Powerpoint Assignment

Required Content for Powerpoint
This is not a test. Discuss with other students in the class.
Ask for help often! Make your TA's work!
Email your Powerpoint files to emartz@microbio.umass.edu.

Please put the slide number on each slide

Slide 1

Your name.
Your email address.
Name and function of your molecule.
PDB Code of your molecule.
Resolution of this model.

Slide 2

Number of protein, DNA, and RNA chains in the asymmetric unit (published PDB file). Snapshot.

Slide 3

What secondary structures are present? Is the molecule mostly one secondary structure?
Number of disulfide bonds within chains? Between chains?

Slide 4

What are the 3-letter codes, and full names of the ligands present?

Slide 5

Is there a hydrophobic core? Snapshot.

Slide 6

Is your molecule soluble? Snapshot.

Slide 7

Snapshot of a close-up of a few noncovalent bonds, using Contacts in FirstGlance. Show only a subset of all the contacts, such as some of the putative hydrogen bonds.

Slide 8

Number of chains in the molecule according to PQS. Two snapshots showing the PQS result and the asymmetric unit side by side.

Slide 9

Are there any patches of all positive or all negative charges? Snapshot.
Choose a chain for charge calculations. Specify the one-letter name of the chain.
What is the isoelectric pH of the chain?
What is the charge of this chain at pH 4?
What is the charge of this chain at pH 7?
What is the charge of this chain at pH 10?

Slide 10

Does your protein have any non-standard amino acids? If yes, list their names.
List the residues (e.g. Phe87:A with Lys212:A) for one energetically significant cation-pi orbital interaction. (":A" means in chain A.)
Show a snapshot of the listed cation-pi interaction with a distance monitor.

Slide 11

Color your molecule by uncertainty.
List one residue with a high temperature (e.g. in the format Glu114:B).
Put halos around the atoms of the listed residue with Find.
Show a snapshot of your molecule spacefilled, colored by temperature. Orient the molecule to show the region with highest temperature, and the halos on the listed residue.

Slide 12

List the gaps in your model as ranges of missing amino acids. For example, for 2ACE, the list would be:
- Chain A*: 1-3
- Chain A: 485-489
- Chain A: 536-537
*Note: If your PDB file contains only one chain, it may be listed by S2C as chain 0 instead of chain A.

Slide 13

List two highly conserved residues on the surface of your protein, one expected and one unexpected. In order to be unexpected, the residue should not be Gly or Pro.
Say why you expected conservation of one residue.
Show a snapshot of the ConSurf result for your molecule with halos on the two residues of interest (from Find.).

Slide 14

List the number of your Proteopedia Sandbox page (for example, Sandbox 14).
Show a snapshot of your Sandbox page including your first green link, and the molecular scene produced by that link.

Slide 15

Show a snapshot of your Proteopedia Sandbox page including your second green link, and the molecular scene produced by that link.

Slide 16

Show a publication-quality view of your molecule created with Polyview-3D.

Slide 17

Show a publication-quality rotating animation of your molecule created with Polyview-3D. Keep the animation small (300 pixels) to avoid overloading the server. Also, rotate through 30 degrees in 2 degree steps to minimize server load.