Hemoglobin

Brian J. Zachau

Karin A. Fossum

Introduction

Hemoglobin is an oxygen binding protein whose function is to transport dioxygen from outside the body to the capillaries. The hemoglobin protein is a tetramer of two alpha subunits and two beta subunits, and it has four heme groups covalently bound to it. The hemes are located in the hydrophobic crevices in the protein. The heme group contains protoporphyrin IX and a ferrous ion; it is the heme group that binds dioxygen. Hemoglobin exists in two conformational states: the taunt (T) form, in which dioxygen is not bound, and the relaxed (R) form, in which dioxygen is found. The T state is stabilized by 8 salt bridges. Upon binding dioxygen, a major conformational change occurs at the place where the alpha and beta subunits are connected. The protein's conformation is thus shifted to the R form, and the salt bridges are broken. The hemoglobin tertramer can bind up to four molecules of dioxygen. The binding of dioxygen by hemoglobin is cooperative. The conformational changes that occur when one molecule of dioxygen binds may increase the affinity of the other remain three sites for dioxygen, because they bind to hemoglobin at a faster rate after the first is bound. Both protons and carbon dioxide bind hemoglobin at allosteric sites, which also affects the affinity of hemoglobin for dioxygen. The binding of protons decreases the heme groups' affinity for dioxygen because the additional protons cause salt bridges to form, thus stabilizing the T state.

First things first:

  1. In order to rotate the molecule, point the mouse button on to the object and HOLD the LEFT mouse button.  You can then rotate the molecule by moving the mouse.
  2. Second to ZOOM IN and ZOOM OUT, select the mouse button as before, but HOLD DOWN the SHIFT KEY.
  3. When you come across lettering in Blue, please follow the commands as listed by, putting the mouse over the molecule, and press the RIGHT mouse button, then follow the commands in order.
  4. At any time the molecule doesn't seem to function properly please select ORIGINAL SETTINGS in the command menu found on the left side of the browser.
  5. Enjoy

Structural Features

As mentioned in the introduction,  hemoglobin is a tetramer.  In order to "see", and understand the function examine the backbone chain, with and without sidechains using the buttons below.

Backbone chain

Backbone chain plus side groups

Now change the color by selecting

  1. Color/Amino Acid
  2. Color/Group

This as good view to see that this molecule is a tetramer.  Also, note that the two colored groups found in the center of the molecule are the two heme groups, which are the binding sites of dioxygen.

  Select the following displays.  You can see with the line model, and the cartoon display, the secondary structure of the molecule.  It is comprise mostly of helixes, with helix-loop-helix tertiary structure.

 Line models    space filling models     cartoon display (2nd structure) A good color to use is Color/Structure

To examine the stability and the structure of hemoglobin a Charm Energy and Charm minimization analyses were run.

Reset

Binding Site

As mentioned in the introduction, hemoglobin binds to oxygen in its relaxed form, but is not bound in the taut form with dioxygen.  In the taut form there is a conformational change between the alpha and beta chains.  To see a model of the four complexes that bind to oxygen Press ME. In order to view the ligand, with the mouse color/monochrome....then, select/hetero/ligand.....then select/change color to/red.  Once this sequence of commands is followed, the molecule should appear white, with the oxygen binding ligand appearing in red.  The ferrous iron is anchored to the molecule by the Nitrogen atom found on the histine residue.  In order demonstrate the binding site, the hemoglobin molecule was minimized to just show the molecule around the region of the active site.    PRESS ME.  Select Color/Group  In this view you can see the binding sites (should be in green).  This is just the view of the molecule and the neighboring area of the molecule around the heme group.  In order to see a another view of the heme groups, click on the still picture link below.

Picture of Still image of Heme Groups

 

 

Ramachandran Plot

wpe6C.jpg (23370 bytes)
From this Ramachandrian plot, most of the allowable phi/psi angles fall (0,-45/-90,-40).  This is the area outlined in purple, which corresponds to a right handed alpha-helical structure.  This plot corresponds with the secondary structure found in the molecule, due to the relationship of the allowable helical structure due to the phi/psi angles, and to what is found in the actual structure (right handed alpha-helixes.)  According to the plot, there is also beta sheet structure, but this structure has many fewer phi/psi angles that allow that structure.

Solvent Accessibility to Surface Area

In order to view the charged and hydrophilic/hydrophobic regions of the molecule, follow the accompanying directions.  To view the charge regions of the molecule, select select/protein/charge...then select/change color to/orange....color/monochrome.  From this view you can see that the charged regions of the protein are found on the outside of the molecule, which is due to protein stabilization.  To view the hydrophobic regions select/protein/hydrophobicity. From this view, you can see that the hydrophobic regions of the molecule are found on the inside, and the hydrophilic regions are found on the outside.  This is  also due to protein stabilization properties; the outside of the molecule binding to water, and the inside regions remaining unexposed.