Sandbox Reserved 1578 - Revision history

John Means at 13:43, 4 December 2019

2019-12-04T13:43:58Z

←Older revision		Revision as of 13:43, 4 December 2019
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	{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
	==SAM Riboswitch==		==SAM Riboswitch==
		+	<StructureSection load='2gis' size='340' side='right' caption='SAM Riboswitch' scene=''>

	==Overview==		==Overview==

-	<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />
	S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>		S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>

John Means at 02:54, 4 December 2019

2019-12-04T02:54:40Z

←Older revision		Revision as of 02:54, 4 December 2019
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-	~~<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>~~{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->	+	{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
	==SAM Riboswitch==		==SAM Riboswitch==

Sarah Moffett at 20:18, 1 December 2019

2019-12-01T20:18:11Z

←Older revision		Revision as of 20:18, 1 December 2019
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	== Structural Highlights ==		== Structural Highlights ==

-	The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />	+	The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand, as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />

	The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix. <ref name="ref1" />		The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix. <ref name="ref1" />
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	== Function ==		== Function ==

-	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed ~~before~~ hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression. <ref name="ref1" />	+	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch, the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed previously hold the ligand in place for productive binding, and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression. <ref name="ref1" />

	== References ==		== References ==
	(1) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.		(1) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.

Sarah Moffett at 18:15, 30 November 2019

2019-11-30T18:15:22Z

←Older revision		Revision as of 18:15, 30 November 2019
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	<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
	==SAM Riboswitch==		==SAM Riboswitch==
		+
		+	==Overview==
		+
	<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />		<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />
	S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>		S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>


-	== Structural ~~highlights~~ ==	+	== Structural Highlights ==

	The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />		The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />

Sarah Moffett at 18:12, 30 November 2019

2019-11-30T18:12:18Z

←Older revision		Revision as of 18:12, 30 November 2019
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	==SAM Riboswitch==		==SAM Riboswitch==
	<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />		<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />
-	S-adenosylmethionine (~~SMA~~) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>	+	S-adenosylmethionine (SAM) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>

Sarah Moffett at 18:11, 30 November 2019

2019-11-30T18:11:14Z

←Older revision		Revision as of 18:11, 30 November 2019
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	==SAM Riboswitch==		==SAM Riboswitch==
	<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />		<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />
-	S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name=~~“ref1~~">PMID:16810258</ref>	+	S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name="ref1">PMID:16810258</ref>


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	The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />		The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />

-	The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.<ref name="ref1" />	+	The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix. <ref name="ref1" />

	The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(orange). <ref name="ref1" />		The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(orange). <ref name="ref1" />
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	== Function ==		== Function ==

-	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression.<ref name="ref1" />	+	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression. <ref name="ref1" />

	== References ==		== References ==
	(1) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.		(1) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.
-	(2) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.

Sarah Moffett at 17:10, 30 November 2019

2019-11-30T17:10:21Z

←Older revision		Revision as of 17:10, 30 November 2019
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	<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-	==SAM ~~Riboswith~~==	+	==SAM Riboswitch==
	<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />		<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />
	S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name=“ref1">PMID:16810258</ref>		S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name=“ref1">PMID:16810258</ref>
Line 11:		Line 11:
	The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.<ref name="ref1" />		The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.<ref name="ref1" />

-
	The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(orange). <ref name="ref1" />		The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(orange). <ref name="ref1" />
-

Sarah Moffett at 17:08, 30 November 2019

2019-11-30T17:08:53Z

←Older revision		Revision as of 17:08, 30 November 2019
Line 1:		Line 1:
	<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		<scene name='82/824623/Helix_interactions/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_JMeans}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-	==SAM Riboswith ~~(2GIS)~~==	+	==SAM Riboswith==
	<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />		<Structure load='2gis' size='350' frame='true' align='right' caption='SAM Riboswitch' scene='SAM Riboswitch' />
	S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name=“ref1">PMID:16810258</ref>		S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.<ref name=“ref1">PMID:16810258</ref>
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	== References ==		== References ==
	(1) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.		(1) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.
-		+	(2) Montange, R. K.; Batey, R. T. Structure of the S-Adenosylmethionine Riboswitch Regulatory MRNA Element. Nature 2006, 441 (7097), 1172–1175. https://doi.org/10.1038/nature04819.
-	~~<referneces~~/>	+

Sarah Moffett at 17:06, 30 November 2019

2019-11-30T17:06:55Z

←Older revision		Revision as of 17:06, 30 November 2019
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	== Structural highlights ==		== Structural highlights ==

-	The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions.	+	The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions. <ref name="ref1" />

-	The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (~~in color~~). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.	+	The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (purple). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.<ref name="ref1" />


-	The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(~~color~~).	+	The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(orange). <ref name="ref1" />


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	== Function ==		== Function ==

-	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression.	+	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression.<ref name="ref1" />

	== References ==		== References ==

Sarah Moffett at 16:56, 30 November 2019

2019-11-30T16:56:00Z

←Older revision		Revision as of 16:56, 30 November 2019
Line 18:		Line 18:
	== Function ==		== Function ==

-	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression.~~<ref name="ref1" />~~	+	Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target. Genetic regulation by RNA is often used in bacterial cells. In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place. Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression.

	== References ==		== References ==