User:Eric Martz/Antibody Answers

Answers to Open-Ended Questions about Antibody

Here are answers to the questions provided in a document with the Antibody tutorial available through MolviZ.Org. Suggestions and feedback to Eric Martz.

Antibody bound to foreign microbes flags them for destruction. This is called "opsonization". Antibody triggers various white blood cells to kill microbes. Antibody bound to viruses can render them non-infectious. Binding of antibody to toxins can neutralize their toxicity. Mothers can give some of their antibodies (primarily IgA) to their babies through their breast milk.

Antibody can cause auto-immune diseases, such as Lupus, rheumatoid arthritis, and Grave's disease. When too much antigen enters the body, antibody:antigen complexes can clog filtration in the kidneys, causing kidney damage called glomerulonephritis.

People with a rare genetic birth defect called agammaglobulinemia are unable to make antibodies. They are susceptible to recurrent infections caused by bacteria that do not "hide" inside cells of the host's body: extracellular infections. These include Staphylococci, Streptococci, Hemophilus influenzae, Mycoplasma, Pseudomonas, and Vibrio cholerae. The best therapy is intravenous injection of purified antibodies pooled from healthy donors.

Immunoglobulin G. (Immunoglobulins are members of a class of proteins called gamma globulins, based on their electrophoretic mobilities.)

"Fab" is the Fragment, Antigen Binding. Each IgG molecule has three "arms", two of which are Fab. Fab retains the ability to bind to its cognate antigen. It loses the ability to recruit various immune defense functions, which require the Fc arm, such as opsonization to recruit macrophages and other leukocytes, and activation of complement. However, simply by binding to antigen, Fab may neutralize toxins and decrease the infectiousness of microbes, especially viruses.

"Fc" is the Fragment, Constant (historically, Crystalline). It is one of the three "arms" of an IgG molecule. When separated by itself, Fc can no longer bind antigen. Thus, Fc loses all of the defense functions of antibody against specific pathogens.

Constant domains have the same amino acid sequences for all molecules of a given subtype of antibody, regardless of antigen specificity. Variable domains have different amino acid sequences for each antigen specificity. Within a variable domain, most of the amino acid sequence is a constant framework to enable the domain to fold properly. Only the CDRs are variable. Both constant and variable domains are immunoglobulin domains. They are similar in size, secondary structure (two beta sheets), one disulfide bond between the beta sheets, and in having their amino- and carboxy-termini at opposite ends.

The thinnest part functions as a hinge. It enables flexibility, which allows the two paratopes to bind to two epitopes with differences in spacing.

An epitope is the portion of the surface of an antigen molecule that directly contacts bound antibody. A single antigen molecule can have multiple, different epitopes, each recognizable by a different antibody specificity. The paratope is the surface of the Fab arm of antibody that directly contacts the bound epitope. Each IgG antibody molecule has two Fab's, so two paratopes.

Epitopes of protein antigens are usually discontinuous. That means they are made up of different segments of the antigen's polypeptide chain that come together in the folded antigen protein to form a single epitope. Epitopes are usually fairly flat, but not always. In contrast to epitopes recognized by antibodies, epitopes recognized by T lymphocytes are a continuous peptide fragment of the protein antigen. Such T cell epitopes bind into the gooves of major histocompatibility molecules (MHC), which present the peptides to T lymphocytes. MHC is not involved in the binding of antibody to antigen, but plays a role in activating T helper cells required to activate B lymphocytes to produce antibody in the first place.

Your drawing should show two CDR3's in the middle of the paratope, one from the light chain and one from the heavy chain. The CDR3's contribute the most to antigen specificity, since they are the most variable of the CDR's. The CDR3's are flanked by 4 other CDR's, 2 from the light chain and 2 from the heavy chain.

Antibody binds to antigen by non-covalent bonds, such as hydrogen bonds and salt bridges, and sometimes some hydrophobic interactions. It is important that the epitope and paratope surfaces, which are not completely flat, fit together tightly, without gaps. This is called shape complementarity.

The analogy is to a single immunoglobulin domain. The two beta sheets are the "bread"; the butter is the hydrophobic core; and the toothpick represents the disulfide bond.