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”.

9) Take a screen shot of your protein, as above, and insert it into your electronic report. Label it appropriately (eg. Step

9). 1 MARK.

10) Now insert screen shots of your protein in “New Cartoon” representation, coloured according to “Structure” (1 MARK) and

“ResType” (1 MARK).

11) What are the meanings of these two colour codings? (2 MARKS)

12) Change the colour back to “Structure”.

13) So far you’ve only displayed the protein, but the PDB file also contains information about the structure and binding

location of ligands (drugs, inhibitors, agonists, etc.). You can display these “non-protein” molecules by creating a second

representation as follows: Graphics -> Representations -> Click Create Rep. Now you’ve created a second “Rep” which actually

overlays on top of the first one, but you can’t tell yet because they’re both the same (“All”).

14) You can display all non-Protein molecules in a different way to that of the Protein, so that they can easily be seen.

Select the second “Rep” as above (highlighted in yellow). In the “Selected Atoms” text box, delete “all”, and type in “not

protein”, and press enter. Then change the Drawing Method to “VDW”, and the Coloring Method to “Name”. Take a screen shot and

insert it
(1 MARK).

15) You will see a lot of red spheres. To find out what they are, you can label them as follows: Mouse -> Label -> Atoms;

then click a red sphere on the protein graphics window. The atom you selected will then have a green label next to it. If the

text is obscured, try making the atoms transparent: Graphics ->  Representations -> Click “Opaque”, then drag and select

“Transparent”. What do the red spheres represent? (1 MARK)

16) To remove the red spheres, change the second “Rep” to “not protein and not resname HOH”. Insert a screen shot once this

is done (1 MARK).

17) You should see a number of molecules in “large spheres” (VDW) format all around the protein.

Rotate the protein around by clicking on the protein and holding the left mouse button while moving the mouse around. The

main ligand is the one bound deep inside a binding pocket of the enzyme (white arrow above). Try making the protein (first

Rep) “Transparent”, and insert a screen shot that clearly shows the ligand in the binding site, such as below (1 MARK).

Label and name 2 protein Amino Acid residues that are in close contact with the ligand (2 MARKS) (eg. HIS108 and SER 120).

18) Edit the second “Rep” so that ONLY the main ligand is visible. Insert a screenshot which shows only the protein (in

cartoon form) and the main ligand (in VDW form), as below.

Hint: You will need to know the “resname” of the ligand. You can do this by labelling one of its atoms, and looking at the

information displayed in the messages window, which looks like this:

19) You can temporarily turn off the first Rep by double clicking it, which will make it turn grey.

You should then only see your ligand in VDW format in the graphics window.

20) You can explicitly display the protein residues which make tight contacts with the ligand by displaying only the protein

amino acids with lie within a certain distance of the ligand. Create a third “Rep”. Delete “all” in the text box, and type in

the following: “protein and same residue as within 5 of resname XXX”, where “XXX” is the resname of your main ligand (in this

example, E20). This displays all protein residues within 5 Angstroms of the ligand. Change the Drawing Method of the third

Rep to, eg. Bonds. You should see something like the graphic below. Insert a screenshot (1 MARK).

21) Insert a screenshot, similar to one above, except with all protein residues within 3 Angstroms of the main ligand (1

MARK).

22) Insert a screenshot with only the ligand and the single CLOSEST protein residue in contact with it; name this residue (1

MARK) and the distance it lies to the protein (1 MARK). (Note: strictly speaking, this method displays residues for which any

of the ligand’s atoms lies within X Angstroms to any protein atom).

23) You can explicitly label bond distances. Using the Mouse -> Label menu options, insert a screenshot showing the labelled

distance between any ligand atom and any protein atom
(1 MARK).

24) Discuss the main interactions between the ligand and the protein. What types of compounds would be most suitable to act

as inhibitors? (3 MARKS)

TOTAL: 20 MARKS

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Biology

Answer questions
(150 words) This week we started learning about evolution, so the two articles you will be comparing in this conference deal with the evolution of the Peppered Moth during the Industrial Revolution in England.
Read the following articles and address the questions listed below.
1. Which article in your opinion was of more scientific merit? Why? Be sure to use concrete examples from the articles to support your claims.
2. Which article did you find more compelling? Why? Again, be sure to use concrete examples from the articles to support your claims.
3. Both articles cite other sources, how does this impact your opinion of the merit/credibility of the articles? How does the source of the article impact your perception of its merit?
4. A compelling argument can sometimes lack scientific merit, what are some strategies you can employ to avoid being “taken in” by a compelling, but not accurate argument? Consider here other arguments you come across in your daily life – commercials for products, advertisements for diet pills, etc.
Article 1: The Peppered Moth – An Update by Kenneth Miller – http://www.millerandlevine.com/km/evol/Moths/moths.html

Article 2: The Peppered Moth as found on Truth in Science
http://www.truthinscience.org.uk/tis2/index.php/component/content/article/127.html

(125 words) Like other living organisms, humans are part of ecosystem and have impacts that go far beyond those of animal species on the ecosystem.
Pick an environmental problem you found in the book, say chlorofluorocarbon damage to the ozone, describe the problem, then describe how we can be part of the solution. What can we do to save our planet and protect our fragile biosphere?