Calculate the secondary structure of T4 lysozyme (2LZM) using both dssp and stride. Prepare the strip diagram (sequence on one line, secondary structure assignment on the next, aligned from N to C) with sequence and secondary structures assigned by both methods. Explain your results in terms of the algorithms and protein structure. stride will produce a strip diagram as part of the normal output (Secondary structure summary section). To generate a similar view from dssp, use dssp2strp in a pipeline similar to the example shown below (note the dssp2strp output will mark residues in the coil with "-" in order to more easily allow you to maintain register with stride output).

Using both assignments of secondary structure, plot two ribbon diagrams of T4 lysozyme, once using the dssp derived secondary structure and once using stride. Prepare both plots in the same color(s) and orientation, just change the definitions of the secondary structure. Which definition is more aesthetically pleasing to you in the ribbon diagram and why?

Prepare a Ramachandran diagram for RNase A (7RSA) using STRIDE to calculate φ & ψ dihedral angles. To help with this, csvram will extract φ & ψ angles from the STRIDE ouput as comma-separated values (the venerable CSV file, loved by all from accountants to zoologists).

You can't place the termini, residues 1 & 124, on this plot, just delete the first and last lines which contain the number 360.0. Compare your plot to the secondary structure assignment made by STRIDE. Pay particular attention to the number of residues in the α–helical region. Do the number of residues in this area match the number of residues assigned to the helix (H) by STRIDE? Explain.

Chou and Fasman (1974) ran their statistical calculations for amino acid conformational preference on a set of fifteen proteins. In 1974, this was a rather large set of proteins (the PDB lists the number of structures it contained in 1976 as thirteen), but today, there are far more structures represented in the protein databank.

Run secondary structure calculations for the November 2017 PDBselect list using dssp. Now, that list is based on polypeptide chains, which may come in structures with other polypeptides and many water molecules. In order to simplify our analysis logic later, use an option of gfp, the -c option, to output only the specified chain. This option requires a five character input code, the four characters of the PDB ID and the one character chain ID. The program rundssp will automate the assignment of secondary structure by dssp (it cuts down the work of the program to just secondary structure assignment as well as solving the redirect to a file problem). Issue the command from the directory containing your structure files.

The program cf will replicate Tables I and II from the Chou and Fasman paper (note that the two tables use different amino acid codes, and are alphabetized differently).

Using Table II, compare the results of this statistical procedure using fifteen proteins with the results using roughly four thousand proteins. Comment on the differences you see in the propensity toward forming the α–helix (Pa). What does this tell you about protein structure in regard to amino acids found in helicies?

Compare this scale of helical propensity to the measured values in Scholtz and Pace (1998). Use the "AVERAGE" values in Table 2 (note: these values are normalize GLY -> ALA, 1.00 to 0.00, you might want to scale, and reverse, one dataset in order aid in comparison). Does the rank order of helical propensity of the amino acids in both scales agree? Are there any noticeable shifts in rank order? Why might that be?

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