Introduction to protein structure: Difference between revisions

--Quest #8b) Channels, holes, or pockets in a protein?

'''Explain your answers'''.

We will begin with the <scene name='57/575866/Cartoon/4'>cartoon</scene> structure of an alpha helix from hemoglobin.  From this view, can you determine:

Hold the mouse over each end of the alpha helix.  A yellow box should appear, with [VAL]17:A:CA:#120.  This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.  If there are two identical chains, one of the chains may be numbered slightly differently (like adding 200 to each residue number) to distinguish the residues.

Rotate the helix so that you are looking down the helix.  What does the middle of the helix look like?

Right click on the mouse, choose style, then scheme, then CPK spacefill.  

Let's try changing to another view.  Right click on the mouse, choose style, then scheme, then ball and stick.  Based upon what you know about peptide composition or by holding the mouse over the atoms determine the color scheme:

Notice that hydrogens are not shown on this model.  Xray crystallography is not able to resolve hydrogens, so they are omitted from the images.  This also simplifies the data set, as there are many fewer atoms to position.

Jmol can be used to make measurements of various properties of the alpha helix, such as the dihedral angle.  <scene name='57/575866/No_sidechains/1'>This structure</scene> has the side chains removed (though the alpha carbons show where the side chain would be).  Right click in the structure box.  In the Measurements menu, select "double click begins and ends measurements".  Double click on one of the nitrogens, then click once on the following atoms in order:  the attached Calpha, carbonyl C, and N.  Record this dihedral angle (a psi angle) in a table, recording the number of the Calpha.  Repeat, starting at the N you ended on.  Notice each click gives a different property:  the first is the bond length, the second is the bond angle, and the third is the dihedral (torsional) angle.  You may need to rotate around the helix to see the atoms you want to measure; repeat for four psi angles. After you have completed it for the psi angles, repeat for the phi angles by clicking on the carbonyl C, Calpha, N and carbonyl C.  If you are having problems making the measurements, here is one with the <scene name='57/575866/No_sidechains/2'>psi angles</scene> and one with the <scene name='57/575866/Phi_angles/1'>phi angles</scene>.   

Since hemoglobin doesn't have any beta sheets, we will switch to another protein:  <scene name='57/575866/1cyo_rainbow/1'>cytochrome B5</scene>, PDB code 1CYO.