Some terms: An antigen is a molecule or pathogen capable of eliciting an immune response

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1 Overview of the immune system We continue our discussion of protein structure by considering the structure of antibodies. All organisms are continually subject to attack by microorganisms and viruses. The immune system identifies and destroys foreign invaders. Two types of immunity have been distinguished: 1. Cellular immunity: T cells 2. Humoral immunity: B cells B cells produce antibodies - immunoglobulins - which will be the focus of our discussion. Some terms: An antigen is a molecule or pathogen capable of eliciting an immune response The part of a foreign substance that is recognized by an antibody is called an epitope Antibodies were at one time called gamma globulins; the major type is now called immunoglobulin-g (IgG) Haptens are small molecules (<5000 mw) that are antigenic only when linked to larger proteins

2 Structure of IgG B cells make immunoglobulins - these are secreted into the blood. IgG is the major class of antibody molecule, and one of the most abundant proteins in the blood. Antibodies are also the most positively charged proteins in the blood. Four polypeptides make up IgG: 2 large ones called heavy chains, and two light chains. They are linked by noncovalent and disulfide bonds into a 150 kd complex. IgG architecture Pairs of heavy and light chains form a Y-shaped molecule; two antigen-binding sites are formed by the combination of variable regions from one heavy (V H ) and one light (V L ) chain. In 1950, Rodney Porter found that a protease called papain cleaves IgG into two fragments: one crystallized easily, showing it has a regular structure and sequence. He called this fragment F c. The other fragment bound to antigen; he called this F ab.

3 The immunoglobulin fold Porter used digestion with trypsin, chymotrypsin and cyanogen bromide to break the Fc fragments into peptides that he could sequence by Edman degradation. Gerald Edelman was the first to sequence an Fab, using monoclonal antibodies from myeloma cells - a type of cancerous B cell. Porter and Edelman received the Nobel Prize for this work in Later, when IgG was crystallized and the complete structure was solved, it was clear that the constant domains have a characteristic structure called the immunoglobulin fold (all beta sheets/turns).

4 CH1

5 VH1 CH1 VH1 CH1 VL

6 VH1 CH1 VL CL VH1 CH1 VL CL

7 VH1 CH1 CL VL Elbow Hinge Flexibility and motion of immunoglobulins Fv Elbow Fv Fv Fb Hinge Fb Fb Fv Fv

8 Fv VH1 CH1 Fb CL VL Fab Elbow Carbohydrate Fc Hinge IgG-antigen binding The 2 heavy chains are (gray) and the 2 light chains (blue) are held together by disulfide bonds. Four disulfides occur between the polypeptide chains: papain cleaves beyond the two at the top of the heavy chains. Antigens bind in the pockets created by the variable regions, often by a mechanism called induced fit.

9 Immunoglobulins are Bifunctional Proteins Immunoglobulins must interact with a finite number of specialised molecules - Easily explained by a common Fc region irrespective of specificity - whilst simultaneously recognising an infinite array of antigenic determinants. In immunoglobulins, what is the structural basis for the infinite diversity needed to match the antigenic universe? Variability of amino acids in related proteins Wu & Kabat Variability Cytochromes C Amino acid No. 100 Variability Human Ig heavy chains Amino acid No.

10 Distinct regions of high variability and conservation led to the concept of a FRAMEWORK (FR), on which hypervariable regions were suspended. Framework and Hypervariable regions Most hypervariable regions coincided with antigen contact points - the COMPLEMENTARITY DETERMINING REGIONS (CDRs) FR1 CDR1 FR2 CDR2 FR3 CDR3 FR4 100 Variability Amino acid No. Hypervariable CDRs are located on loops at the end of the Fv regions Hypervariable regions

