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There are several programs that allow the inspection and manipulation of 3-D structural protein data. In the past we used the swiss protein data bank viewer, aka Deep View or SPDBV.
While this is an excellent choice, in part becasue it also provides an interface to the Swiss Protein databank modeling software, the program pymol has generated a large following, and it can be more easily adapted to do interesting things.
The pymol program is available free of charge for educational purposes. You can down load executables from the pymol site (check with the instructor for the password), or you can get the latest version form sourceforge, older versions are also available through different servers (see here for a windows example), More information on how to install pmol is available in th pymok-wiki
There are several excellent on-line tutorials available to learn the use pymol, the most authorative is part of the pymol wiki, but there are dozens of you-tube clips on how to do things in pymol (a discussion on how to align structures is here)
Task 1: Install pymol on your computer
Start pymol either through typing pymol in the terminal window (in case you downloaded the sourceforge version for unix) or by double cliccking on the Pymol or MacPyMOL icon.
You can retrieve pdb files from the NCBI, or from the protein structure data bank at Rutgers University. (To do so search for the file, click the explore link and right click on the link that indicated download uncompressed pdb file.) (My favorite ones are also available here).
1HEW - getting to know pymol part 1
To get to know pymol, type fetch 1hew in the pymol command line. The text window should display information on the file, the graphics window should display the structure. (You also can download the file 1hew.pdb from the pdb databank, and then use the file menu to open the file. To familiarize yourself with pdb files, go to the pdb databank, search fro 1HEW and display the pdb file.)
What molecule is depicted in 1hew ?
To the right of the graphics window are four buttons
The bottom right gives the settings for the mouse, you can select the mouse that you use in the mouse menu on top.
For the 1HEW structure, H everything, then S cartoon, then C by chain -> chainbow.
Explore different display options, view and cursor options.
At the bottom right is the Select button. click it, this displays the sequence of the lysozyme. At the end of the amino acids are the non amino acid atoms that are part of the structure. Select the N-Acetyl Glucosamine (NAG) trimer. This opens a new row of ASHLC buttons. select S sticks and C one of the chnops coloring schemes.
If you get lost, right-click the background of the viewer, and select reset from the Main Pop-Up. The model should return to view.
Try to depict the protein as a meshed surface and the substrate as space filling balls. (Challenge: Can you find a way to depict the surface according to charge? What commands did you use?)
To make a simple movie select movie in the main menu, then ->Program->Camera->Y-Roll-> 32 Seconds
then press the play button on the lower right. Unselect loop frame, add some other movie parts such as nutate, or rock.
Getting to know pymol part 2
Repeat the above exercise with four favorite molecule.
To create a high resolution movie using ray tracing
We will color a protein according to its
conservation profile and determine where the inteins sit in the VMA protein
You will need the conservation profile and
protein .pdb file
Lets work with the excel file first
(note: a perlscript that creates a conservation profile from a multiple sequence alignment is here)
this file the first column gives the alignment position and the second column is
the conservation score - the lower the more conserved
(the number of aa types in a sliding window)
the profile on the second column smallest to largest
assign colors in the third column for now working with a ROYGB color scheme
Label 0-2 Red
Label 2-5 Orange
Label 5-8 Yellow
Label 8-11 Green
Label 11 – the rest Blue
your file and put it a side for now
Now will work with the protein files
1VDZ.pdb in PyMOL
On the right under the all object click H everyting, then S ribbons
In the PyMOL> bar type
color gray, all
We are going to make each color group an object.
This will be helpful if we want to go back and change the colors for the group
For each color we marked off in the excel file
select the amino acids from the first column
So for the reds select those copy them then in
another cell right click > paste special and select transpose
Copy the transposed list and paste it in text
Then copy the space between the numbers
Paste into the top box and replace all with what
between, the quotes here ‘ resi ‘ so space resi space
Back to pymol
RED, resi then copy and paste the line from text wrangler into the PyMOL>
all those amino acids are grouped together
the same for the rest of the colors replacing the object identifier “RED” with
the appropriate color name.
Once all the groups are made they should show up
on the side bar
Make one more group for the inteins
intein insertion site, select intein_site, resi 249 resi 269
Color each group
To make the intein insertion sites pop out
against the rest of the protein select intein on the side bar click S >as
Where are the inteins sitting?
Other intersting structures:
small intein without homing endonuclease (HE) from Mycobacterium xenopi mini intein (PMID: 9437427, 1AM2)
intein with HE from vacuolar ATPase in yeast (PMID: 9160747, 1VDE)
intein with HE from yeast bound to DNA (PMID: 12219083, 1LWS)
Histone core (8 histones) with DNA wound around it (1AOI)
ATP synthase head group (F1) from beef heart mitochondria (1bmf)