of T-cell immune response.

Nerya created this molecular visualization of the LINGO-1 self-interacting tetramer using PyMol for her examination of  its structure and significance in the central nervous system.

References

H.M. Berman, K. Henrick, H.Nakamura, J.L. Markley (2007) The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data Nucleic Acids Res. 35 (Database issue): D301-3; 

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