Fab Lysozyme

A Mouse Monoclonal Antibody Interacting with Hen Egg White Lysozyme

On the right is a wire frame structure of an Fab fragment of mouse anti-lysozyme antibody (HY-HEL63) bound to hen egg white lysozyme. The light chain Fab fragment is shown in blue and the heavy chain Fab fragment is shown in green-blue. The lysozyme is in green-yellow.

For our purposes, it is often easier to see the interactions between the chains when they are shown as ribbons, strands or backbone. You can change these now

Antibody light chain

[Ribbons Backbone Strands Wireframe ]

Antibody heavy chain

[Ribbons Backbone Strands Wireframe ]

Lysozyme (Antigen)

[Ribbons Backbone Strands Wireframe ]

Now let's look at the residues of the of the antigen, lysozyme, that make contact via hydrogen bonds with the antibody (switch on red spacefill: here) These are amino acids 15, 16, 20, 21, 73, 93, 96, 97,98, 100, 101, 102 and 103

To see which residues of the light chain variable region interact with the lyzozyme, use this button: (switch on yellow spacefill: here). In the light chain, these are amino acids 31, 32, 53, 92 and 96

To see which residues of the variable region of the heavy chain interact with lysozyme use this button: (switch on orange spacefill: here). In the heavy chain, these are amino acids 30, 32, 33 50, 52, 53, 54, 56 and 58

The molecule can be rotated at any time by left clicking the mouse on the molecule and dragging the image with the left button depressed or you can switch on rotation here: Rotate On Rotate Off

You can also zoom in on your changes here [ Zoom 150% Zoom 200% Zoom 300% Reset Zoom Rotate On Rotate Off ]. The zoom defaults to the center of the molecule. Hold down the control key to drag the molecule to the position that you want with the right mouse button.

We have now made quite a few changes to the molecule and you may want to reset the original image here .

To orient ourselves, let's look at the antibody in more detail. First let's see where the ends (N-terminal and C-terminal) of the two chains lie:

Light chain N-terminal (switch on light blue spacefill: here).
Light chain C-terminal (switch on dark blue spacefill: here)
Heavy chain N-terminal (switch on light green spacefill: here).
Heavy chain C-terminal (switch on dark green spacefill: here)

The Fab region of the molecule has been formed from a whole antibody molecule by using a proteolytic enzyme (papain) that removes the Fc region (which does not interact with the antigen). This allows the protein to crystallize more readily.

To see the variable region of the light chain click here (switch on light blue spacefill: ). Now space-fill the constant region of the light chain (switch on blue spacefill: ).

The same process can be done with the variable and constant region of the heavy chain. To see the variable region of the light chain click here (switch on light green spacefill: ). Space-fill the constant region of the light chain (switch on green spacefill: ).

To return to the original wire-frame structure, reset the image here .

Finally, let's look at the secondary structure of the molecules. This is best seen by converting the image to stands and coloring the molecule so that alpha-helices are in purple, beta-sheet in orange and random coil in gray. Do this here . You can see that the antibody has very little helical structure and a lot of beta sheet

Now look at the part of the antigen that is recognized by the antibody (switch on spacefill: here). The antibody appears to be recognizing a helical structure in the antigen and we refer to this as a three dimensional (conformational) determinant

The protein database file is here Get Chime here