understanding biology through structurescourse work 2006 understanding immune recognition

Understanding biology through structures Course work 2006

Understanding Immune Recognition


Antigen Recognition

• B cells can recognise antigens via their surface Ig molecules

• T cells can only recognise antigen in association with a Major Histocompatibility Complex (MHC) molecule.


The Immunoglobin Fold


Immunoglobin Fold

• V and C domains share the basic Ig fold

• Differences between the two domains

• C domain is built of seven -strands arranged so that four strands form one sheet and three strands form a second sheet.

• The strands are closely packed together and joined by a single disulphide bond

• Most of the invariant residues of the constant domain are in the sheets

• Overall structure of the V domain

very similar but there are nine strands instead of seven. The two additional strands harbour CDR2


Structure of antibody


Complementarity Determining Regions in Ig


• Six loops of the VH (H1, H2 and H3) and VL (L1, L2 and L3) domains create a great variety of surfaces

• Deep binding cavities: such as those seen in some antibody-hapten complexes

• Wide pockets : seen in certain antibody-peptide complexes

• Flat surfaces : seen in antibody-protein interactions

• H3 is the most variable of the loops and in all crystallographically solved antibody-antigen complexes makes several contacts with antigen

The Complementarity Determining Regions


What Do Antibodies Recognize?

1. Proteins (conformational determinants, denatured or proteolyzed determinants)

2. Nucleic acids3. Polysaccharides4. Some lipids5. Small chemicals (haptens)


• Antibodies bind to antigens by recognizing a large surface, and through surface complementarity.

• Thus, these complexes have a very high affinity for each other.

Antigen:Antibody complex


• The interaction between an antigen and antibody can be very strong, and yet all of the forces involved are considered to be relatively weak. How can weak hydrogen bonds, electrostatic attractions, hydrophobic forces, and van der Waals contacts lead to a high affinity?

• Contact between antigen and antibody occurs over a wide surface area, allowing multiple weak interactions that give a strong affinity

• Hydrogen bonds join the antibody and antigen over a wide surface area. Other weak forces, including van der Waals forces, electrostatic attractions and hydrophobic forces, add to the strength and specificity of antibody/antigen binding

Weak forces vs high affinity


• Haptens, having a limited total surface area, deeply embed themselves into the VL/VH dimer interface

• Hapten binding antibodies frequently show a deep central cavity, long CDR L1 loops and a CDR H3 loop with an "open" conformation, allowing the hapten to bind as much as 80% of its total surface in the interaction.

Antibody-Hapten Complex


Intimate interaction between Ab and Hapten


Peptide Antibody Complex


• In contrast, proteins preferentially to a relatively flat binding surface

• In a "closed" CDR H3 conformation, the CDR H3 loop packs down onto the central cavity, and the protein antigen binds on top of it.

Protein Antibody Complex


Effector response is mediated via Ig-FcR complex formation

• Antibodies not only must recognize antigen, but also must invoke responses – effector functions – that will remove the antigen and kill the pathogen.

• Variable regions of antibody are the sole agents of binding to antigen.

• The heavy chain constant region (CH) is responsible for interactions with other proteins (e.g. complement), cells (elements of innate immune system), and tissues that result in the effector functions of the humoral response.

• FcR recognize the Fc portion of antibodies not antigens


The Fc-Fc Receptor complex• FcR plays important role in antibody mediated immune responses

• Ig and FcR binding activates effector functions

• Fc Receptor interacts with the CH2 and CH3 domains of Immunoglobulins


Mode of interaction of FcR with difference Ig molecules


Immune Recognition :MHC and TCR

interactions


Antigen Recognition

• B cells can recognise antigens via their surface Ig molecules

• T cells can only recognise antigen in association with a Major Histocompatibility Complex (MHC) molecule.


T cells

• T cells display TCR as their antigen recognition protein

• When stimulated they become Cytotoxic or Helper T cells

• Secrete cytokines that recruit other cells of the IS

• TCR’s only recognise short peptides.


MHC & T cells • T cells have a requirement to recognise both the

ANTIGEN and the MHC molecule. This is because the molecular structure of the MHC-Antigen complex is arranged so that some of the polymorphic amino acids of the MHC molecule are in direct contact with the TCR – Therefore T cell recognition of antigen is said to be

MHC ‘restricted’.


Antigen Processing and Presentation

• Fragmentation of protein into peptides• Association of peptide with an MHC molecule• Transport to cell surface for expression• Different cellular pathways for association of peptide

with MHC class I and class II molecules


MHC & Antigens• MHC Class I

– present endogenously derived peptides.

