User:Tom Gluick/glutamine synthetase: Difference between revisions
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<span style="color:green">'''Assignment 1: IIA. Quaternary Structure:'''</span> 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.<ref name="review">Eisenberg, D., et.al., Structure-function relationships of glutamine synthetases, Biochim Biophys Acta 2000: 1477, 122-145.</ref><br/> | <span style="color:green">'''Assignment 1: IIA. Quaternary Structure:'''</span> 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.<ref name="review">Eisenberg, D., et.al., Structure-function relationships of glutamine synthetases, Biochim Biophys Acta 2000: 1477, 122-145.</ref><br/> | ||
<span style="color:green">'''Assignment 2: IIB. Tertiary Structure:''' </span> Map the two | <span style="color:green">'''Assignment 2: IIB. Tertiary Structure:''' </span> Map the two Pfam domains in the GS; Include in your discussion what Pfam database records<ref>Bateman, ''et.al.,''The Pfam Protein Families Database, Nucl Acids Res, 2000: 28, D263-D266;Bateman, ''et.al.,''The Pfam Protein Families Database, Nucl Acids Res, 2004: 32, D138-D141 </ref>; 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. Your experience may be different. Show the general design of the active site; reference 1 contains useful material<ref name="review"/>.<br/> | ||
<span style="color:green">'''Assignment 3: IIB. Tertiary Structure:'''</span> Map the two CATH domains in the GS; Include in your discussion what CATH database records<ref>Pearl, F., ''et.al.''The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis, Nucl. Acids Res. 2005 22: D247-D252</ref>; 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 Library Jmol[http://www.imb-jena.de/IMAGE.html], which can be access through PDBsum[http://www.ebi.ac.uk/pdbsum/] to assist you in mapping the CATH domains. The RSCB site may not list the domains correctly.[http://www.rcsb.org/pdb/home/home.do] | <span style="color:green">'''Assignment 3: IIB. Tertiary Structure:'''</span> Map the two CATH domains in the GS; Include in your discussion what CATH database records<ref>Pearl, F., ''et.al.''The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis, Nucl. Acids Res. 2005 22: D247-D252</ref>; 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 Library Jmol[http://www.imb-jena.de/IMAGE.html], which can be access through PDBsum[http://www.ebi.ac.uk/pdbsum/] to assist you in mapping the CATH domains. The RSCB site may not list the domains correctly.[http://www.rcsb.org/pdb/home/home.do] <ref name="review"/><br/> | ||
<span style="color:green">'''Assignment 4: IIB: Tertiary Structure:''' </span> 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.<ref name="struct">Yamashita, M. M., ''et.al.,'' Refined Atolnic Model of Glutamine Synthetase at 3.5 A Resolution, J Biol Chem 1989 264: 17681-17690.</ref> | <span style="color:green">'''Assignment 4: IIB: Tertiary Structure:''' </span> 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.<ref name="struct">Yamashita, M. M., ''et.al.,'' Refined Atolnic Model of Glutamine Synthetase at 3.5 A Resolution, J Biol Chem 1989 264: 17681-17690.</ref> | ||
<span style="color:green">'''Assignment 5: IIC: Secondary Structure:''' </span> Dissect a monomer into secondary structure elements. You may want to include a wiring diagram or use the wiring diagram in PDBsum[http://www.ebi.ac.uk/pdbsum/] as an aid in presenting. Briefly comment on the significance of the elements when required. | <span style="color:green">'''Assignment 5: IIC: Secondary Structure:''' </span> Dissect a monomer into secondary structure elements. You may want to include a wiring diagram or use the wiring diagram in PDBsum[http://www.ebi.ac.uk/pdbsum/] as an aid in presenting. Briefly comment on the significance of the elements when required.<ref name="struct"/> | ||
<span style="color:green">'''Assignment 6: IID: Primary Structure:'''</span> 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/> | <span style="color:green">'''Assignment 6: IID: Primary Structure:'''</span> 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. <ref name="review"/> <br/> | ||
<span style="color:green">'''Assignment 7: IIIA: β-loop:'''</span> Map the interactions stabilizing quaternary structure. Explain how these interactions contribute to quaternary structure stability.<br/> | <span style="color:green">'''Assignment 7: IIIA: β-loop:'''</span> Map the interactions stabilizing quaternary structure. Explain how these interactions contribute to quaternary structure stability. <ref name="review"/><ref name="struct"/><br/> | ||
