For our final project, we chose to help Quentin organize some information that he had been acquiring for his preliminary exam. At first, Emily and Kate had little idea what Quentin’s project was on. Quentin was quoted to say “Glycosyltransferase…it puts sugars on lots of stuff”. To unravel the mystery surrounding this enzyme, the trio worked together with a few tools that were learned during this weeks workshop.
- Wordle: Generation of the wordle showed key words and phrases that hinted at the functioning of this enzyme. We used the first paragraph from wikipedia to create this wordle.
- End-note: The main method that Quentin used to organize his literary resources was End-Note. Emily and Kate created accounts so they could have access to the journal articles. We found that EndNote was a great tool to not only organize resources but to create in-text citations and bibliographies.
Some of the journal articles listed above pointed out how glycolsylation is a pivotal biological phenomena that allows enzymes to recognize other proteins and compounds. For example, the HIV virus uses a shield of sugars to mask itself from the immune system. In fact, some research focuses on recognition mechanisms for antibodies against the HIV virus.
- Gapminder: HIV has become a pandemic in the global society. Being curious individuals, we explored some of the data available through Gapminder to see what demographics (like the Human Development Index) show strong correlation with the incidence of HIV.
The enzyme family responsible for attaching carbohydrate molecules onto other proteins or molecules are called glycosyltransferases. The enzyme we chose to study further from this broad family was bifunctional N- and O- glucosyltransferase. For more information on this enzyme, we visited the RCSB Protein Database . One of the most easy to find but extremely important pieces of information on this enzyme is its PDB # (in this case 2VCH). This categorization system for proteins gives each molecule a unique ID that can help identify it across many exploration tools, like PyMol (shown below).
- PyMol (Structural Discovery Program): Viewing a structure can many times shed light on the functionality of an enzyme. So, both Quentin and Emily used PyMol to discover some attributes of the enzymes structure that are pertinent to Quentin’s Prelim.