User:Tom Gluick/glutamine synthetase: Difference between revisions
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<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. Show the general design of the active site.<ref name="review"><br/> | <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. Show the general design of the active site.<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 | <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] <br/> | ||
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] <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="review"><ref name="35structure">Yamashita, M. M., ''et.al.,'' Refined Atolnic Model of Glutamine Synthetasea t 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="review"><ref name="35structure">Yamashita, M. M., ''et.al.,'' Refined Atolnic Model of Glutamine Synthetasea t 3.5 A Resolution, J Biol Chem 1989 264; 17681-17690.</ref> | ||
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<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 PDBsumhttp://www.ebi.ac.uk/pdbsum/] as an aid in presenting. Briefly comment on the significance of the elements when required.<ref name="review"><ref name="35structure"> | <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 PDBsumhttp://www.ebi.ac.uk/pdbsum/] as an aid in presenting. Briefly comment on the significance of the elements when required.<ref name="review"><ref name="35structure"> | ||
<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. | <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.<ref name="review"><ref name="35structure"><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="35structure"><br/> | ||
<span style="color:green">'''Assignment 8: IIIB: Central-loop:''' </span> Map the interactions | <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="35structure"><br/> | ||
<span style="color:green">'''Assignment 9: IIIC: Helical thong:''' </span> Map the interactions | <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="35structure"><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="35structure"><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="35structure"><br/><ref name="atp">Liaw, S-H., Interactions of Nucleotides with Fully Unadenylylated Glutamine Synthetase from | ||
Salmonella typhimurium, Biochemistry 1994, 33: 11 184-1 1188 <ref> | |||
<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; 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/> | <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; 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/> | ||