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Open the pdb file 1iak.pdb in DeepView which is located in the PDB Files folder in course documents.
The model shows the extracellular portion of an MHC class II molecule with an antigenic polypeptide (P) bound to its combining site. The MHC class II molecule consists of two polypeptide chains (A and B). The C-terminal regions of both the A- and B-chains are folded into discrete domains, while the N-terminal regions of these chains are folded into a single complex domain, which forms the combining site for the antigenic peptide.
T lymphocytes have receptors (T cell receptors) that recognize and bind specifically (but non-covalently) to the complex of the MHC molecule plus the antigenic peptide, i.e. they interact with residues from both the MHC molecule and the peptide.
By examining the model, answer the following questions:
(a) Describe the C-terminal domains of the A- and B-chains of the MHC class II molecule, with particular reference to their secondary structure. What type of module do these domains represent?
(b) What structure do amino acid residues 107 and 163 of the A-chain form?
(c) Describe the domain which forms the combining site for the antigenic peptide, with particular reference to its secondary structure.
(d) There are three residues which are covalently bound to the MHC class II molecule, but which do not form part of the polypeptide chains: two are attached to the A-chain and one to the B-chain. What type of residues are they? What is the description of this type of modification of the protein? Where in the cell and how did these residues become linked to the polypeptide chain?
(e) The antigenic polypeptide in this model consists of residues 50–62 of hen egg white lysozyme. Some of the side-chains of these residues project into the peptide binding site to interact with residues from the MHC molecule whereas others project out of the binding site, and could potentially interact with a T cell antigen receptor.
For each of the residues Asp52, Tyr53, Leu56, and Gln57, state whether the side-chain of the residue projects into the binding site or out of the binding site.
(f) If the residue Asn59 was mutated to an alanine residue, do you think that the polypeptide would still bind to the MHC molecule? Do you think it would have any effect on the ability of the MHC/peptide complex to be recognized by a T cell? Explain your reasoning.
(g) Produce a molecular model on a white background which shows the peptide binding domain of the MHC molecule, shown as a solid ribbon, without side-chains, and with the A-chain in one colour and the B-chain in a different colour. The antigenic peptide should be shown as a stick atomic model. The view should show the side that faces towards the T cell antigen receptor (i.e. looking towards the cell expressing the MHC molecule). Label the A-chain, the B-chain and the antigenic peptide, using your word processor.
Open the pdb file 1AAY.pdb in DeepView which is located in the PDB Files folder in course documents. Use Deep View to explore the structure and answer the following questions.
(a) How many nucleotide residues are present in the two DNA strands, and how many of these nucleotide residues form base-pairs? Explain your answer.
(b) How many zinc fingers are visible in this model? Explain how you reach this conclusion. (note:- zinc-finger structures that consist of a short alpha helix and two anti-parallel B-sheets)
(c) How do the zinc fingers interact with the DNA – relate the position of the zinc fingers to the structure of the double-helix.
(d) Identify four amino acid residues that are coordinated with the zinc ion, ZN203
(e) From what you have learnt from the structure of the DNA double helix, can you state whether the helix in this structure is distorted from the expected structure of a B-form helix by its interaction with the transcription factor? If so, describe how it is distorted. If not, say why you think not.
(f) What function do Zinc-finger proteins perform within cells and what evidence suggests that this group of proteins appear to be particularly important in eukaryotes?
(g) Identify the zinc finger which is formed from the stretch of amino acids between residues 163 and 185. Within this region, two amino acid residues within the zinc finger form hydrogen bonds with guanidine bases in the DNA. What are the two amino acid residues?
(h) Make a molecular model, which shows one of the amino acid residues identified in (g) above and the base-pair it interacts with. The model should show only:
Your model should show all three residues together with any hydrogen bonds that they form. Label all three of the residues within the structure, one amino acid and two nucleotides.
Present the model on a white background (you may also have to change the colour of the carbon atoms and labels to black in order to achieve a good picture), and save the model and place it into your report. (The residues can be labelled either using the label function within Deepview or by adding labels using your word-processing programme.)
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