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In-class problems

In-class problems#

In-class Problems Week 9

For this exercise we are going to study the structural similarity and potential dynamics of the spike (S) protein of SARS-CoV-2. We are going to use the PDB entry 7FCD as the reference structure for analyses.

Using the information provided before, use the bio3d library to load the 7FCD structure.Before moving forward create a new structure object that only has the atoms from chain A.

Follow the same set of steps as done for the 5J5X example and perform a blast search against the PDB sequences. Retrieve the top 10 hits, align them using MUSCLE, perform a structural alignment and calculate the RMSD between them.

  • What is the mean RMSD among the 10 structures, approximate to the first decimal (A:5.3)

  • Perform the hierarchical clustering of the structural similarity using as a distance the RMSDs.

  • What is the structure that is most similar to 7BYR_A (A:7A25_A)

Try to understand what are the most important structural differences in the different structures of the spike protein. You can do this by opening two representative structures from the clustering analysis. A more advanced analysis would be to generate interpolated structures along the first principal complement as illustrated for the 5J5X example.