Required Powerpoint Report (2015)
This is not a test.
It is to show your practical work and understanding.
However, your completed Powerpoint will be graded.
Don't worry about your English. My Japanese is much worse!
If I can understand you, you get credit.
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 martzeric@yahoo.com.
(You may also use emartz@microbio.umass.edu but there may be problems.)
Name your Powerpoint file with your name:
namba.ppt, minamino.ppt
Please show the Question Number on each slide.
You may make more than one slide to answer one question.
Name of Professor of your laboratory research group.
Topic of your research project.
You have 2 PDB codes:
PDB code assigned to you by Minamino-san.
PDB code that you chose.
Give the following information (on separate "Question 1" slides)
for each of these PDB codes:
PDB Code.
Name and function of the molecule.
Resolution, R value, and Free R of this model.
FirstGlance.Jmol.Org gives R and Free R.
What reliability "grade" does FirstGlance give to the Free R?
Question 2 - Number of chains
(Use the PDB that YOU CHOSE.)
Number of chains of protein, DNA, and RNA
in the asymmetric unit (published PDB file).
(A "chain" is a covalently linked linear polymer of amino acids
or nucleotides. "Distinct" means the sequences are different.)
Snapshot of Cartoon.
If there are zero, say 0 chains of DNA, etc.
Indicate which chains, if any, have identical sequences.
Suggestion: Copy the report from FirstGlance, Molecule Information Tab.
including the Chain Details.
When you need Ångstroms, copy this into Powerpoint: Å
Question 3 - Ligands and non-standard residues
Answer for both of your PDB codes:
What are the 3-letter codes, and full names of the
ligands and non-standard residues?
Suggestion: Copy the list from FirstGlance in the
Molecule Information Tab.
Question 4 - Full length vs. crystallized sequence
(Use the PDB that YOU CHOSE.)
For each protein chain, give the length of the crystallized
fragment (number of amino acids), and the length of the full-length protein.
Pick one chain and do a sequence alignment between the full-length protein and
the crystallized fragment.
Snapshot showing the alignment.
If the crystallized sequence is shorter than the full-length sequence,
which parts were removed before crystallization: the C terminus, the N terminus,
or both?
Suggestion: FirstGlance in Jmol, Molecule Information tab (PDB code
tab), Sequences. At the bottom is a link to instructions for making
the sequence alignment.
Question 5 - Secondary structure
(Use the PDB that YOU CHOSE.)
What secondary structures are present? Is the molecule mostly one
secondary structure?
Snapshot.
Suggestion: FirstGlance in Jmol, Views tab, Secondary Structure.
Question 6 -- Charge distribution.
(Use the PDB that YOU CHOSE.)
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. Use the sequence of the
crystallized protein (possibly a fragment, not the full-length
sequence, unless the full-length was crystallized).
What is the isoelectric pH (pI) of the chain?
Suggestion: FirstGlance, Views tab, Charge.., follow instructions there
for calculations.
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?
Question 7 - Local uncertainty
(Use the PDB that YOU CHOSE.)
Display your molecule as sticks (Views tab, Vines, check
more detail) then
color by Local Uncertainty (Views tab).
List one residue with a high temperature (for example "Glu114 in chain B").
Put halos around the atoms of the listed residue with Find.
Show a snapshot including the minimum, average, and
maximum temperature report at the upper right of Jmol. (To slide the molecule,
double-click and drag on the second click.)
Orient the molecule to show
the region with highest temperature, and the halos on the listed
residue.
Question 8 - Hydrophobic cores
(Use the PDB that YOU CHOSE.)
Are there hydrophobic cores?
Snapshot. (Don't just show a snapshot.
Answer the question!)
Note: there will be a separate
hydrophobic core in each water soluble domain.
Suggestion: FirstGlance in Jmol, Views tab, Hydrophobic/Polar.
Question 9 - Water solubility
(Use the PDB that YOU CHOSE.)
Is your molecule soluble in water?
Please say the reason for your conclusion.
Snapshot.
Question 10 - Disulfide bonds
Show the PDB you chose. If it has NO disulfide
bonds, also show the PDB given to you by Minamino-san.
If it has NO disulfide bonds, also show 9ins.
Number of disulfide bonds?
Number within chains?
Between chains? ("Within" means from one Cys in a chain to
another Cys in the same chain. "Between" means from a Cys in
one chain to a Cys in a different chain.)
Snapshot.
Suggestion: FirstGlance in Jmol, Tools tab, Disulfides.
