smart teams: students modeling a research topic jmol training 101!
TRANSCRIPT
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SMART Teams:Students Modeling A Research Topic
Jmol Training 101!
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There are three methods that may be used to determine structures deposited in the protein data bank:
X-ray CrystallographyStructure 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
Methods Used to Determine Molecular Structures
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X-Ray Crystallography
Determination of the three-dimensional structure of molecules by means of diffraction patterns produced by x-rays of crystals of the molecules rr
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X-Ray Crystallography
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X-Ray Crystallography
Crystal of the Molecule of Interest
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X-Ray Crystallography
X-Ray
Crystal of the Molecule of Interest
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X-Ray Crystallography
X-Ray
Crystal of the Molecule of Interest
X-ray film
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X-Ray Crystallography
Series of Computations
X-Ray
Crystal of the Molecule of Interest
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X-Ray Crystallography
Defines the X, Y, and Z coordinates for each atom in a molecule
Series of Computations
X-Ray
Molecule of Interest
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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
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Building a Model
What you see + What you think = What you get
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Final Model
3D models take visual representation toa new level of awesomeness!
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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.
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NMR
http://phet.colorado.edu/en/simulation/mri
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Cryo-EM
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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 FileCopy and paste the pdb file of the protein to be modeled (Instructions to follow)
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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
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The Protein Databank
Molecule of the Month!
Search Bar
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PDB File Search
You may search by:
Search Bar
• Molecule name• Scientist name• File name
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PDB File Download
File Name
• 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
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Primary CitationYou 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
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More Summary Tab Information
Method
Scroll down the screen while on the “Summary” tab to find information about:• Ligands• Structure Determination Method
Ligand
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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
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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
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Opening Your File in Jmol
•Open Jmol.jar
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Opening Your File in Jmol
•Your screen should look like this:
Model Design BoxConsole Box:
Type your commands here
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Opening Your File in Jmol
Drag and drop the PDB File into the black screen.
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You Are Ready to Design!
The Jmol Quick Reference Sheet is your lifeline for protein model design!
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You Are Ready to Design!
Try the Mouse Movements!
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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)
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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
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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
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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
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Highlighting a Specific Chain
To select a specific section of a molecule, type: select :b and backbone
To color the backbone, type: color green
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Highlighting a Specific Chain
To select a specific section of a molecule, type: select :a and backbone
To color the backbone, type:color yellow
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Highlighting Secondary Structures
To highlight secondary structures, type:select :a and backbone and helixcolor red
select :a and backbone and sheetscolor blue
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Adding a Sidechain
To Display SidechainsRefer 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 1.25wireframe 1.0
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Adding a Sidechain
Click on the amino acid and check the information provided in the script console box.
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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!
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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
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Coloring a Sidechain
To color only the sidechain and not the backbone, type:select glu177 and sidechaincolor cpk
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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
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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 sheetscalculate hbondshbonds 1.0set hbonds solidset hbonds backbonecolor hbonds <lemonchiffon>
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Adding Disulfide Bonds
Disulfide bonds can be an important part of the molecular story of your protein.
•To display disulfide bonds, type:select allssbonds onssbonds 1.0set ssbonds backbonecolor ssbonds purple
You may also chose to highlight the cysteine sidechains responsible for forming the disulfide bond instead.
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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 allcalculate strutsstruts 1.0color struts tan
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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
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Opening Your Saved Work
To Open:
Your folder MUST have
• PDB file
• Shortcut to Jmol
• *.jpg