Required Content for Powerpoint
This is not a test. Discuss with other students in the class.
Ask for help often! Your TA's can help you!
Your completed Powerpoint will be graded.
Email your Powerpoint files to emartz@microbio.umass.edu.
Please put the slide number on each slide: "Slide 1", etc.
Slide 1
Your name.
Your email address.
Name of Professor of your laboratory research group.
Topic of your research project.
Name and function of your molecule.
PDB Code of your molecule.
Resolution, R value, and Free R of this model.
Slide 2
Number of chains of protein, DNA, or RNA
in the asymmetric unit (published PDB file).
Snapshot.
How to Make a Snapshot
These instructions are for FirstGlance in Jmol, but work equally well
for molecular scenes in Proteopedia.
When you need Ångstroms, copy this into Powerpoint: Å
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. Zoom in. Show only a subset of all
the contacts, such as some of the putative hydrogen bonds. Show distances.
Slide 8
Number of chains in the molecule according to PQS.
Two snapshots showing the PQS result and
the asymmetric unit side by side.
GRAY SLIDES ARE NOT REQUIRED IN 2009.
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 amino acids (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 - Evolutionary Conservation
List two highly conserved amino acids on the surface of your
protein, one expected and one unexpected. In order
to be unexpected, the amino acid should not be Gly, not Pro, not Met1.
(Why is conservation of Gly and Pro expected on the surface?)
Sometimes there is no conserved amino acid that is unexpected. In that case,
say "There is no conserved amino acid that is unexpected", and put halos on
only the expected conserved residue.
Say why you expected conservation of the one residue you chose.
Show a
snapshot
of the Evolutionary Conservation result for your molecule with halos on the two residues of interest
(from Find.).
Slide 14
List the number of your Proteopedia Sandbox Reserved page (for example, Sandbox Reserved 14).
Show a snapshot of your Sandbox Reserved page including your first green link, and
the molecular scene produced by that link.
Slide 15
Show a snapshot of your Proteopedia Sandbox Reserved 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.