– these can be either self or derived from viruses

– because MHC Class I is present on all cells any cell can interact with T cells if infected by a virus

• MHC Class II– present exogenous

antigen which has been phagocytosed and processed.eg. Bacteria

– This is performed by professional antigen presenting cells eg macrophages


MHC

• MHC Class I– detected on all

nucleated cells– very highly

polymorphic– Tight fit for

peptides of only about 9 aa

– consists of an -chain of 3 domains associated with -2 microglobulin

• MHC Class II– seen only on the

‘professional antigen processing cells’ e.g macrophage

– slightly less polymorphic

– accepts peptides of up to 15 aa acids


CD4 T-CELL

TCR CD4

CD3

9 aa peptide15 aa

peptide

CD8 T-CELL

CD8

TCR

CD3

ANTIGEN PRESENTING CELL

MHCCLASS II

11

2 2

Major histocompatibility complex (MHC); human=Human Leukocyte Antigen (HLA); mouse=H-2Gorer and Snell identified a genetic basis for graft rejection and Snell named it histocompatibility 2 (H-2). Nobel prize awarded to Snell.Highly polymorphic genes organized in a complex on chromosome 6 (human) and 17 (mouse).Glycoproteins expressed on the surface of cells. MHC class I is composed of one polypeptide, non-covalently associated with 2microglobulin. MHC class II is composed of two polypeptides, referred to as and .

MOLECULES OF T LYMPHOCYTE RECOGNITION

CLASS IMHC 2m

2 1

3

ANTIGEN PRESENTING CELL


MHC Class I and Class II Proteins• Class I

– Alpha Chain• 3 External domains• 1 Transmembrane• 1 Cytoplasmic tail• Encoded in MHC

– Beta-2 Microglobulin• 1 External domain• No transmembrane• No Cytoplasmic tail• Not encoded in MHC

• Class II– Alpha Chain

• 2 External domains• 1 Transmembrane• 1 Cytoplasmic Tail• Encoded in MHC

– Beta Chain• 2 External domains• 1 Transmembrane• 1 Cytoplasmic Tail• Encoded in MHC


MHC Class I and Class II Proteins


Peptides bind to MHC molecules in a polyproline II conformation


Class I:Peptide Binding


MHC-II Structure


Peptide Binding by Major Histocompatibility Complex (MHC) Antigen-presenting Proteins

• Peptides of intracellular origin

• Peptides 9-10 residues long

• Deep pockets bind peptide sidechains

• Deep pockets bind peptide N- and C-termini

• Peptides of extracellular origin

• Peptides 15 residues or longer

• Shallow pockets bind peptide sidechains

• Peptide termini free• H-bonds to peptide

backbone

MHC I MHC II


• Both Class I and Class II genes are highly polymorphic

• Most polymorphic residues of Class I are in the alpha 1 and alpha 2 domains

• Most polymorphic residues of Class II are in the alpha 1 and beta 1 domains

MHC Polymorphism


Location of Polymorphic Residues


Allelic variation in MHC occurs at the peptide binding site and on the top/sides of the binding cleft


T-cell Receptor


The T cell receptor (TCR) is a complex of integral membrane proteins that participates in the activation of T cells in response to the presentation of antigen. Specific recognition and binding by the clonotype-specific a/b heterodimer leads to activation of transcription and commitment of the T cell to CD4+ or CD8+ fate. This activation involves other subunits of the receptor complex as well as other membrane-associated molecules that couple the extracellular liganding event to downstream signaling pathways such as protein phosphorylation, the release of inositol phosphates and the elevation of intracellular calcium levels.


TCR binds peptide/MHC with a restricted (but variable) orientation


peptide binding interface: 21-34%proportion of TCR contacts with the peptide:26-47%contact are different between TCR-MHC complex

-the contribution to the binding energy is still uncleared!

Bandovich and Garcia. 2003. Immunity 18,7-11


-CDR1 and CDR2 interact with MHC molecules (helices)

-CDR3 interacts with the peptide

-interaction always in the same orientation-45 to 70 degrees angle related to peptide-V see N-ter of the peptide-V see C-ter of the peptide

TRI-MOLECULAR COMPLEX CHARACTERISTICS


TRI-MOLECULAR COMPLEX CHARACTERISTICS

- most of the binding interface is between the TCR and MHC helices

- conformational change in the TCR CDR loops enhances TCR crossreactivity

- no conformational change in the TCR constant region (except in one complex out of ten)


Recognition of the Super Antigens


Antigen Recognition by Antibodies (Ab) and T-cell

Receptors (TCR)

• Surface area ~ 2x750 Å2

• Epitope discontinuous in antigen (Ag) sequence

• Surface area ~ 2x1000 Å2

• Ag peptide contributes only 40% of surface area

• Epitope continuous in Ag sequence

• Otherwise similar to Ab - Ag recognition

Ab - Ag TCR – MHC/peptide


PARADOX

-TCR-MHC interaction has a weak affinity-affinity ~ 10 M-half-life ~10s

-restricted numbers of ligands (~100) are displayed at the surface of antigen presenting cells

-T cell activation requires a long interaction with antigen presenting cells (>2h)

understanding biology through structurescourse work 2006 understanding immune recognition

Documents

understanding biology

structurescourse work

antibody complex slide

ig slide

structure of antibody

immunoglobin fold slide

immune recognition slide

antigen recognition