代做BIOC 334/434 NMR HOMEWORK代做Python程序

NMR HOMEWORK (YEE) Due 11:59 p.m. THURSDAY OCTOBER 31, 2024

(For both BIOC 334 and 434)

For this homework assignment, you will need to use the two interactive graphics computer programs: PyMOL and COOT (or WinCoot)

Questions:

1. From the Protein Data Bank website, download the 8voi.pdb file.

What is the full name and the normal biological source of the proteins in this structure?  Describe an important biomedical function for each of the proteins in one sentence each.

How many different NMR experiments were carried out to solve this structure?  How many of them involved 2D pulse sequences?  How many of them involved 3D pulse sequences?  How many of them involved 4D pulse sequences?

What was the typical protein concentration used for most of the NMR experiments?

In this NMR structure, how many models/conformers were calculated?  How many models/conformers are included in the 8voi.pdb file?

What methods were used to refine this NMR structure?

2.  Edit 8voi.pdb to generate a new *.pdb file that contains only Model 1, which is the “representative conformer” in the ensemble (keep the header lines containing “ORIGX” and “SCALE” in your new edited *.pdb file).   Similarly create a new *.pdb file that contains only Model 10.  You should now have 3 *.pdb files:  the original with all of the conformers, and two containing only Models 1 and 10 respectively.

You are now familiar with both PyMOL and COOT/WinCoot.  Use these 3 *.pdb files and the appropriate program to answer the remaining questions.

How many amino acids and atoms does Model 1 contain?  How many amino acids are in each of chains A and B?

What atom type is included in the Model 1 coordinates that was not present in the EM or X-ray structures that were used in the EM and X-ray homework?

3.  Use PyMOL (and the all_states command) to draw the entire ensemble of conformers as Cα traces that are color-ramped from blue N-termini to red C-termini.

Which polypeptide chain shows the most disorder?

Rotate the structure so that the most disordered protein is on the bottom.  Save the image as a png, insert the figure below, and scale it so that the protein structure is 10-12 cm wide.

4.  Use PyMol and the intra_fit command to calculate the overall rmsds using only Cα atoms and Model 1 as the reference.  PyMol will calculate an overall rmsd between model 1 and each of the other models in the NMR structure.

According to these rmsd values, which is the model that is most similar to Model 1, and what is the rmsd?  Which model is most different from Model 1, and what is the rmsd?  What is the rmsd between Models 1 and 10?

5.  Use PyMol and the split_states command to create individual objects for each of the models.  Display only Model 1 and the model that is most different from it, both as cartoons showing secondary structure.  Color Model 1 cyan and the other model magenta.

Which polypeptide chain is most different in conformation between these two models?  Rotate the structure so that the most conformationally different region is on the right. Save the image as a png, insert the figure below, and scale it so that the polypeptide chain is 10-12 cm wide.

6.  Use COOT/WinCoot to display Models 1 and 10 as Cα traces.

Use “LSQ superpose” in COOT/WinCoot to calculate additional values.

What is the rmsd between Models 1 and 10 using the Cα atoms for only chains A?  Describe how this superposition looks – how well do chains A superimpose, and how well do chains B superimpose?

What is the rmsd between Models 1 and 10 using the Cα atoms for only chains B?  Describe how this superposition looks – how well do chains B superimpose, and how well do chains A superimpose?

Compare the chain A-only and chain B-only rmsds calculated by COOT with the the overall rmsd calculated in PyMol, i.e. which is/are larger?

What do these three rmsd values tell you about the primary conformational/dynamics difference between Models 1 and 10?