In-class problems

In-class Problems Week 8

We are going to be looking into the structure of the spike or surface glycoprotein (S) protein of SARS-CoV-2. This protein forms a trimmer whereby three copies of the same protein form a complex. This protein has been intensively studied by structural approaches since it is a key protein involved in the entry of the virus into the target cells and the key protein used for the development of vaccines. We are going to use the PDB entry 7FCD as the reference structure for analyses.

Using the information provided above use the bio3d library to load the 7FCD structure

This structure is very large because it has 3 copies of a very large protein. Before moving forward create a new structure object that only has the atoms from chain A.

• What is the number of helices found in the structure of chain A (use the R length function) ?

• What is the size in amino-acids of the first helix ?

• Calculate the distances between all alpha carbons in the structure of chain A

• What is the distance in angstroms between the amino-acids with the 10th and 20th indices ?