Transcript Jmol Training Powerpoint

SMART Teams:
Students Modeling A Research Topic
Jmol Training 101!
Methods Used to Determine
Molecular Structures
There are three methods that may be used to determine
structures deposited in the protein data bank:
X-ray Crystallography
Structure must be in a crystallized form
Nuclear Magnetic Resonance (NMR)
Structure may be in solution
Cryo-electron microscopy (Cryo-EM)
Used primarily for large multiprotein assemblies
X-Ray Crystallography
Determination of the
three-dimensional
structure of molecules
by means of diffraction
patterns produced by xrays of crystals of the
molecules rr
X-Ray Crystallography
X-Ray Crystallography
Crystal of the Molecule of
Interest
X-Ray Crystallography
X-Ray
Crystal of the Molecule of
Interest
X-Ray Crystallography
X-Ray
Crystal of the Molecule of
Interest
X-ray film
X-Ray Crystallography
X-Ray
Series of
Computations
Crystal of the Molecule of
Interest
X-Ray Crystallography
Defines the X, Y, and Z coordinates
for each atom in a molecule
X-Ray
Series of
Computations
Molecule of
Interest
What Do You See?
• collect images around crystal to
record the position of all the
spots
• spots represent where x-rays
were deflected by electrons in
the molecule
• resolution is reflection
of how well ordered
the atoms are in the crystal
phenylalanine
Building a Model
What you see
+
What you think
=
What you get
Final Model
3D models take visual representation to
a new level of awesomeness!
The Case of the Missing Hand
• Sometimes a clear model is
difficult to produce.
• Uncertainty may occur in
interpreting data collected
from a crystal if a portion
of the molecule has
multiple conformations.
For example, the photograph on the left demonstrates the
blurry image that is produced if a student moves their
hand while being photographed.
NMR
http://phet.colorado.edu/en
/simulation/mri
Cryo-EM
Let’s Begin Jmol: Create a Folder
First create a folder to store the information needed to
design your model.
Include a Copy of Jmol
Copy and paste a copy of the Jmol.jar file into the folder
you created
Include the PDB File
Copy and paste the pdb file of the protein to be modeled
(Instructions to follow)
Retrieve a PDB File
The Protein Data Bank (pdb) is the worldwide repository for
the processing and distribution of 3-D biological
macromolecular structure data.
http://www.pdb.org
The Protein Databank
Search Bar
Molecule of the Month!
PDB File Search
You may search by:
• Molecule name
• Scientist name
• File name
Search Bar
PDB File Download
• Type the file name in the search bar. We will use 2AAI.
• Click on the Download Files and select PDB File (Text)
• Place this file in the folder that you have created
File Name
Primary Citation
You may find the following information on the “Summary” tab:
• Title of the primary citation
• Authors of the primary citation
• Journal in which primary citation was published
• Abstract
More Summary Tab Information
Scroll down the screen while on the “Summary” tab to find
information about:
• Ligands
• Structure Determination Method
Method
Ligand
PDB File Search
Click on the “Sequence” tab.
Information about primary and secondary structure of the
protein may be found here!
Primary and
Secondary Structures
Jmol Version
Be sure to use the correct version of Jmol!
We will not be able to view your files if you use a version
other that the one specified!
This year we will use version:
Jmol 14.2.15
Opening Your File in Jmol
•Open Jmol.jar
Opening Your File in Jmol
•Your screen should look like this:
Model Design Box
Console Box:
Type your
commands here
Opening Your File in Jmol
Drag and drop the PDB File into the black screen.
You Are Ready to Design!
The Jmol
Quick
Reference
Sheet is your
lifeline for
protein
model
design!
You Are Ready to Design!
Try the Mouse Movements!
Changing the Background Color
Type all commands into the console box.
To change the background color, type:
background white
(you may want to try a few other colors)
Jmol Colors
Jmol Colors
To explore other Jmol color options you can investigate the
following site: http://jmol.sourceforge.net/jscolors
Scroll down until you
see: JavaScript Colors
Alpha-Carbon Backbone Format
Type commands in the
console box.
To display the alpha carbon
backbone, type:
backbone 1.5
You will notice a “funny
line” in the backbone – the
cartoon display is still
turned on. Type:
cartoon off
Restrict Command
To “get rid of the water
molecules”, type:
restrict not water
Notice the other ligands are
still displayed. To remove
them, type:
restrict not hetero
Highlighting a Specific Chain
To select a specific section of a molecule, type:
select :b and backbone
To color the
backbone, type:
color green
Highlighting a Specific Chain
To select a specific section of a molecule, type:
select :a and backbone
To color the
backbone, type:
color yellow
Highlighting Secondary Structures
To highlight secondary structures, type:
select :a and backbone and helix
color red
select :a and backbone and sheets
color blue
Adding a Sidechain
To Display Sidechains
Refer to the primary citation to determine the relevant
sidechains to display in your model design.
One such side chain in ricin is glutamic acid 177, as it is a
key catalytic amino acid in the active site.
To display this sidechain, type:
select glu177 and (sidechain or alpha)
spacefill 1.25
wireframe 1.0
Adding a Sidechain
Click on the amino acid and check the information
provided in the script console box.
Adding a Sidechain
If you do not include
(sidechain or alpha)
you will get what is known as
a “bumpy backbone”, shown
to the right.
AVOID the dreaded bumpy
backbone at all costs!
Adding a Sidechain
AVOID the dreaded bumpy backbone and add Arginine
180 to your practice model!
$ select arg180 and (sidechain or alpha)
8 atoms selected
$ wireframe 1.0
$ spacefill 1.25
[ARG]180:A.NH2 #1417 20.909 64.017 53.14
Coloring a Sidechain
To color only the sidechain and not the backbone, type:
select glu177 and sidechain
color cpk
Coloring a Sidechain
A common error is to color
the backbone as well as the
sidechain (shown at right).
Avoid this error by using the
commands on the previous
slide.
Now correctly color arg180
Adding Hydrogen Bonds
In some models you will want to display the hydrogen
bonds (especially in the beta sheets)
To add hydrogen bonds to beta sheets, type:
select sheets
calculate hbonds
hbonds 1.0
set hbonds solid
set hbonds backbone
color hbonds <lemonchiffon>
Adding Disulfide Bonds
Disulfide bonds can be an important part of the molecular
story of your protein.
•To display disulfide bonds, type:
select all
ssbonds on
ssbonds 1.0
set ssbonds backbone
color ssbonds purple
You may also chose to highlight the cysteine sidechains
responsible for forming the disulfide bond instead.
Adding Struts
In some models you will need to stabilize the model or
connect a ligand to the model. To do this you will need to
add struts.
To add struts, type:
select all
calculate struts
struts 1.0
color struts tan
Saving Your Work
Be sure to save your work!
To save:
Click on the camera icon
Name your file
It should now be saved in
the folder you created
Opening Your Saved Work
To Open:
Your folder MUST have
• PDB file
• Shortcut to Jmol
• *.jpg