User:Tom Gluick/glutamine synthetase/Assignment 3: Difference between revisions
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== | ==Assignment and Intent== | ||
<span style="color:red">'''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:red">Intent and Hope: </span> I hoped the students would be able to illustrate the domains and structures of glutamine synthetase as defined by CATH website. I hoped the students would incorporate information found in the references into their presentation. | |||
==Student Contribution== | |||
<applet load='1f1h' size='400' color='white' frame='true' align='right' caption='Glutamine synthetase from Salmonella typhimurium' /> | <applet load='1f1h' size='400' color='white' frame='true' align='right' caption='Glutamine synthetase from Salmonella typhimurium' /> | ||
Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. | Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. | ||
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==References== | ===References=== | ||
<references /> | <references /> | ||
===Student Contributions=== | |||
Sindhu Lakkur<br/> Ejiofor Ezekwe<br/> Steven Tuyishime | |||
==Assessment== | |||
The students completed the assignment successfully. They showed the two domains in the context of the complex, showed each domain and its architecture using the SAT. The visuals were designed very well. The assignment was relatively straightforward with most information easily accessible. | |||