User:Tom Gluick/glutamine synthetase: Difference between revisions

'''Project 1:  IIA. Quaternary Structure:'''  Provide an overview of the quaternary structure of ''Salmonella typhimurium''  Glutamine Synthetase.  Your explanation ought to include stoichiometry, how the monomers are joined to from the quaternary structure, a clever way to show the symmetry, an indication of the active site location.<br/>

'''Project 2:  IIB. Tertiary Structure:'''   Map the two PFAM domains in the GS; Include in your discussion what PFAM database records; Define the role of each domain in the protiein.  You can use the viewers provided in the PFAM site, but I had some difficulties with all three;  JMOL did not load the molecule properly;  Astex, never did load the molecule, and SPICE did, but the viewer is complicated to operate.  Show the general design of the active site.<br/>

'''Project 3:  IIB. Tertiary Structure':''  Map the two CATH domains in the GS; Include in your discussion what CATH database records; explain the significance of each domain.  In your discussion show the features of the CATH  architecture and topology that provides them with the designation.  As a hint you may want to use the JENA site, which can be access through PDBsum to assist you in mapping the CATH domains. The RS.. site does not list the domains. <br/>

'''Project 4:  IIB:  Tertiary Structure:'''   Map polar/nonpolar or charged and uncharged regions of GS monomers.  Use space filling model.  Map where polar and nonpolar residues are located in the protein.  Comment on significance.  

'''Project 5: IIC:  Secondary Structure:''' Dissect a monomer into secondary structure elements.  You may want to include a wiring diagram or use the wiring diagram in PDBsum as an aid in presenting.  Briefly comment on the significance of the elements when required.

'''Project 6: IID:  Primary Structure:'''  Map the conserved residues on an individual subunit.  Comment on the significance of the conservation using applets or images to enhance discussion of the topic.  See discussion of Wiki Colors in Help:  Editing to be used to enhanced your presentation.  <br/>

'''Project 7: IIIA:  B-loop:'''  Map the interactions stabilizing quaternary structure.  Explain how these interactions contribute to quaternary structure stability.<br/>   

'''Project 8: IIIB:  Central-loop:''' Map the interactions stabilizing quaternary structure.  Explain how these interactions contribute to quaternary structure stability.<br/>

'''Project 9: IIIC:  Helical thong:''' Map the interactions stabilizing quaternary structure.  Explain how these interactions contribute to quaternary structure stability.<br/>

'''Project 10:  IVA: ATP Binding site:'''   Map the ATP binding site; indicate which residues stabilize  ATP binding; indicate which residues are important for activity and how they contribute to catalysis. <br/>

'''Project 11: IVB:  Glu binding site:'''   Map out the Glu binding site  and explain how Glu binds, you will need to consider the inhibitor phosphothricin as a good analog of glutamate; use ref # ( Gill, H and Eisenberg, D., Biochemistry 2001 40, 1903-1912).  Indicate which amino acid residues are important in stabilizing Glu in the binding site.  Indicate which residues are involved in catalysis.<br/>

'''Project 12:  IVC:  Ammonium Binding Site:''' Map the Ammonium binding site and explain how it contributes to cataysis.<br/>

'''Project 13:  IVD:  Inhibitors:'''  Explain how a competitor inhibitor binds to the active site. <br/>

'''Project 14:  VA:''' Transition State  Analogs:  Map the transition state in ''Mycobacterium tuberculosis'' crystal structure.  Show the important interactions involved in chemical steps directly <br/>

'''Project 15:  VIA:''' Map the Adenylylation site on the tertiary and quaternary structure of GS with an explanation of how it happens and how the covalent modification affects enzyme activity.<br/>

'''Project 15:  VIB:''' Map the ADP-ribosylation site on the tertiary and quaternary structure of GS with an explanation of how it happens and how the covalent modification affects enzyme activity.<br/>

'''Instructor Project:  I and II:'''  The introduction and the conclusion.