Protein Structure

Yesterday (January 29th), I went to RPI for more interesting analysis! We started with a summary of protein structure, which was really cool because we recently learned about protein synthesis and structure in AP Bio, so it was really cool to apply it to research! Protein structure is divided into different levels of structure. Primary structure (1˚) consists of the amino acid sequence of the protein. To form secondary structure (2˚), different amino acids that are not adjacent in the sequence can react and cause twists in the amino acid strand. The two common secondary structure forms are the α helix and the β pleated sheet. Today, as I will explain later, I focused on α helices. Tertiary structure (3˚) is formed when the secondary structure folds on itself, forming a three-dimensional structure. Finally, the quaternary structure (4˚) gives the protein form and function by adding molecules such as sugars and phosphates or combining different proteins together. Below is a diagram showing the different protein structures.

Source: Madison Technical College Lab Manual on Protein Structure

Today, my task was to look at a protein structure using MOE software. We are looking for a site to bind another molecule, especially the α helix sites. Two α helix forms can aggregate like a zipper, like the bindings of two spiral notebooks. I identified all of the different helix sites and recorded them by amino acid sequence numbers. After they were identified, I color coded them on the model so we could see where they were located in the three-dimensional surface structure of the protein. It was so interesting to see the relationship between the amino acid sequence and the final structure of the protein! It added a lot to my knowledge of protein structure and allowed me to apply something I learned in class.

As usual, I can’t wait to see what comes next!