Homology Modeling Part-I - assigned 10/8/08

You are to make a homology model of the enzyme mouse group-IID phospholipase A2 (mGIID PLA2) using the Swiss Model server.  Later (10/29/08), in part-II of our modeling work, we will learn how to make homology models using the program Modeller.   The mGIID PLA2 is a secreted 14 KDa protein and has the NCBI accession codes: AAD51391 or gi|5771422|.  A usefull review article for this project can be downloaded here [Schaloske, R.H. and Dennis, E.A. (2006) Biochim. Biophys Acta 1761, 1246-1259.] When selecting templates for this homology modeling assignment, select at least one template structure which includes an active site ligand bound at the enzyme's active site.  This template will be important for the second picture you will be asked to make, see below.

websites visited in class
Swiss Model  - http://swissmodel.expasy.org//SWISS-MODEL.html
NCBI PubMed - http://www.ncbi.nlm.nih.gov/sites/entrez/
Deepview - http://spdbv.vital-it.ch/
Deep View Tutorial - http://www.usm.maine.edu/~rhodes/SPVTut/index.html
PyMol - http://pymol.org/
Connect to UD network - http://www.udel.edu/help/getting_connected.html
UDeploy software site - https://udeploy.udel.edu/

Other Usefull Links
Protein Data Bank - www.pdb.org
Principles of Protein Structure, Comparative Protein Modeling and Visualisation
ExPASy  (http://us.expasy.org/) - the main page that will cover most of what CLUSTALW (http://www.ebi.ac.uk/clustalw/)
- a program that generates multi-sequence alignments in several formats 
BOXSHADE (http://www.ch.embnet.org/software/BOX_form.html)
- takes output from Clustalw and makes nice figure  you need for this assignment. 
Biology Workbench (http://workbench.sdsc.edu/) - an all inclusive option to sequence alignments

1) Explain your choice of templates used for the modeling assignment.  In your answer make sure to make a convincing arguement of why you chose the templates you did.

2) Prepare a multi- protein sequence alignment of your choice of templates aligned with the target sequence.  You could use the programs ClustalW/Boxshade (demonstrated in class) or other programs of your choosing.  In addition to turning in your final sequence alignments, you should use this approach to help make decisions of what templates to include (part 1).

3) Forward to me (Bahnson@udel.edu) the e-mail, which includes your mGIID-PLA2 model aligned with each of the templates you used to make the homology model.   This file should be a pdb format file.   When you receive your results back, open up the *.pdb file in Deep View. 

4) You need to turn in two figures of your homology model using Deep View, PyMol,  or another appropriate program.  Rendering hints: it would be best to render these on a white background.   Display - OpenGL rendering, render in solid 3D;  Color- by CPK;   Preferences- Labels, 3D rendering. 
Picture 1:  Show a ribbon diagram of the mGIID PLA2 homology model with the template structures superimposed in stick format.
Picture 2:  Show a ribbon diagram of the mGIID PLA2 homology model together with only the active site ligand of one of the modeling templates superimposed in ball and stick format.  Label the figure to identify the active site ligand and template it was taken from.

5) Sometimes, homology models that are constructured from several templates versus a homology model that is made from only the best template can give complementary information.  Is that the case for your homology modeling of mGIID PLA2?  Incorporate information derived from parts 1-4 above,  to answer the question posed here.  Explain. 

6) If you were going to use a homology model to help solve a crystal structure of  the  mGIID PLA2 by molecular replacement, which homology model from part-5 would you use and why?  Also, would you make any changes to the homology model in order to use it as a molecular replacement search model?  Describe the changes you would make and explain why. 

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