Introduction to protein structure: Difference between revisions

== Levels of Protein Structure ==

'''Questions based upon these scenes:'''

'''Questions based upon these scenes:'''

'''Explain your answers'''.

In this section, you will both learn about secondary structure properties and manipulating structures in Jmol.  We will begin with some basic manipulation strategies so that you can analyze secondary structures.  Try the following manipulations with the mouse:

Clicking the right mouse button in the structure box brings up an extensive menu. This exercise will use commands in the style, color,zoom, measurements, and set picking categories.

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:

Rotate the helix so that you are looking down the helix.   

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:

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.  

The coloring in this view is a N-->C rainbow, with the N terminus being blue and the C terminus red.

Next, we will look at two of the <scene name='57/575866/1cyo_20_32_transparent/1'>beta strands</scene>. The side chains have been faded out to make the backbone more obvious.

===Turns and loops===

{{Clear}}

A domain is an independently folded region of a protein that has a particular function.  In contrast to motifs, domains can exist as separate, functional proteins.  Often domains of proteins have different functions.  For example, [[glyceraldehyde-3-phosphate dehydrogenase]] has <scene name='57/575866/G3pd_domains/1'>two domains</scene>:  a NAD+ binding domain and a glyceraldehyde-3-phosphate binding domain.  The NAD binding domain is found in many proteins that bind NAD+, even though the reactions they catalyze are very different.

</StructureSection>

=='''Content Donators'''==

Created with content from [[Structural Templates]] written by [[User:Alexander Berchansky|Alexander Berchansky]], [[User:James D Watson|James D Watson]], [[User:Eran Hodis|Eran Hodis]]