opium

opium

opium is one of the world’s oldest drugs and related drugs are used to relieve severe pain’ opioids
produce analgesia by binding to and activating the G-protein-coupled p-opioid receptor (p-oR) in
the central nervous system. After many years of effort several GPCR structures have been solved
recently due to a novel protein engineering strategy that facilitates crystalisation (-1-2)’ The pdb to
download for the p-opiod GPCR is 4DKL’
Attach a comPleted coversheet.
Restrict text to a maximum of 1000 words which includes figure legends’ lnclude one or more
Pymolimages.

Using appropriate headings answer the following:
A) lntroduction – Explain why is it useful to have structural information about GPCRs in general
and this receptor in particular. Briefly summarize the innovation that permitted researchers to
solve the structures of GPCRs’ (Text 2 marks)
B) Results – Construct and annotate a figure (you can make several parts (images) to this figure)
that illustrates the structure. Use the sequence viewer to select the GPCR domain (the N-terminal
protein domain) and present it in green cartoon format. select the T4 lysozyme fusion protein in
the sequence viewer and present it in red stick format. select the morphine-like ligand (BFo) by
finding it using sequence viewer and present it in spheres, coloured by element ( NC )’ Capture
an image of the overall structure’
Find residue D147 which forms an electrostatic interaction with the amine moiety (l’l) of the
ligand. Zoom into the region of this amino acid. Measure and report the distances between the
carboxylic oxygen {o) of D147 and the amine moiety (N) of the BFo ligand’ capture an image of
the ligand binding site and the interaction with D147′ (Figure 2 marks; Figure legend 2 marks;
Distance 1 mark)
C) Discussion – Describe the overall structure of the p-opioid GRCR eg the type of secondary
structure (helices or sheets?). Describe the nature of the region of the protein that is membraneassociated.
How many transmembrane segments? ls the ligand-binding site buried or accessible at
the GPCR surface? (Text 3 marks)
TOTAL = 10 marks
FORMAT OF THE ASSIGNMENT
Please present the assignment as follows:-
(1) Use a header ” Assignment (TilleY)”
Then in the main Lody of the assignment include the following:-
(2) Student number
{3) Paper title {as above), authors, journal, volume and page numbers
(4) Under the title “lntroduction” provide a short summary of the paper (4-5 lines) in your own
words (do NOT plagiarize the abstract of the paper)
– 1ot2′
(5) Under the title “Results” show the associated PyMol irnage of the p-opiod GPCR as
instructed in steps (i) to (iii) below. lnsert this into your assignment document as a PNG file {with a
white background) and label with a detailed figure legend (including the PDB lDs) as “Figure 1”.
(6) Under the title “Discussion” answer the questions in Part C above.
PyMol instructions
ti) Open 4DKL and show {S) the structure in cartoon image and hide (H) all non-bonded atoms
and lines.
(ii) Create a cartoon image of the ligand-bound structure.
{iii) Now select the ligand and show as spheres. [HINT: Select the sequence of the ligand bound
structure and using the “selecting” option in the bottom right hand corner of the viewing screen,
select “Molecules” mode.]
How to make an image in PyMol.
Once you have your structure positioned as you like it:-
i)type in the command line: “ray”
ii) without moving the image, go to the menu “file” -> “Save lmage” -> give the file a name and
save it in a directory of your choice
iii) The file is a png file which can be inserted into a document file.
1. Rosenbaum, D. M., Rasmussen, S. G., and Kobilka, B. K. (2009) The structure and function
of G-protein-coupled receptors, Natu re 459, 35G363.
2. Rosenbaum, D. M., Cherezov, V., Hanson, M. A., Rasmussen, S. G’, Thian, F. S., Kobilka, TS.,
Choi, H. J., Yao, X. J., Weis, W. I., Stevens, R. C., and Kobilka, B. K.(2007) GPCR engineering
yields high-resolution structural insights into beta2-adrenergic receptor function, Science 378,
L266-t273.
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