Comparing structural classifications of fungal (1aru) and human (1cxp) peroxidases
Now you will compare the structural classification of the human 1CXP to a fungal heme-dependent peroxidase in order to learn how to analyze the structural similarities and differences between the two similar functioning enzymes from two very different organisms. Search the PDB for "1ARU", a peroxidase structure from Arthromyces ramosus, a fungal species.
Q6 Which levels of the SCOP and CATH classifications do 1ARU and 1CXP have in common, and at what level of classification do they begin to differ? You will see that while the two enzymes are functionally related, they have significant structural differences. As a side note, the sequence similarity of the two enzymes is less than 10%, and 1CXP is composed of two chains, while 1ARU is composed of only a single amino acid chain.
Now you will visualize the two peroxidase enzymes to examine a common substructure shared between them within the catalytic site. Download the PDB structure files for both 1ARU and 1CXP from the PDB.
Draw the protein backbone in vmd
First open 1ARU.pdb in VMD. There are many different ways of visualizing the protein. Open the molecular representation menu of VMD by clicking "Graphics" and then selecting "Representations..." from the menu, which will open a new menu window. Change the "Drawing Method" to "NewCartoon" to draw only the backbone of the protein and display all alpha helices in helix form. Change the "Coloring Method" to "ResType", which will color each amino acid in the backbone by the residue type to which it corresponds: non-polar residues (white), basic residues (blue), acidic residues (red) and polar residues (green).
Draw the catalytic substructure
Now you will highlight a substructure within the catalytic site of the 1ARU. In the "Graphical Representations" window where you previously changed the drawing type of the whole protein, click the "Create Rep" button to create a new representation. Select the new representation (the selected representation will be highlighted in yellow within the menu). Now change the text in the "Selected Atoms" field from it's current value ("all") to "resid 52 56 93", which will select only residue numbers 52, 56, and 93 (you will not see any changes in the visualization window yet). Now so that you can distinguish these amino acids from the rest of the protein, change the "Drawing Method" to "DynamicBonds" and the "Coloring Method" to "Name". You will now see the side chains of these catalytic site amino acids within a pocket/cleft of the protein.
Draw the heme group
There is also a heme group within this pocket near the catalytic amino acids that we will highlight now. Create another molecular representation by clicking "Create Rep" again. Select the new representation. Change the "Selected Atoms" to "resname HEM" which will select the only heme group within the protein. You will see that the heme group is co-located with the amino acids you have just highlighted. Rotate the molecule and zoom in on the catalytic site that we have just revealed. Output a picture of the catalytic site for your submission by going to "File ->Render..." and then selecting "PostScript" from the "Render using" menu. One free utility for viewing PostScript files is GhostView.
Compare fungal (1aru) and human (1cxp) proteins
Now you will repeat the process for 1CXP, except that the amino acids for the catalytic site should be selected with "resid 91 95 239". Again output a picture of the catalytic site, this time for 1CXP.
Q7 Examine the structures of 1CXP and 1ARU in VMD and list 3 differences between the enzymes that you see.
For submission
Please follow this list closely.
Deliverables
Describe in one paragraph what the role of CI2 is and in whatreactions it is involved. You may use any source (including the PDB).
List some reasons for having more than 16different structures for CI2.
List the experimental methods used for resolving 1CIQ, 1CIR, and 1COA,the organisms from which these structures were extracted, and the
respective resolutions reported (some of this information may be inside the PDB file, but some may be found in the structure's page within the PDB). Please explain why reporting theresolution is essential to resolving the structure for a protein.
Compute the LRMSD of all the conformations provided in 1coa_confs.crd withrespect to the very first conformation in the same file.
Plot their LRMSD on the Y-axis and the conformation ID on the X-axis. Youcan use Excel, Gnuplot, SM, Matlab, or any
other plotting software. Please submit this plot.
Name two protein families, as defined by EC nomenclature, within the "1.11.1" classification.
In terms of CATH and SCOP classifications, how are 1ARU and 1CXP similar and where do they differ?
With VMD (or the visualization tool of your choice), create an image for each of the two corresponding catalytic substructures, one within 1ARU and one within 1CXP. List 3 differences that you see between the structures 1ARU and 1CXP.
Note: While you are welcome to use any method (MS Word, LaTeX, etc.),
please typeset
your deliverables . Although we have assumed you are using VMD in writing the assignment, you are free to use any visualization software for molecular
structures or even write your own. Only VMD will be supported by the TA, however.
Appendix: installing vmd
VMD can be installed easily in Windows/Linux/Solaris by getting the latest version from
here . Just click on the "Download VMD" link on the left and choose the right platform. The page will ask you to register if it's the first time, so simply choose a username and password and accept the usual "no-commercial-use" license agreement.
If you want to use VMD in the Owlnet Windows machines, you will need to install it locally, so get the Windows VMD installer from the link above and execute it. It has an intuitive graphical installation process.
If you use Linux/Solaris (either at home or an Owlnet machine) you can get the appropriate version and install it. The UNIX distributions usually are tarball files. After you download them, you can un-tar them with:
tar zxvf vmd-1.8.5.bin.PLATFORM.opengl.tar.gz Which will create an installation directory. CD to this directory and follow the short instructions in the README file.
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Source:
OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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