MHC and T Cell Receptors
Updated 23/10/00

Resources	Objectives	Procedures	Marks
Kuby's Immunology	Immunology Reference Shelf	Carney's Learning Techniques	To Tortora's Microbiology	Immunology Laboratory

This Lab exercise contains a Description of the needed source materials, a list of objectives, a detailed description of each of the objectives and the marking scheme

OBJECTIVES:

1. To use the Protein Data Bank
2. To use RasMol to construct three dimensional models of protein
3. Build a model showing the structure of MHC-1
4. Build a model showing the structure of MHC-2
5. Build a model showing the structure of the T cell receptor (TCR)
6. Build a model showing the structure of the T cell receptor- Antigen-MHC complex

OBJECTIVE 3: Build a model showing the structure of MHC-1

• If you have not already done so download and install Windows 95 version of Rasmol & its user manual to your computer.
• If you do not have Windows 95 go to the Rasmol Home Page and download the version appropriate for your system.
• Download the protein database file MHC-1.pdb file to your own computer
• Open the file MHC-1.PDB in Ras Mol editor.
• Use the Rasmol command line editor construct your answers to the following assignments
• Use the EXPORT menu of RasMol to save your results in GIF format on a 3.5 " floppy disk with the filename MHC-1.GIF Submit written answers as required in a file MHC-1.TXT constructed in MS Notepad

Assignmentss for MHC-1

• show each of 3 alpha chain domains .
• how many amino acids are there in each domain?
• show the peptide binding cleft
• which domains are involved in formation of the peptide binding cleft
• count beta strands which are involved in formation of the peptide
• binding cleft
• how many amino acids contains peptide found in the cleft?
• show the microglobulin molecule
• name the secondary structure found in alpha 3 and microglobulin
• what kinds of bonds are involved in maintaining the domain fold?
• name molecule with similar fold
• does microglobulin interact with all 3 domains of MHC I?

OBJECTIVE 3: Construct a model showing the structure of MHC-2

• If you have not already done so download and install Windows 95 version of Rasmol & its user manual to your computer.
• If you do not have Windows 95 go to the Rasmol Home Page and download the version appropriate for your system.
• Download the protein database file MHC-2.pdb file to your own computer
• Open the file MHC-2.PDB in Ras Mol editor.
• Use the Rasmol command line editor construct your answers to the following assignments
• Use the EXPORT menu of RasMol to save your results in GIF format on a 3.5 " floppy disk with the filename MHC-2.SPT Submit written answers as required in a file MHC-2.TXT constructed in MS Notepad

Assignments for MHC-2

• show the two chains constituting the single MHCII molecule
• show each domain present
• show the domains involved in formation of the peptide binding cleft
• which domains have immunologlobulin homologous fold?
• how are peptide-binding clefts oriented on the dimers?

OBJECTIVE 4: Build a model showing the structure of the T cell Receptor

• If you have not already done so download and install Windows 95 version of Rasmol & its user manual to your computer.
• If you do not have Windows 95 go to the Rasmol Home Page and download the version appropriate for your system.
• Download the protein database file TCR.pdb file to your own computer
• Open the file TCR.PDB in Ras Mol editor.
• Use the Rasmol command line editor construct your answers to the following questions
• Use the EXPORT menu of RasMol to save your results in GIF format on a 3.5 " floppy disk with the filename TCR.GIF Submit written answers as required in a file TCR.TXT constructed in MS Notepad

OBJECTIVE 5: Build a model showing the structure of the T cell Receptor-Antigen-MHC complex

• If you have not already done so download and install Windows 95 version of Rasmol & its user manual to your computer.
• If you do not have Windows 95 go to the Rasmol Home Page and download the version appropriate for your system.
• Download the protein database file TCRAGMHC.pdb file to your own computer
• Open the file TCRAGMHC.PDB in Ras Mol editor.
• Use the Rasmol command line editor construct your answers to the following Assignments
• Use the EXPORT menu of RasMol to save your results in GIF format on a 3.5 " floppy disk with the filename TCRAGMHC.GIF Submit written answers as required in a file TCRAGMHC.TXT constructed in MS Notepad

Assignments T Cell Receptor-AG- MHC Complex

• Show the hypervariable regions of the T cell receptor as a space filling model
• Show the contact sites of the T cell receptor with the MHC in a distinctive colour
• show the contact sites of the antigen with the T cell Receptor in a distinctive colour