User:Tom Gluick/glutamine synthetase/Assignment 3 - Revision history

Tom Gluick: /* Assessment */

2008-12-29T15:53:02Z

Assessment

←Older revision		Revision as of 15:53, 29 December 2008
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	==Assessment==		==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 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.

Tom Gluick: /* Assessment */

2008-12-29T06:24:57Z

Assessment

←Older revision		Revision as of 06:24, 29 December 2008
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	==Assessment==		==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.

Tom Gluick: /* Student Contributions */

2008-12-29T06:11:01Z

Student Contributions

←Older revision		Revision as of 06:11, 29 December 2008
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	Sindhu Lakkur<br/> Ejiofor Ezekwe<br/> Steven Tuyishime		Sindhu Lakkur<br/> Ejiofor Ezekwe<br/> Steven Tuyishime
		+
		+	==Assessment==

Tom Gluick: /* Assignment and Intent */

2008-12-29T06:10:26Z

Assignment and Intent

←Older revision		Revision as of 06:10, 29 December 2008
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	==Assignment and Intent==		==Assignment and Intent==
-	<span style="color:red">'''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: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.		<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.

Tom Gluick: /* Assignment and Intent */

2008-12-29T06:08:51Z

Assignment and Intent

←Older revision		Revision as of 06:08, 29 December 2008
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	==Assignment and Intent==		==Assignment and Intent==
		+	<span style="color:red">'''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: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==		==Student Contribution==

Tom Gluick: /* Student Contributions */

2008-12-29T06:00:34Z

Student Contributions

←Older revision		Revision as of 06:00, 29 December 2008
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	===Student Contributions===		===Student Contributions===

-	~~Undergraduate student at UMBC, Group consisits of~~ Sindhu Lakkur, Ejiofor Ezekwe ~~and~~ Steven Tuyishime~~- Dr. Thomas Gluick Biol 430~~	+	Sindhu Lakkur<br/> Ejiofor Ezekwe<br/> Steven Tuyishime

Tom Gluick: /* Glutamine Synthetase CATH Domains */

2008-12-29T05:59:18Z

Glutamine Synthetase CATH Domains

←Older revision		Revision as of 05:59, 29 December 2008
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-	==~~Glutamine Synthetase CATH Domains~~==	+	==Assignment and Intent==
		+
		+	==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>.

Tom Gluick: /* Glutamine Synthetase CATH Domains */

2008-12-29T05:58:07Z

Glutamine Synthetase CATH Domains

←Older revision		Revision as of 05:58, 29 December 2008
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	==Glutamine Synthetase CATH Domains==		==Glutamine Synthetase CATH Domains==
-		+	<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>.

Tom Gluick: /* Student Contributions */

2008-12-29T05:57:38Z

Student Contributions

←Older revision		Revision as of 05:57, 29 December 2008
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	Undergraduate student at UMBC, Group consisits of Sindhu Lakkur, Ejiofor Ezekwe and Steven Tuyishime- Dr. Thomas Gluick Biol 430		Undergraduate student at UMBC, Group consisits of Sindhu Lakkur, Ejiofor Ezekwe and Steven Tuyishime- Dr. Thomas Gluick Biol 430
-
-	<applet load='1f1h' size='400' color='white' frame='true' align='right' caption='Glutamine synthetase from Salmonella typhimurium' />

Tom Gluick: /* References */

2008-12-29T05:57:01Z

References

←Older revision		Revision as of 05:57, 29 December 2008
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-	==References==	+	===References===

	<references />		<references />
		+
		+	===Student Contributions===
		+
		+	Undergraduate student at UMBC, Group consisits of Sindhu Lakkur, Ejiofor Ezekwe and Steven Tuyishime- Dr. Thomas Gluick Biol 430
		+
		+	<applet load='1f1h' size='400' color='white' frame='true' align='right' caption='Glutamine synthetase from Salmonella typhimurium' />