User:Wayne Decatur/Interactions between Antibiotics and the Ribosome - Revision history

Wayne Decatur at 04:40, 3 January 2010

Wayne Decatur — Sun, 03 Jan 2010 04:40:01 GMT

←Older revision		Revision as of 04:40, 3 January 2010
Line 7:		Line 7:
	*Data optimized for viewing online in Jmol. This includes limiting much of the files to simply alpha carbon and phosphate atoms and, significantly, combining data split split across multiple PDB coordinate files so the entire ribosome structure is visible at once, an issue the RCSB Protein Data Bank has recently attempted to address, as described [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20091208 here].		*Data optimized for viewing online in Jmol. This includes limiting much of the files to simply alpha carbon and phosphate atoms and, significantly, combining data split split across multiple PDB coordinate files so the entire ribosome structure is visible at once, an issue the RCSB Protein Data Bank has recently attempted to address, as described [http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20091208 here].
	==Pages for the Antibiotics bound to the Ribosome==		==Pages for the Antibiotics bound to the Ribosome==
		+	<!--Seems the table layout in single row at least needs to be same size to work right. I used 516 by 516 for Azithromycin.-->
	{\| align="center"		{\| align="center"
-	\| <table width='~~200~~' align='center' cellpadding='5'><tr><td>	+	\| <table width='300' align='center' cellpadding='5'><tr><td>
	<imagemap>		<imagemap>
-	Image:Azithromycin50s.~~jpg~~\|left\|300px\|alt=1m1k image	+	Image:Azithromycin50s.png\|left\|300px\|alt=1m1k image
	default [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin]]		default [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin]]
	desc none		desc none
	</imagemap>		</imagemap>
	</td></tr><tr><td><center>'''[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin\|Azithromycin (zithromax)]]'''</center></td></tr></table>		</td></tr><tr><td><center>'''[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin\|Azithromycin (zithromax)]]'''</center></td></tr></table>
-	\|\| <table width='~~200~~' align='center' cellpadding='5'><tr><td>	+	\|\| <table width='300' align='center' cellpadding='5'><tr><td>
	<imagemap>		<imagemap>
-	Image:~~Unremediated1rpuWithPolyview3D~~.png\|left\|300px\|alt=~~1rpu~~ image	+	Image:Par.png\|left\|300px\|alt=1m1k image
	default [[User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin]]		default [[User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin]]
	desc none		desc none
	</imagemap>		</imagemap>
	</td></tr><tr><td><center>'''[[User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin\|Paromomycin]]'''</center></td></tr></table>		</td></tr><tr><td><center>'''[[User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin\|Paromomycin]]'''</center></td></tr></table>
-	\|\| <table width='~~200~~' align='center' cellpadding='5'><tr><td>	+	\|\| <table width='300' align='center' cellpadding='5'><tr><td>
	<imagemap>		<imagemap>
-	Image:~~Unremediated1rpuWithPolyview3D~~.png\|left\|300px\|alt=~~1rpu~~ image	+	Image:Par.png\|left\|300px\|alt=1m1k image
	default [[User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin]]		default [[User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin]]
	desc none		desc none

Wayne Decatur at 07:47, 31 December 2009

Wayne Decatur — Thu, 31 Dec 2009 07:47:28 GMT

←Older revision		Revision as of 07:47, 31 December 2009
Line 11:		Line 11:
	<imagemap>		<imagemap>
	Image:Azithromycin50s.jpg\|left\|300px\|alt=1m1k image		Image:Azithromycin50s.jpg\|left\|300px\|alt=1m1k image
-	default [[User:Wayne Decatur/~~Sandbox~~ Haloarcula Large Ribosomal Subunit With Azithromycin]]	+	default [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin]]
	desc none		desc none
	</imagemap>		</imagemap>
-	</td></tr><tr><td><center>'''[[User:Wayne Decatur/~~Sandbox~~ Haloarcula Large Ribosomal Subunit With Azithromycin\|Azithromycin (zithromax)]]'''</center></td></tr></table>	+	</td></tr><tr><td><center>'''[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin\|Azithromycin (zithromax)]]'''</center></td></tr></table>
	\|\| <table width='200' align='center' cellpadding='5'><tr><td>		\|\| <table width='200' align='center' cellpadding='5'><tr><td>
	<imagemap>		<imagemap>

Wayne Decatur at 07:44, 31 December 2009

Wayne Decatur — Thu, 31 Dec 2009 07:44:08 GMT

←Older revision		Revision as of 07:44, 31 December 2009
Line 10:		Line 10:
	\| <table width='200' align='center' cellpadding='5'><tr><td>		\| <table width='200' align='center' cellpadding='5'><tr><td>
	<imagemap>		<imagemap>
-	Image:~~Unremediated1rpuWithPolyview3D~~.~~png~~\|left\|300px\|alt=~~1rpu~~ image	+	Image:Azithromycin50s.jpg\|left\|300px\|alt=1m1k image
	default [[User:Wayne Decatur/Sandbox Haloarcula Large Ribosomal Subunit With Azithromycin]]		default [[User:Wayne Decatur/Sandbox Haloarcula Large Ribosomal Subunit With Azithromycin]]
	desc none		desc none

