4 peptide chains
Viewing the molecule
Display Menu
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Amphipathicity of the Alpha Helix

Hydrophobicity, Polarity and Charge

Click on the "X" button opposite "The hemoglobin molecule is made up of four polypeptide chains ....".  This should load a rotating model of the hemoglobin molecule in the left frame.  The rotating model of hemoglobin shows several things:

• It is composed of four separate chains of amino acids (polypeptides).  Each polypeptide is displayed in a different color.

• Each polypeptide binds one heme group which is displayed in red.

Engineers refer to the position of an object in 3 dimensions using the terms pitch (movement around the Z axis), yaw (movement around the Y axis) and roll (movement around the X axis), as shown in the thumbnail to the left.

The viewer displays different aspects of the hemoglobin molecule as follows:

• Translate X or Y (moved left or right; up or down).  with the mouse by holding down the control key and the right button on the mouse.
• Yaw and Roll.  The image can be yawed (rotated left and right about the Y axis ) or rolled (rotated up or down about the X axis)  with the mouse by holding down the left button on the mouse.
• Pitch.  The image can be pitched (rotated clockwise or counterclockwise) about the Z axis with the mouse by holding down the shift key and the right button of the mouse.

Zoom.  The image can be resized with the mouse by holding down the shift key and the left button on the mouse.

A menu for changing the display is accessed by holding down the right button of the mouse

• Rotation:  This function can be toggled on or off.
• Display:   The "Display" menu allows us to view different aspects of the structure:
1. Hold down the right mouse button.  Choose "Display" --- "Spacefill" --- "Van der Waals  Radii".
2. Resize the molecule by holding down the shift key and the left mouse button.  Move the mouse up or down to zoom in or out.  Reduce the molecule to the height of your window.
3. Manipulate the molecule with your mouse to stand it up vertically.
4. Hold down the right mouse button.  Choose "Options" --- "Stereo Display".
• Reset:   Click on the "X" button opposite "The hemoglobin molecule is made up of four polypeptide chains ...."

The following options are available for color display.  Play with them.

• Monochrome - self explanatory
• CPK (carbon grey; hydrogen white; oxygen red; nitrogen blue; phosphorus gold)
• Amino Acid - every amino acid is displayed in a different color
• Shapely - the amino acids are displayed according to the chemical properties of their side chains
• Group - this emphasizes the different elements of secondary structure and the ends of each polypeptide chain.  It is most useful when used in the "ribbon" or "cartoon" display mode.
• Chain - each of the polypeptide chains is displayed in its own color
• Structure - this emphasizes the different secondary structures.  Alpha helix is displayed in rose; beta pleated sheet in gold; random coil in thin blue/white lines.  It is most useful when used in the "ribbon" or "cartoon" display mode.

Temperature and User:  not useful for our purposes.

We know that proteins have shape because it is necessary for them to bind something in order to perform their function.  For example and enzyme has an active site into which the substrate fits.  More generally we refer to these as the binding site on the protein and the ligand which fits into it.

In Hemoglobin we can display the protein chains and the ligand (the Heme group) in different ways.   We can display hemoglobin to emphasize the shape of the binding site:

• Hold the mouse button down.  Go to Select; then go to Hetero; then go to Ligand ("hetero" refers to any other atoms and molecules which are not part of the polypeptide chains).
• Go to the Color menu and select "CPK"
• Go back to Select;  then go to Protein.
• go to the Display menu and select "Wireframe"
• You should now see something like this.

  Each chain holds a heme group containing one Fe++ atom. 
Heme group = porphyrin ring (colored in red) + Fe²⁺ atom chelated in the center. 
There are 4 hemes because there are 4 chains.

  The heme-iron complexes are colored red because they give hemoglobin its red color.  Actually, it is the yellow colored atom in the center which gives the Heme group the red color.  This atom is Iron. Heme has a red color because oxidized iron (rust) is red!  This is also why oxygenated blood is red.

  Now the heme molecules have been colored by element.  The Heme groups displayed using CPK colors.

  Spacefill view of atoms that make up a single heme molecule.  The Heme group displayed to show the true size of each atom, and the real shape of the molecule.

