Sandbox 42 - Revision history

Student: /* Introduction */

2012-10-15T03:20:05Z

Introduction

←Older revision		Revision as of 03:20, 15 October 2012
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	<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />		<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />
	==Introduction==		==Introduction==
-	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The two chains are identical and so structural elements can be examined by focusing on one chain. The space filling section of the protein is the ligand, which is bound to the active site in this representation.	+	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. This protein is an enzyme that converts one molecule of ATP and one molecule of AMP into two molecules of ADP. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The two chains are identical and so structural elements can be examined by focusing on one chain. The space filling section of the protein is the ligand, which is bound to the active site in this representation.

	==Structural Elements==		==Structural Elements==

Student: /* Structural Elements */

2012-10-15T03:19:11Z

Structural Elements

←Older revision		Revision as of 03:19, 15 October 2012
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	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that water permeates the molecule at least part way. However, as has just been shown, the path to the active site contains a large number of polar and charged amino acid residues, so this is really not surprising. The solvated ligand enters through the channel where water is still present before it becomes unsolvated, at which point it can bind to the protein.		In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that water permeates the molecule at least part way. However, as has just been shown, the path to the active site contains a large number of polar and charged amino acid residues, so this is really not surprising. The solvated ligand enters through the channel where water is still present before it becomes unsolvated, at which point it can bind to the protein.

-	The <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. This view shows how the ligand binds to the protein via interactions with protein side chains, as well as that it binds where we expect from the location of the internal polar and charged residues. <scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> are colored purple for this view.	+	The <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. This view shows how the ligand binds to the protein via interactions with protein side chains, as well as that it binds where we expect from the location of the internal polar and charged residues. <scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> are colored purple for this view. This shows some very important information. Three of these residues are bound to the ligand, which show how it is anchored into place to the protein. The other two residues, however, are centered on the chain connecting the two parts of the ligand. Since it is a longer, non-hydrolyzable ligand, no chemistry will happen. However, if it were ATP and AMP that were bound, these two catalytic resides would be positioned over the bond that would be broken to form two molecules of ADP. These two residues are clearly important in facilitating the reaction, either by some electron transfer or a conformational change.

Student: /* Structural Elements */

2012-10-15T03:13:35Z

Structural Elements

←Older revision		Revision as of 03:13, 15 October 2012
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	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that water permeates the molecule at least part way. However, as has just been shown, the path to the active site contains a large number of polar and charged amino acid residues, so this is really not surprising. The solvated ligand enters through the channel where water is still present before it becomes unsolvated, at which point it can bind to the protein.		In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that water permeates the molecule at least part way. However, as has just been shown, the path to the active site contains a large number of polar and charged amino acid residues, so this is really not surprising. The solvated ligand enters through the channel where water is still present before it becomes unsolvated, at which point it can bind to the protein.

-	The <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. This view shows how	+	The <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. This view shows how the ligand binds to the protein via interactions with protein side chains, as well as that it binds where we expect from the location of the internal polar and charged residues. <scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> are colored purple for this view.
-	<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple	+

Student: /* Structural Elements */

2012-10-15T03:09:07Z

Structural Elements

←Older revision		Revision as of 03:09, 15 October 2012
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	The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.		The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.

-	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that	+	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that water permeates the molecule at least part way. However, as has just been shown, the path to the active site contains a large number of polar and charged amino acid residues, so this is really not surprising. The solvated ligand enters through the channel where water is still present before it becomes unsolvated, at which point it can bind to the protein.

-	<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.	+	The <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. This view shows how
	<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple		<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple

Student at 03:04, 15 October 2012

2012-10-15T03:04:24Z

←Older revision		Revision as of 03:04, 15 October 2012
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	The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.		The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.

-	The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.	+	The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.
-	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. ~~What is most interesting about this view is that ...~~	+
-	<scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>~~Water~~</scene> in ~~yellow - ball/~~stick	+	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that
		+
	<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.		<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.
	<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple		<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple

Student: /* Structural Elements */

2012-10-15T02:58:35Z

Structural Elements

←Older revision		Revision as of 02:58, 15 October 2012
Line 10:		Line 10:

	The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.		The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.
-	<scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> ~~in yellow -~~ secondary structure	+	In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. What is most interesting about this view is that ...
	<scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>Water</scene> in yellow - ball/stick		<scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>Water</scene> in yellow - ball/stick
	<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.		<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.
	<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple		<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple

Student: /* Structural Elements */

2012-10-15T02:53:26Z

Structural Elements

←Older revision		Revision as of 02:53, 15 October 2012
Line 9:		Line 9:
	The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.		The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.

-	<scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> in gray	+	The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated.
-	<scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> in brown	+
	<scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> in yellow - secondary structure		<scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> in yellow - secondary structure
	<scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>Water</scene> in yellow - ball/stick		<scene name='Sandbox_42/Wes_-_water-ball_and_stick/1'>Water</scene> in yellow - ball/stick
	<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.		<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent.
	<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple		<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple

Student: /* Introduction */

2012-10-15T02:48:31Z

Introduction

←Older revision		Revision as of 02:48, 15 October 2012
Line 4:		Line 4:
	<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />		<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />
	==Introduction==		==Introduction==
-	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The two chains are identical and so structural elements can be examined by focusing on one chain.	+	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The two chains are identical and so structural elements can be examined by focusing on one chain. The space filling section of the protein is the ligand, which is bound to the active site in this representation.

	==Structural Elements==		==Structural Elements==

Student at 02:46, 15 October 2012

2012-10-15T02:46:12Z

←Older revision		Revision as of 02:46, 15 October 2012
Line 4:		Line 4:
	<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />		<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />
	==Introduction==		==Introduction==
-	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.	+	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The two chains are identical and so structural elements can be examined by focusing on one chain.
		+
		+	==Structural Elements==
		+	The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.

	<scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> in gray		<scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> in gray

Student at 00:47, 15 October 2012

2012-10-15T00:47:39Z

←Older revision		Revision as of 00:47, 15 October 2012
Line 4:		Line 4:
	<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />		<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />
	==Introduction==		==Introduction==
-	Adenylate kinase consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.	+	Adenylate kinase is a protein that is found in the bacterium ''yersinia pestis''. It consists of two chains, <scene name='Sandbox_42/Wes_-_1ake/1'>Chain A</scene> and Chain B. The <scene name='Sandbox_42/Wes_-_secondary_structure/1'>secondary structure</scene> is highlighted here, with alpha helices (shown in green) and beta sheets (blue). <scene name='Sandbox_42/Wes_-_hydrogen_bonds/1'>Hydrogen bonds</scene> are shown in black. These bonds show that the beta sheets are connected in parallel, as the hydrogen bonds are angled and not parallel to one another.

	<scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> in gray		<scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> in gray