Human Leukocyte Antigen
Created by Brian Francica
HLA (Human leukocyte antigen) molecules are key components of the human immune system. Known more broadly as MHC (major histocompatibility complex) molecules, these molecules are broken up into many different categories depending on their specific roles in the immune system. The general function of an MHC molecule is to bind antigen (which has already been processed by the cell) and then present it on the cell surface to T-cell receptors. While Class II MHC molecules present peptides found outside of the cell, Class I MHC molecules are responsible for presenting peptides found in the intracellular space. This correlation between class molecules and peptides they present signals the immunes system as to the type of threat it is dealing with. (Parham)
After translation in the ER, the Class I molecule is incorporated into intracellular membranes of the Golgi where it is subject to proteins that are in the cytosol of the cell. Protein antigens will attach to the HLA molecule as it is on its way to the surface of the cell. Once on the surface of the cell, the HLA molecule serves as a ligand to the T-Cell Receptor (TCR). Through the process of central tolerance, T-Cells that recognize HLA molecules presenting peptide sequences innate to the human body are removed from the body. However, if foreign antigen is presented by the HLA Class I molecule, a TCR-HLA interaction occurs. (PFam, Parham)
The TCR is associated with a protein CD3 on the cell surface and the MHC molecule is associated with CD8 (See picture in Doc1_1). This secondary interaction is also critical for full protein-ligand interaction and thus signal transduction. Each T-Cell expresses many copies of a unique TCR and each presenting cell, if infected, will express on its surface many HLA complexes with the same foreign antigen. If an estimated 100 TCR-HLA and CD8/CD3 interactions occur, the CD8+ killer T cell is activated to not only undergo clonal expansion, a process by which thousands of copies of the orginial T-Cell are produced, but also to induce apoptosis (programmed cell death) of the HLA presenting cell. By these mechanisms, infected cells can be cleared from the body without the infection spreading. (Parham)
Introduction to General Structure of HLA A2 Class I MHC
The HLA Class I MHC molecule (PDB ID: 3MYJ) is a total of 89790.71 daltons and consists and 375 base pairs. It is a heterodimer comprised of two chains: a MHC alpha chain (heavy chain), and abeta2-microglobulin chain (light chain), where only the alpha chain spans the membrane. (PDB)
The alpha chain has three extracellular domains (alpha 1-3, with alpha1 being at the N terminus), a transmembrane region and a C-terminal cytoplasmic tail.(EBI) A1 Comprises amino acids 1-90, A2 91-182, and A3 183-270. B2 is comprised of B1-100. The A1 and A2 are structurally almost exactly alike, and A3 and B2 are similarly analogous. (EBI)
The A1 and A2 (also in mesh) Variable Domains of the alpha chain are referred to as the recognition region, because the peptide antigen (recall from the introduction that HLA molecules present peptide antigen to T cell receptors) binds in a deep groove between these two domains. They are called the variable domains because there is a number of differing genes that encode for the same general structure, but with slightly different amino acids. This variability in sequence confers the ability for a person to have a set of different HLA molecules that can recognize a wide variety of peptides. A1 and A2 are defined by two, four stranded antiparallel beta sheets with a 70 degree left handed twist. Loops of varying length connect each beta sheet that alternate above and below the beta sheet. The sheets from A1 and A2 are joined so that a larger sheet is created. Two almost parallel alpha helices that follow the twist of the beta pleated sheets and form the peptide binding region of the molecule. Each helix spans from one corner of the sheet to the other corner. The junction of A1 and A2 helices is such that the two helices are slightly above the beta sheets and outline the sheet to create a cleft with the beta sheet as a bottom. The A2 domain, if taken as a replica of the A1, is simply rotated 178 degrees. (Saper)
A3 and B2 microglobulin do not bind ligand and thus do not perform in the primary function of the protein, but are essential none the less. A3 associates the protein to the cell membrane and the soluble extracellular B2microglobulin associates with A3 and is necessary for MHC stability. (PFam)
Structure as Related to Function:
The two Alpha helices of A1 and A2 that create the binding cleft are formed so that not only do they bind antigen, a crucial process for T-cell specificity, but also are complimentary to the T-Cell Receptor. The specificity of these residues (A1 56-85 and A2 137-180) (Sapert )determines what type of molecules the MHC molecule binds. Remember that it is important to note that these to variable regions are encoded by several different genes. This variability allows the body to have a host of MHC complexes that are specific (Borbulevych) for different peptides. Without this variability, the body would be greatly limited to the number of peptides, and thus, number of invasive pathogens, that it could recognize. (Parham)
A3 and B2m are known as the constant region of the MHC complex. They do not have any interaction with peptide or T-cell receptor and thus do not need to have the same variability. A3 not only structurally allows the complex to be anchored to the membrane, but also associates with B2microglobulin which is crucial for the complexs stability. A3 and B2m have a host of interactions between beta sheets that lead to conformational stability, as the microglobulin interacts both with the 8 stranded beta sheet of A1 as well as A2 and A3. (PDB, Sapert)
MHC contact with T Cell Receptor:
Variable loops 1,2, and 3 of TCR alpha chain contact A2-alpha helix. CDRb3 (Complimentarity determining region, same as variable loop) extends across a1 at residue 72 and ends by contacting the a2 domain at 149,150,151, and 155. Variable loops surround y5. CDR residues G4 and Y5 make contact with a1 alpha helix residues 65,66,68, and 69. CDR1a contacts the a helices of a1 and a1 domains, making a footprint like CDR3.
While the TCR is mostly specific for the the peptide, and thus has more involved contacts with the peptide, there are a few crucial residues where the TCR makes contact with the HLA molecule. Variable loops 1,2, and 3 of the T cell receptor alpha chain contact A2-alpha helix. One such loop ,called CDRb3 (Complimentarity determining region, same as variable loop), contacts A1 at residue 72 and ends by contacting the A2 domain at 149,150,151, and 155. Variable Loops (viewed longways and sideways) surround the Y5. CDR residues G4 and Y5 of the TCR interact with a1 alpha helix residues65,66,68, and 69. CDR1a contacts the a helices of A1 and A2 domains, making a footprint like CDR3. (Othman, Garboczi)
Attachment to the membrane:
HLA molecules are all attached to the membrane as a part of their function. However, the alpha helix that serves as an anchor is a separate domain not shown in this software and is generally ignored by research. I feel that it is important to note that there is a C-terminal apha helix that links the protein to the membrane, but the structure is not outstanding in any other way. (Parham, EBI)
Structural Similarities:
As i previously mentioned, HLA molecules are highly polymorphic, allowing htem to display different antigens and make synapses with different T cell receptors. There are different classes of HLA molecule such as HLA-B, that perform similar tasks, but in different parts of the body. This molecule is HLA-B*2709 (PDB ID: 3BP7), and shows very similar structural similarity even though it is only 70% similar residue for residue. (Dali Server)
Another protein MHC class 1 H-2k (PDB ID: 1KPU), has only 30% sequenc similarity, but the the structural similarity is obvious. MHC molecules all have very similar functions, but each isotype is specialized to act in a slightly different way and present slightly different antigen. (Dali Server)