To distinguish within/between, check Color Disulfide Bonds By Chain.
Question 11 - Missing residues
Show the PDB you chose. If it has NO missing residues,
also show the PDB given to you by Minamino-san.
List missing residues. If there are none, say so.
Suggestion:
In FirstGlance, Molecule Information Tab, Missing Residues.
Take a
snapshot of the Summary by Chain table.
Take a
snapshot showing the "empty baskets".
How many incomplete amino acid sidechains?
Suggestion:
In FirstGlance, Molecule Information Tab, the number of incomplete sidechains
is given under Asymmetric Unit.
Question 12 - Non-covalent interactions
Use the PDB code that you chose. If it has
no ligand, you can target one amino acid, or if the PDB given to you
by Minamino-san has ligand, you may use that.
Snapshots of close-ups of two
different kinds of non-covalent bonds, using Contacts and Non-Covalent Interactions
(Tools tab) in
FirstGlance. Zoom in to show the bonds clearly.
Show distances for only those two bonds. Do not show more than two distances.
Say the kind (type, name)
of each non-covalent bond you are showing.
Question 13 - Biological unit (If the PDB you chose is an X-ray structure, use it.
If the PDB you chose is an NMR structure, use the PDB from Minamino-san.)
Number of chains in the biological unit:
two snapshots showing
the asymmetric unit side by side with biological unit.
Label each snapshot clearly and say the number of chains in each.
Suggestion:
In FirstGlance, Resources tab, Biological Unit.
Question 14 - Evolutionary Conservation (Use the PDB you chose.)
Select a chain for analysis. ConSurf can analyze only one chain at a time.
Check NO, you will not be uploading a multiple sequence alignment. (ConSurf will create
one for you.)
Leave all parameters at their pre-set defaults.
(OPTIONAL: If you want a research grade result, check "Let me select the sequences for the analysis
manually out of BLAST results", and see
Limiting ConSurf Analysis to Proteins of a Single Function.)
Enter your email address at the bottom of the form (this is important so you don't lose
your results). Optionally enter a job title.
Click the button Submit.
It may take an hour or more to complete this calculation.
When it is finished, under Final Results, click the link View ConSurf Results with
FirstGlance in Jmol.
Include the web address of the ConSurf result in your report!
Functional site (patch of highly conserved amino acids)
Gly in turn
Pro* in turn
Met1 at N-terminus
Cys in disulfide bond
Asp, Glu, Arg, Lys in salt bridge
An isolated single highly conserved
amino acid on the protein surface
that is not an expected case.
* 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
Highly conserved Pro290: expected.
Highly conserved Glu188: unexpected.
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
conservation.
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.).
If you used the ConSurf server, paste the address (URL) of your
result into your slide!
Question 15 - Proteopedia Scene I
(Use the PDB that YOU CHOSE.)
List the number of your Proteopedia Sandbox Reserved page (for example, Sandbox Reserved 14).
Show a
Snapshot
of your Sandbox Reserved page (show the entire browser window please)
including your first green link, and the molecular scene produced
by that link.
Question 16 - Proteopedia Scene II
(Use the PDB that YOU CHOSE.)
Show a
Snapshot
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.
Question 17 - Cation-pi interaction (Use the PDB you chose. If it has NO energetically significant
cation-pi interactions, please also show the PDB from Minamino-san.)
List the amino acids (for example, Phe87:A with Lys212:A) for only oneenergetically significantcation-pi interaction.
(":A" means in chain A.)
Show a snapshot of the listed
cation-pi interaction with a distance monitor.
Suggestion: FirstGlance, Tools tab, Salt Bridges/Cation Pi.
Question 18 - Polyview-3D static image
(Use the PDB that YOU CHOSE.)
Show a publication-quality view of your molecule created with Polyview-3D.
Question 19 - Polyview-3D animation for Powerpoint
(Use the PDB that YOU CHOSE.)
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.
Question 20 - Intrinsically disordered regions
Pick one chain of your protein.
Predict whether any parts of the crystallized protein chain are intrinsically disordered.
Show a snapshot of the prediction graph.
Are there missing residues in any of these parts?
(The FoldIndex server makes no prediction about the ends of
protein chains. It uses a 50-residue moving window, so there is no
prediction for the first and last 25 residues.)
Also run the intrinsic disorder prediction for the full length
sequence.
Show a snapshot of the prediction graph.
Were parts of the protein predicted to be disordered removed
before crystallization? (Compare with Question 4.)