Required Powerpoint Slides
This is not a test, but it is to show your practical work and understanding.
Don't worry about your English. My Japanese is much worse!
If I can understand you, you get credit. Ask for help.
Your completed Powerpoint will be graded.
Discuss with other students in the class.
Ask for help often! Your TA's can help you!
You will not present your Powerpoint with the projector. It will simply be a record of your work.
Email your Powerpoint files to email@example.com.
Name your Powerpoint file with your name:
Please put the slide number on each slide: "Slide 1", etc.
Save file as Powerpoint 1997-2004 .ppt (not .pptx).
- Your name.
- Your email address.
- Name of Professor of your laboratory research group.
- Topic of your research project.
You have 2 PDB codes: One that you selected, and one that was given to you by Minamino-san
and the TA's.
If the PDB code that you selected does not have ligand, give the following information
on Slide 1 for two PDB codes: your selected code, and your given code:
- Name and function of the molecule.
- PDB Code.
- Resolution, R value, and Free R of this model. (See #34 on the Syllabus.)
If the PDB code that you selected has ligand, use
it for all slides below.
If the PDB code that you selected has NO ligand, use
the PDB code given to you for Slides 3 and 7.
Use the PDB code that you selected for all the other slides.
- Number of chains of protein, DNA, and RNA
in the asymmetric unit (published PDB file).
If there are zero, say 0 chains of DNA, etc.
Suggestion: Proteopedia tells you the total number of chains under
About This Structure.
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 (Which PDB code? See note above.)
- What are the 3-letter codes, and full names of the:
- Non-standard residues?
Suggestions: Use Proteopedia's green links.
- What secondary structures are present? Is the molecule mostly one
secondary structure? Snapshot.
- Number of disulfide bonds within chains? Between chains?
Suggestion: FirstGlance in Jmol, More Views.., Disulfide Bonds.
- Is there a hydrophobic core?
- Is your molecule soluble? Please say the reason for your conclusion.
Slide 7 (Which PDB code? See note above.)
- 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.
Say the kind of non-covalent bond for each one you are showing.
Slide 8 - Evolutionary Conservation
- In Proteopedia, show evolutionary conservation for your molecule.
- Click on the link Complete Results at ConSurfDB (in Evolutionary Conservation).
- At ConSurfDB, View Conservation in FirstGlance.
- Find two highly conserved amino acids on the surface of your molecule,
one expected and one unexpected.
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?)
Gly in turn
Pro* in turn
Met1 at N-terminus
<--Nothing on left
(No known function)
* Pro is "helix breaking".
- Identify the two residues by clicking on them, for example on 4enl
you could select Pro290 and Glu188.
- Go to the FirstGlance Control Panel and use Find.. to put halos
on these two residues. (In the example, you would find "pro290,glu188".)
- On your slide, say the two residues you selected (for example
Sometimes there is no highly conserved (level 9) amino acid that is unexpected.
In that case, find an amino acid conserved at level 8 with unexpected
Say why you expected conservation of the one residue you chose.
of the Evolutionary Conservation result for your molecule with halos on the two residues of interest
- Highly conserved Pro290: expected.
- Highly conserved Glu188: unexpected.
Number of chains in the biological assembly:
two snapshots showing
the asymmetric unit side by side with the result(s) from MakeMultimer.
Go to Submit PDB ID, enter your PDB code, click Submit.
Click View in FirstGlance.
List the gaps in your model as ranges of missing amino acids. For example, for 2ACE, the list
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.
List the number of your Proteopedia Sandbox Reserved page (for example, Sandbox Reserved 14).
of your Sandbox Reserved page (show the entire browser window please)
including your first green link, and the molecular scene produced
by that link.
of your Proteopedia Sandbox Reserved page
(show the entire browser window please)
including your second green link, and
the molecular scene produced by that link.
List the amino acids (e.g. Phe87:A with Lys212:A) for one energetically significant
cation-pi orbital interaction. (":A" means in chain A.)
snapshot of the listed cation-pi interaction with a distance monitor.
Suggestion: FirstGlance in Jmol, More Views.., Show cation-pi interactions.
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.
snapshot of your molecule spacefilled, colored by temperature.
Orient the molecule to show the region with highest temperature, and the halos on the
Are there any patches of all positive or all negative charges?
Choose a chain for charge calculations. Specify the one-letter name of the chain.
What is the isoelectric pH (pI) of the chain?
Suggestion: FirstGlance in Jmol, Charge.., follow instructions there
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?
SLIDES 16 AND 17 ARE NOT REQUIRED FOR 2012.
Show a publication-quality view of your molecule created with Polyview-3D.
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.