  Here is how iron is attached to the rest of the heme molecule. Notice that the Fe²⁺ is coordinately bound by 4 heterocyclic ring nitrogens.

  An elemental oxygen molecule binds to the ferrous iron atom in the lungs where oxygen is abundant, and is released later in tissues which need oxygen. Note that there is a difference between a single oxygen atom and an Oxygen molecule which is composed of two oxygen atoms!

  The position of bound elemental oxygen in one chain of hemoglobin.

  Space occupied by the heme bound oxygen in the polypeptide chain. Notice how close is the complementary fit between the heme group and the cavity formed by the alpha helices in the beta globin chain.

  A histidine nitrogen binds to the iron, helping to anchor its position. Actually, there are 2 histidine residues shown here! 

• Histidine 63  (on the right side)  binds to the O₂ molecule, stabilizing it. 
• Histidine 92  (on the left side) binds to the Fe²⁺ atom, holding it in place from the other side.

  A spacefill view (with the exception of the heme molecule) of the hemoglobin polypeptide chain.  This view shows a stick model of the Heme group with the yellow colored iron atom in the center.  The molecules on either side displayed in spacefill mode and CPK color are the side chains of 2 amino acids in the protein chain.

• Hold down the button on your mouse and go to the Options menu.  At the bottom choose Stereo Display.  Adjust the size to look something like this.
Put your nose close up to the screen, and move slowly backward concentrating on the "third" image in the center.  At some point the image should appear 3 dimensional!  This view gives you a good idea of how closely ligands fit into binding pockets  .......... and how important SHAPE is to FUNCTION!!!

When you click on the "X" button, the rotating model of the hemoglobin molecule will load again.  Stop the rotation so you can view the molecule easily.  What you see is one of the four polypeptides and a single heme group (the author does not specify whether this is an a or b globin chain).

The segments of the amino acid chain which fold into a helix are shown in red.  Random coil (the segments which do not fold into a helix) are shown in white.  Start the rotation again so you can see the overall 3D structure.

This coloring scheme helps to trace out the chain from the beginning which is colored blue -- light blue -- teal -- green -- yellow -- orange -- red, which is the end.

• Where is the a helix?
• Where is the Random Coil?

• Where is the a helix?
• Where is the Random Coil?

  Here is the isolated alpha helix.

  The backbone representation connects alpha carbon positions in this alpha helix. These lines do not represent the positions of any actual chemical bonds.

Stop the rotation.  Use the mouse to manipulate the molecule into a vertical position.  Reposition the model to the center of your window.  Resize the model so that the entire length fits in your window.  Using the mouse menu go to Options; then Stereo Display. Turn the rotation on. View the image in stereo.

Using the mouse menu go to Color; then Amino Acid.  Then Display; as Sticks) Now you can see the individual amino acids in the chain which is coiled into the a helix. Using the mouse menu go to Option; then labels. Now you can see exactly how the amino acid chain coils to form this secondary structure.

• Were you correct in identifying the individual amino acids?
• How many amino acids are in this short polypeptide? 

Stop the rotation.  Use the mouse to manipulate the molecule into a vertical position.  Reposition the model to the center of your window.  Resize the model so that the entire length fits in your window.  Using the mouse menu go to Options; then Stereo Display. Turn the rotation on. Now it should be possible to visualize why alpha helices form stiff, rod-like structures!

• The Hydrogen bonds form between what atoms?

This graphic shows a space-filling model of a beta globin chain with the polar residues in blue or green, and the non-polar residues in gray. The heme group is colored light pink.

Turn the stereo option on. Turn on rotation.

When viewed in stereo, do the hydrophilic residues appear more often on the surface, and the hydrophobic residues more often on the interior?

Open the menu. Select "Options", then "Slab Mode", as shown in the thumbnail to the left. 

Now hold down both the Control and Left mouse keys, and move the cursor up or down to slice through the molecule. The views should look something like this.

The Slab option clearly demonstrates how hydrophobic residues are shielded by the hydrophilic residues from the aqueous environment surrounding the molecule.