• Secondary

EU name: 3D-301

 (From: ../step5 ) (Date: Aug 24 2016 ../step)

After completing the "Secondary structure" part of the Structure section you will:
Be able to recognize secondary structure elements in a 3D structure on the screen.
Know the characteristic backbone hydrogen bonding pattern of the alpha helix.
Know the characteristic backbone hydrogen bonding pattern of the parallel and anti-parallel beta-sheet.

In this section you can look at, and analyze some small, nearly perfect parts of molecules with a regular secondary structure.

Helix

Figure 54. Load the file HELIX.pdb in Yasara. This is obviously not a real protein, but something we made up to make it easy for you to get used to looking at protein structures.

Question 60: Describe the distribution in space (relative to the helix) of the side chains of the hydrophobic and hydrophilic residues.

Answer

Question 61: Describe the hydrogen bonding of the backbone atoms of the glutamic acid. Do the same for two other residues in the middle of the helix. Do you see a pattern emerge?

Answer

Question 62: Although this helix is energetically already rather favourable (compared to the unfolded form), it is not yet perfect. How can you improve the stability by changing its sequence?

Answer

EU name: 3D-303

 (From: ../step5 ) (Date: Aug 24 2016 ../step)

Antiparallel sheet

Figure 55. Load the file BETA1.pdb in yasara. This is obviously not a real protein, but someting we made up to make it easy for you to get used to looking at protein structures.

Question 63: Load the file BETA1.pdb in yasara.
Draw the 2D-projection of the backbones of the two strands. Include the hydrogenbonds as dashed lines.

Answer

Question 64: Describe the hydrogen bonding pattern for the backbone of Phe-10.

Answer

Question 65: And now, without clicking in yasara, describe the hydrogen bonding pattern of Arg-9.

Answer

Question 66: Describe the spatial distribution (i.e. the distribution in three dimensions) of the side chains of the hydrophobic and hydrophilic residues. Do you see systematic effects in this distribution?

Answer

EU name: 3D-304

 (From: ../step5 ) (Date: Aug 24 2016 ../step)

Parallel sheet

Figure 56. Load the file BETA2.pdb in yasara. This, again, is not a real protein, but something we made up.

Question 67: Draw the 2D-projection of the backbones of the two strands. Include the hydrogenbonds as dashed lines.

Answer

Question 68: Describe the hydrogen bonding pattern of Thr-3.

Answer

Question 69: Describe the hydrogen bonding pattern of Phe-4.

Answer

Question 70: Describe the spatial distribution in three dimensions of hydrophobic and hydrophilic residues.

Answer