User:Tom Gluick/glutamine synthetase: Difference between revisions

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'''Assignment 2: IIB. Tertiary Structure:''' 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; reference 1 contains useful material.

'''Assignment 3: IIB. Tertiary Structure:''' 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">~~

'''Assignment 3: IIB. Tertiary Structure:''' 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] See reference 1 for more details.

'''Assignment 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.<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>

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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;  reference 1 contains useful material.<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] <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] See reference 1 for more details.<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>