<span style="color:green">'''Assignment 8: IIIB: Central-loop:''' </span> Map the interactions involving the central loop that stabilize quaternary structure. Explain how these interactions contribute to quaternary structure stability.<br/> | <span style="color:green">'''Assignment 8: IIIB: Central-loop:''' </span> Map the interactions involving the central loop that stabilize quaternary structure. Explain how these interactions contribute to quaternary structure stability.<ref name="review"/><ref name="struct"/><br/> | ||
<span style="color:green">'''Assignment 9: IIIC: Helical thong:''' </span> Map the interactions involving the helical thong that stabilize quaternary structure. Explain how these interactions contribute to quaternary structure stability.<br/> | <span style="color:green">'''Assignment 9: IIIC: Helical thong:''' </span> Map the interactions involving the helical thong that stabilize quaternary structure. Explain how these interactions contribute to quaternary structure stability.<ref name="review"/><ref name="struct"/><br/> | ||
<span style="color:green">'''Assignment 10: IVA: ATP Binding site:''' </span> Map the ATP binding site; indicate which residues stabilize ATP binding; indicate which residues are important for activity and how they contribute to catalysis. <ref name="review"><ref name=" | <span style="color:green">'''Assignment 10: IVA: ATP Binding site:''' </span> Map the ATP binding site; indicate which residues stabilize ATP binding; indicate which residues are important for activity and how they contribute to catalysis. <ref name="review"/><ref name="struct"/><br/><ref name="atp">Liaw, S-H., Interactions of Nucleotides with Fully Unadenylylated Glutamine Synthetase from Salmonella typhimurium, Biochemistry 1994, 33: 11184-11188 </ref><br/> | ||
Salmonella typhimurium, Biochemistry 1994, 33: | |||
<span style="color:green">'''Assignment 11: IVB: Glu binding site:''' </span> 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 | <span style="color:green">'''Assignment 11: IVB: Glu binding site:''' </span> 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.<ref>Gill, H & Eisenberg, D., Biochemistry 2001 40: 1903-1912</ref> Indicate which amino acid residues are important in stabilizing Glu in the binding site. Indicate which residues are involved in chemistry.<ref name="review"/><ref name ="myco">Krajewski, W. W., ''et.al.,''Structure of ''Mycobacterium tuberculosis'' glutamine synthetase in complex with a transition-state mimic provides functional insights, Proc Natl Acad Sci 2005, 102; 10499-10504.</ref><br/> | ||
<span style="color:green">'''Assignment 12: IVC: Ammonium Binding Site:''' </span> Map the Ammonium binding site and explain how it contributes to cataysis.<br/> | <span style="color:green">'''Assignment 12: IVC: Ammonium Binding Site:''' </span> Map the Ammonium binding site and explain how it contributes to cataysis.<ref name="NH4"/>Liaw, S-H, ''et.al.,''Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site Protein Sci. 1995 4: 2358-2365</ref><br/> | ||
<span style="color:green">'''Assignment 13: IVD: Inhibitors:'''</span> Explain how a competitor inhibitor binds to the active site. <br/> | <span style="color:green">'''Assignment 13: IVD: Inhibitors:'''</span> Explain how a competitor inhibitor binds to the active site. <ref name="review"/><ref name="inhib">Liaw, S-H., ''et.al.,''Feedback inhibition of fully unadenylylated glutamine synthetase from ''Salmonella typhimurium'' by glycine, alanine, and serine, Proc Natl Acad Sci 1993 90: 4996-5000.</ref><br/> | ||
<span style="color:green">'''Assignment 14: VA:''' </span> Transition State Analogs: Map the transition state in ''Mycobacterium tuberculosis'' crystal structure. Show the important interactions involved in chemical steps directly <br/> | <span style="color:green">'''Assignment 14: VA:''' </span> Transition State Analogs: Map the transition state in ''Mycobacterium tuberculosis'' crystal structure. Show the important interactions involved in chemical steps directly.<ref name="Myco"/> <br/> | ||
<span style="color:green">'''Assignment 15: VIA:''' </span> 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/> | <span style="color:green">'''Assignment 15: VIA:''' </span> 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.<ref name="review"/> <br/> | ||
<span style="color:green">'''Assignment 15: VIB:''' </span> 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/> | <span style="color:green">'''Assignment 15: VIB:''' </span> 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.<ref name="review"/><br/> | ||
<span style="color:green">'''Instructor Project: I and II:'''</span> The introduction and the conclusion. | <span style="color:green">'''Instructor Project: I and II:'''</span> The introduction and the conclusion. | ||