Sandbox Reserved 791 - Revision history

Student at 05:11, 17 October 2013

Student — Thu, 17 Oct 2013 05:11:08 GMT

←Older revision		Revision as of 05:11, 17 October 2013
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	For chains A and D, the glycerol binds to sites		For chains A and D, the glycerol binds to sites
-	I221, V225, T226, K227, P228, V229, A228, G269 and V270	+	I221, V225, T226, K227, P228, V229, A228, G269 and V270 while CoA binds to these sites G14, T16, G17, S18, Q19, V38, T39, P40, K42, Y71, V72, P73, F76, S80, I95, T96, E97, N122, T123, P124, I136.
-	CoA binds to these sites	+
-	G14, T16, G17, S18, Q19, V38, T39, P40, K42, Y71, V72, P73, F76, S80, I95, T96, E97, N122, T123, P124, I136	+

	For chains B and E, CoA binds to these sites		For chains B and E, CoA binds to these sites
-	R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352	+	R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352.

-	~~Its~~ <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on chains A and B. On <scene name='56/563203/Catalytic_residues_chain_a/1'>chain A</scene>, the glutamic acid residue at position 208 and the histidine residue at position 246 while for <scene name='56/563203/Catalytic_residues_chain_b/1'>chain B</scene> (shown in pink), its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).	+	Succinyl CoA synthetase's <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on chains A and B. On <scene name='56/563203/Catalytic_residues_chain_a/1'>chain A</scene>, the glutamic acid residue at position 208 and the histidine residue at position 246 while for <scene name='56/563203/Catalytic_residues_chain_b/1'>chain B</scene> (shown in pink), its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue). This active sites are responsible for catalyzing the succinate formation from succinyl-CoA.

Student at 04:52, 17 October 2013

Student — Thu, 17 Oct 2013 04:52:18 GMT

←Older revision		Revision as of 04:52, 17 October 2013
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	<scene name='56/563203/Water_interactions_chain_c/1'>Chain D</scene>'s water interactions (in red) are depicted. Its <scene name='56/563203/Waterandsolv_inter_chain_d/1'>ligand </scene> binding sites are also observed (CoA (fuchsia), glycerol (indigo).		<scene name='56/563203/Water_interactions_chain_c/1'>Chain D</scene>'s water interactions (in red) are depicted. Its <scene name='56/563203/Waterandsolv_inter_chain_d/1'>ligand </scene> binding sites are also observed (CoA (fuchsia), glycerol (indigo).
	<scene name='56/563203/Water_interactions_chain_e/1'>Chain E</scene>'s water interactions (in red) are depicted and its		<scene name='56/563203/Water_interactions_chain_e/1'>Chain E</scene>'s water interactions (in red) are depicted and its
-	<scene name='56/563203/Waterandsolv_inter_chain_e/1'>ligand</scene> binding sites are also observed (CoA (fuchsia), sulfate (purple). We exercise caution ~~her~~ in noting what we consider to be the ligands. Sulfate and phosphate are typically solvents located in the crystal structure of the protein, so they are not the true ligands that we are interested in. On the other hand, we are interested in CoA and glycerol as they are the true ligands that are bound to the enzyme to facilitate the catalysis. Noting this caveat, we can also observe the <scene name='56/563203/Ligand_binding_sites/2'>side chain contacts</scene> with the ligands. The color of the ligands are coded as such:	+	<scene name='56/563203/Waterandsolv_inter_chain_e/1'>ligand</scene> binding sites are also observed (CoA (fuchsia), sulfate (purple). We exercise caution here in noting what we consider to be the ligands. Sulfate and phosphate are typically solvents located in the crystal structure of the protein, so they are not the true ligands that we are interested in. On the other hand, we are interested in CoA and glycerol as they are the true ligands that are bound to the enzyme to facilitate the catalysis. Noting this caveat, we can also observe the <scene name='56/563203/Ligand_binding_sites/2'>side chain contacts</scene> with the ligands. The color of the ligands are coded as such:
-	CoA (fuchsia), phosphate (green), sulfate (purple) and glycerol (indigo). ~~The~~ sulfate and phosphate molecules are not particularly important as they are more of solvent molecules rather than ligands. The major species here are the CoA and glycerol molecules. The glycerol molecule is surrounded by hydrophobic residues (depicted by the white-colored side chains) whereas the CoA molecule has hydrophilic residues (Lys) stabilizing the negatively charged phosphate groups while hydrophobic residues (e.g. Ile, Pro,) stabilize the rest of the CoA.	+	CoA (fuchsia), phosphate (green), sulfate (purple) and glycerol (indigo). As mentioned earlier, the sulfate and phosphate molecules are not particularly important as they are more of solvent molecules rather than ligands. The major species here are the CoA and glycerol molecules. The glycerol molecule is surrounded by hydrophobic residues (depicted by the white-colored side chains) whereas the CoA molecule has hydrophilic residues (Lys) stabilizing the negatively charged phosphate groups while hydrophobic residues (e.g. Ile, Pro,) stabilize the rest of the CoA.