11 Space-filling model of (Fab)2, viewed from above, illustrating the surface location of CDR loops Light chains Heavy chains CDRs Green and brown Cyan and blue Yellow Hypervariable loops and framework: Summary The framework supports the hypervariable loops The framework forms a compact! sandwich (sometimes also called barrel ) with a hydrophobic core The hypervariable loops join, and are more flexible than, the! strands The sequences of the hypervariable loops are highly variable amongst antibodies of different specificities The variable sequences of the hypervariable loops influences the shape, hydrophobicity and charge at the tip of the antibody Variable amino acid sequence in the hypervariable loops accounts for the diversity of antigens that can be recognised by a repertoire of antibodies

12 Non-covalent forces in antibody - antigen interactions Electrostatic forces Hydrogen bonds Attraction between opposite charges Hydrogens shared between electronegative atoms Van der Waal s forces Fluctuations in electron clouds around molecules oppositely polarise neighbouring atoms Hydrophobic forces Hydrophobic groups pack together to exclude water (involves Van der Waal s forces) Other Ig classes have similar folds but distinct heavy chains Many vertebrates have 5 classes of Ig, each with a distinct type of heavy chain. IgD and IgE are similar in structure to IgG. IgA is found mainly in secretions - tears, saliva, milk - and can be a monomer, dimer or trimer. IgM is the first antibody made by B cells in the early stages of a primary immune response. It can be either monomeric (and membranebound) or secreted as a disulfide cross-linked pentamer. IgM pentamer

13 Domain Structure of Immunoglobulins Domains are folded, compact, protease resistant structures Fc Fab S S CL VL Light chain C domains " or # Heavy chain C domains $, %, &, ', or µ S S S S S S CH1 F(ab)2 VH Pepsin cleavage sites Papain cleavage sites - 1 x (Fab)2 & 1 x Fc - 2 x Fab 1 x Fc Why do antibodies need an Fc region? The (Fab) 2 fragment can - Detect antigen Precipitate antigen Block the active sites of toxins or pathogen-associated molecules Block interactions between host and pathogen-associated molecules but can not activate Inflammatory and effector functions associated with cells Inflammatory and effector functions of complement The trafficking of antigens into the antigen processing pathways

14 Structure and function of the Fc region C H 3 C H 2 IgA IgD IgG C H 4 C H 3 C H 2 IgE IgM The hinge region is replaced by an additional Ig domain Fc structure is common to all specificities of antibody within an ISOTYPE (although there are allotypes) The structure acts as a receptor for complement proteins and a ligand for cellular binding sites C1q binding motif is located on the C'2 domain Carbohydrate is essential for complement activation Subtly different hinge regions between subclasses accounts for differing abilities to activate complement

15 Phagocytosis of an antibody-bound virus by a macrophage IgG is the major antibody produced in secondary immune responses, initiated by memory B cells. As part of the organism s ongoing immunity to antigens already encountered, IgG is the most abundant Ig in the blood. Fc receptors on the surface of macrophages bind antibody Fc regions, triggering engulfment. Upon binding to a bacterium or virus, macrophages - a type of leukocyte (white blood cell) - are recruited to engulf and destroy the invader. High-affinity antibody-antigen binding Typical antibody-antigen interactions have Kd values of M. The Kd value reflects energy derived from ionic, H-bond, hydrophobic and van der Waals interactions that stabilize the binding. Amino acids lining the antigen binding site tend to be hypervariable, enabling maximum numbers of variants from which to select those with tightest binding to a particular antigen. The complex of an Fab bound to an HIV-derived peptide illustrates the kind of large conformational change (and induced fit) that can occur upon antigen binding. Challenge: Can you find the mistake in Whitford??? It has something to do with the information given on this slide!

16 Antibody-antigen interactions provide important analytical tools Polyclonal antibodies are those produced by many different B cells responding to the same antigen. Polyclonal preparations contain a mixture of antibodies targeting different parts of the protein. Monoclonal antibodies are produced by a population of identical - clonal - B cells. They are homogeneous and all recognize the same epitope. Kohler and Milstein developed the techniques for producing monoclonal antibodies for use as analytical tools.

17 ELISA method LEARN MORE ABOUT ELISA:

18 USING ANTIBODIES IN PROTEIN PURIFICATION/DETECTION: Immunoblotting This is often called a Western blot.

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