Wayne Decatur at 07:35, 31 December 2009

Wayne Decatur — Thu, 31 Dec 2009 07:35:06 GMT

←Older revision		Revision as of 07:35, 31 December 2009
Line 11:		Line 11:
	<imagemap>		<imagemap>
	Image:Unremediated1rpuWithPolyview3D.png\|left\|300px\|alt=1rpu image		Image:Unremediated1rpuWithPolyview3D.png\|left\|300px\|alt=1rpu image
-	default [[User:Wayne Decatur/Sandbox ~~Thermus 70S~~ With ~~Paromomycin~~]]	+	default [[User:Wayne Decatur/Sandbox Haloarcula Large Ribosomal Subunit With Azithromycin]]
	desc none		desc none
	</imagemap>		</imagemap>
-	</td></tr><tr><td><center>'''[[User:Wayne Decatur/Sandbox ~~Thermus 70S~~ With ~~Paromomycin~~\|~~Paromomycin~~]]'''</center></td></tr></table>	+	</td></tr><tr><td><center>'''[[User:Wayne Decatur/Sandbox Haloarcula Large Ribosomal Subunit With Azithromycin\|Azithromycin (zithromax)]]'''</center></td></tr></table>
	\|\| <table width='200' align='center' cellpadding='5'><tr><td>		\|\| <table width='200' align='center' cellpadding='5'><tr><td>
	<imagemap>		<imagemap>

Wayne Decatur at 00:56, 21 December 2009

Wayne Decatur — Mon, 21 Dec 2009 00:56:39 GMT

←Older revision		Revision as of 00:56, 21 December 2009
Line 2:		Line 2:
	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>. Several of these structures highlighted below.		A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>. Several of these structures highlighted below.

-	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the ~~files~~ derived ~~from each structure~~, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this set of pages feature:	+	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the derived coordinate files, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this set of pages feature:
	*Consistent representation and color scheme for the ribosomal subunits, elements and ligands enabling easy visualization of where a particular antibiotic binds.		*Consistent representation and color scheme for the ribosomal subunits, elements and ligands enabling easy visualization of where a particular antibiotic binds.
	*Links to Proteopedia pages covering the essentials of the structures of each subunit and complete ribosome.		*Links to Proteopedia pages covering the essentials of the structures of each subunit and complete ribosome.

Wayne Decatur at 00:55, 21 December 2009

Wayne Decatur — Mon, 21 Dec 2009 00:55:48 GMT

←Older revision		Revision as of 00:55, 21 December 2009
Line 1:		Line 1:
	==Brief Summary of the Scope and Approach of this Set of Pages==		==Brief Summary of the Scope and Approach of this Set of Pages==
-	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.	+	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>. Several of these structures highlighted below.

	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this set of pages feature:		Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this set of pages feature:

Wayne Decatur at 00:28, 21 December 2009

Wayne Decatur — Mon, 21 Dec 2009 00:28:45 GMT

←Older revision		Revision as of 00:28, 21 December 2009
Line 2:		Line 2:
	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.		A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.

-	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this ~~package~~ of pages feature:	+	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this set of pages feature:
	*Consistent representation and color scheme for the ribosomal subunits, elements and ligands enabling easy visualization of where a particular antibiotic binds.		*Consistent representation and color scheme for the ribosomal subunits, elements and ligands enabling easy visualization of where a particular antibiotic binds.
	*Links to Proteopedia pages covering the essentials of the structures of each subunit and complete ribosome.		*Links to Proteopedia pages covering the essentials of the structures of each subunit and complete ribosome.

Wayne Decatur at 00:28, 21 December 2009

Wayne Decatur — Mon, 21 Dec 2009 00:28:06 GMT

←Older revision		Revision as of 00:28, 21 December 2009
Line 1:		Line 1:
	==Brief Summary of the Scope and Approach of this Set of Pages==		==Brief Summary of the Scope and Approach of this Set of Pages==
-	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. ~~Several structures~~ of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and ~~mechanism~~ of inhibition of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.	+	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and the mechanisms of inhibition of several members of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.

	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this package of pages feature:		Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this package of pages feature:

Wayne Decatur at 00:26, 21 December 2009

Wayne Decatur — Mon, 21 Dec 2009 00:26:04 GMT

←Older revision		Revision as of 00:26, 21 December 2009
Line 1:		Line 1:
	==Brief Summary of the Scope and Approach of this Set of Pages==		==Brief Summary of the Scope and Approach of this Set of Pages==
-	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Several structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and mechanism of inhibition<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.	+	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Several structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and mechanism of inhibition of this important class of small molecules<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.

	Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this package of pages feature:		Given the numerous solved structures of antibiotics complexed with ribosomes and ribosomal subunits and the massive size and complexity of the ribosome and the files derived from each structure, several technical and pedagogical issues are obstacles appreciating the elegance and insight provided by these structures. Towards that end this package of pages feature:

Wayne Decatur at 00:24, 21 December 2009

Wayne Decatur — Mon, 21 Dec 2009 00:24:58 GMT

←Older revision		Revision as of 00:24, 21 December 2009
Line 1:		Line 1:
-	==~~Interactions between Antibiotics and~~ the ~~Ribosome~~==	+	==Brief Summary of the Scope and Approach of this Set of Pages==
	A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Several structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and mechanism of inhibition<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.		A major class of [http://en.wikipedia.org/wiki/Antibiotic antibiotics] are those that target protein synthesis. Several structures of antibiotics bound to ribosomal subunits and full [[ribosome\|ribosomes]] have now revealed at atomic-resolution the details of binding and mechanism of inhibition<ref>PMID: 16553874</ref><ref>PMID: 15491801</ref><ref>PMID: 19929179</ref><ref>PMID: 16261170 </ref><ref>PMID: 16111914</ref><ref>PMID: 15680981</ref>.