Lecture 8: Protein Viewing (in-class demonstrations)
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Assigned reading in Campbell: Chapter 4.2-4.5.
The CMU Chime Tutorial has been covered in cluster sessions. Be sure you understand the operation of this structure visualization tool.
(http://stingray.bio.cmu.edu/~rule/chime_tut/chime.html)
The Protein Architecture Tutorial introduces the basic principles of protein 3-D structure using Chime images of Protein G.
(http://info.bio.cmu.edu/Courses/BiochemMols/ProtG/ProtGMain.htm)
Protein Structure Examples: Links to Chime images of the proteins shown in Campbell, Ch. 4 and other representative structures.
(http://info.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm)
A. Structures will be viewed that illustrate some of the protein architecture principles covered in the text and in lectures.
B. Some of the more detailed manipulations on Chime pages that are required for Problem Set 3 will be demonstrated using Rubredoxin from the Protein Structure Examples list.
In the following, the Chime menu cascades (or chain of commands) are written on one line separated by a "¬", as in the CMU Chime Tutorial. The sequence of suggested image changes and the choice of display or coloring is not unique. Play around some and decide on your own preferences for viewing.
- 1. Identify H-bonds and measure their distances:
- Select All
- Display ¬ Cartoons
- Select ¬ Protein ¬ Sheet
- Select ¬ Hide ¬ Not Selected
- Display ¬ Sticks
- Color ¬ CPK
- Options ¬ Display Hydrogen Bonds
- Select ¬ Mouse Click Action ¬ Toggle Distance Monitor
- Now, a click between any two atoms will display their separation (in Å).
- Bring the mouse back to the identifcation mode with:
- Select ¬ Mouse Click Action ¬ Identify
- 2. Look at the residues around a buried atom (Fe3+) in Rubredoxin.
- Select ¬ Atom ¬ FE
- Display ¬ Spacefill ¬ Van der Waals Radii
- Select ¬ Protein ¬ Protein
- Display ¬ Spacefill ¬ Van der Waals Radii
- Color ¬ Monochrome
- Color ¬ Amino Acid
- Options ¬ Slab Mode
- Then drag the mouse (left) with Control key down to slab in and out.
- Display ¬ Ball & Stick
- Select ¬ Protein ¬ Hydrophobic
- Display ¬ Spacefill ¬ Van der Waals Radii
- Identify the layer of hydrophobic residues surrounding the "Cys4 cage".
- 3. Find some ion pairs on the surface of Rubredoxin.
- Select ¬ Protein ¬ Protein
- Color ¬ Monochrome
- Select ¬ Protein ¬ Acidic
- Color ¬ CPK
- Display ¬ Ball & Stick
- Select ¬ Protein ¬ Basic
- Color ¬ CPK
- Display ¬ Ball & Stick
- Select ¬ Mouse Click Action ¬ Toggle Distance Monitor
- Now pick some likely candidates for distances of 3 to 4 Å
- Remember to bring the mouse back to the identifcation mode with:
- Select ¬ Mouse Click Action ¬ Identify
- 4. Related items
a) "The image is too small on the page to manipulate conveniently." - File ¬ Save Moleule As . . .
- Give the file a name and the ".pdb " suffix.
Save it to the desktop (or wherever).
Then open the file in Netscape (with a new window, perhaps) for full page size.
b) "I want to save the current image for later viewing." - Edit ¬ Copy
- This puts the image on the Clipboard.
Paste it into a document directly, or better, create a file using a program like Photoshop. If the image is converted to GIF or JPEG format it can be sent anywhere or viewed on the web.
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