biology

BIOL2119 COMPUTATIONAL BIOLOGY 2012.
ASSIGNMENT 2.
THEME: PROTEIN STRUCTURE VISUALISATION AND SIMPLE ANALYSES

GENERAL INSTRUCTIONS: Read the Background, and complete each of the Tasks below in the order in which they are presented. Pay

close attention, as certain steps involve making screen shots to put in your report, and these are worth various marks as

indicated.

(You may find this a very easy assignment, as it is intended to ensure everyone is familiar enough with basic VMD to

complete the next assignment.)

BACKGROUND

Acetylcholinesterase (AChE) is an enzyme responsible for terminating synaptic transmission in the nervous system. Inhibitors

of AChE, including many insecticides, cause accumulation of acetylcholine in the synaptic cleft, which can result in spastic

paralysis. In this assignment, you will use a popular and user-friendly molecular graphics program (VMD) to generate various

images and simple analysis data for ligand-bound AChE structures. You will continue computational studies of this enzyme and

its inhibitors in Assignment 3.

TASKS

1) Use your own PDB number which is (1ACJ) Note the PDB number assigned to you. This number corresponds to the protein

databank (PDB) structure file that you will be working with for this assignment.

2) Go to the website: www.rcsb.org. Type in the PDB number assigned to you in the SEARCH box and press enter.

3) Click “Download Files”, and select “PDB File (Text)”. Save the PDB file on your hard drive.

4) Go to the website:

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Download and install the latest version of VMD available for your system. You may have to fill out some basic registration

details first.

5) Once installed, start the VMD program.

6) Load the PDB file you downloaded in step 3): File -> New Molecule -> Browse. Select your PDB file, click Open, then click

Load. You should then see the first image of your assigned protein.

7) Take a screen shot of your protein, similar to that shown above, and insert it into your electronic report. Label it

appropriately (eg. Step 7). Worth 1 MARK.

(Note: A number of programs can be used to take screenshots. Eg. MWSnap for PC Windows:

www.mirekw.com/winfreeware/mwsnap.html)

The default view shows the protein in Lines representation, which includes every atom in the PDB, with lines connecting

covalently bound atoms.

8) An alternative representation may be more informative. Change the representation to “New Cartoon” as follows: Graphics ->

Representations. Under the “Draw style” tab, click and hold “Drawing Method”. A large number of possible choices appear.

Select “New Cartoon”.

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