Immunoglobulins
    Immunoglobulin Structure
Intact molecule
Light Chain   Heavy Chain  
Variable Region   Hyper VR

Proteolytic Fragments
    Fab   Fc   Fv  

Super-secondary Structure
Immunoglobulin fold 

Immunoglobulin disulfide bonds  

Antibody-Hapten Interactions:
DNP+Ab   zoom Int   dot  
DNP (Structure of Hapten)

Antibody-Lysozyme Interactions:
Complex  
Light   Heavy   HprV  

Interaction  
Interfacial waters  
zoom

Wht Bkgd   Blu Bkgd   Blk Bkgd  

Go to immunoglobulin lecture
Note: Many of the chime commands will not work on the intact immunoglobulin structure because the coordinate file only contains Ca carbons.
Notes:
  1. Immunoglobulin Structure
    1. Immunoglobulins contain four chains, two light chains, two heavy chains.
    2. Each chain has a variable region and a constant region. The variable region binds the foreign material.
    3. The size of the variable region is about 100 residues. Each variable region contains 3 hyper-variable segments (see section 3).
    4. Fab fragment contains the antigen binding region. It is composed of a complete light chain and one half of a heavy chain.
    5. Fc fragment does not bind antigen. It is composed of two partial heavy chains (constant region).
    6. Fv fragment binds antigen and just contains the variable regions of the light and heavy chain.
    7. The immunoglobulin fold is the smallest independent structural domain in immunoglobulins. Each light chain has two of these domains and each heavy chain has four.
    8. Both inter- and intra-chain disulfide bonds are present.
    9. Immunoglobulins are glycosylated (not shown here)
  2. Antibody-Hapten Interactions
    1. A hapten is a small molecule that is recognized by immunoglobulins. A dinitrophenyl derivative in this particular case.
    2. All types of favorable energetic interactions are observed, hydrophobic, hydrogen bonding, van der Waals, etc.
  3. Antibody-Antigen Interactions
    1. Antigens are larger molecules that are recognized by immunoglobulins. Can be proteins, sugars, nucleic acids. In this example the antigen is the protein lysozyme.
    2. Epitope is the surface of the antigen that binds to the antibody, usually quite large 600-900 A2
    3. Hypervariable regions (complementarity determining regions, CDRS) on both heavy and light chains are used to interact with antigen.
    4. Interface between antibody and antigen is stabilized by same interactions used to stabilize protein folding and protein-protein interactions in general.
    5. Interface between antibody and antigen often contains buried water molecules.
  4. Antibody-Drug Interactions
    1. The PCP-antibody complex is stabilized by hydrophobic interactions
    2. The PCP-antibody complex is also stabilized by van der Waals forces - note the very close packing between PCP and sidechains.

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