	For chains A and D, the glycerol binds to sites		For chains A and D, the glycerol binds to sites

Student at 04:46, 17 October 2013

Student — Thu, 17 Oct 2013 04:46:39 GMT

Student at 04:34, 17 October 2013

Student — Thu, 17 Oct 2013 04:34:17 GMT

←Older revision		Revision as of 04:34, 17 October 2013
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	The form isolated is doubly dimeric protein with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.		The form isolated is doubly dimeric protein with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.

-	As much as we like the ribbon model of proteins, we also need to visualize succinyl CoA synthetase in its <scene name='56/563203/Scs_space-filling/1'>space filling form</scene>. This model gives us a better picture of the Van der Waal radii and packing of the side chains, details usually not obtained by the use of the ribbon model. However, with the ribbon model, it is often easier to visualize the <scene name='56/563203/Hydrogen_bond/1'>hydrogen bonding</scene> present in the enzyme's secondary structure. Here we observe the presence of <scene name='56/563203/Alpha_helices/2'>alpha helices</scene> and <scene name='56/563203/Beta_sheet/3'>beta sheets</scene>. ~~In the beta sheet structure~~, we observe	+	As much as we like the ribbon model of proteins, we also need to visualize succinyl CoA synthetase in its <scene name='56/563203/Scs_space-filling/1'>space filling form</scene>. This model gives us a better picture of the Van der Waal radii and packing of the side chains, details usually not obtained by the use of the ribbon model. However, with the ribbon model, it is often easier to visualize the <scene name='56/563203/Hydrogen_bond/1'>hydrogen bonding</scene> present in the enzyme's secondary structure. Here we observe the presence of <scene name='56/563203/Alpha_helices/2'>alpha helices</scene> and <scene name='56/563203/Beta_sheet/3'>beta sheets</scene>. For succinyl CoA synthetase, we observe that alpha helices are the major contributor to the protein structure, with the <scene name='56/563203/Alpha_helices_hbonding/3'>hydrogen bonding</scene> observed by the white lines connecting the carbon backbone.
-		+	For the beta sheets, we can use the backbone <scene name='56/563203/Beta_sheet/4'>hydrogen bonds</scene> to distinguish the antiparallel and parallel sheets. The antiparallel sheets are denoted by parallel white lines connecting the sheets whereas nonparallel white lines indicate the presence of two adjacent parallel sheets.
-	~~Here's some~~ <scene name='56/563203/~~H-bond_beta_sheet~~/1'>hydrogen bonding</scene> ~~for~~ the beta ~~sheet~~.	+

-	~~Here~~ are the	+	Another important factor in protein analysis is knowing where the hydrophobic and hydrophilic residues are. While the <scene name='56/563203/Hydrophilics/2'>hydrophilic residues</scene> and the <scene name='56/563203/Hydrophobics/3'>hydrophobic residues</scene> in ribbon form are visually appealing, it is usually more useful to approach these residues with a stick/wireframe representation. We can get a clearer picture of the <scene name='56/563203/Hydrophobics_transparency_2/1'>hydrophobic</scene> chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to obtain the <scene name='56/563203/Hydrophilic_transparency_1/1'>hydrophilic chains</scene>, which are shown in light brown. We can see that the hydrophobic residues are mostly located on the interior of the protein while the hydrophilic residues are mostly interacting with the protein's exterior.

-	We can see the <scene name='56/563203/Hydrophilics/1'>hydrophilic residues in ribbon form</scene> here while the <scene name='56/563203/Hydrophobics/2'>hydrophobic residues in ribbon form</scene> are visible as well.	+	Another important factor to consider the solvent accessibility of solvent molecules. Water is often crystallized with the protein, and we can show portions of <scene name='56/563203/Water_interactions_chain_a/1'>chain A</scene> where water molecules (light blue) interacts with the chain. We can also analyze the presence of ligand molecules at <scene name='56/563203/Waterandsolv_inter_chain_a/1'>specific</scene> sites, where CoA (fuchsia), phosphate (green) and glycerol (indigo) bind.
-		+
-	We can get a clearer picture of the <scene name='56/563203/Hydrophobics_transparency_2/1'>hydrophobic</scene> chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to ~~obtain~~ the ~~<scene name='56/563203/Hydrophilic_transparency_1/1'>hydrophilic chains</scene>, which are shown in light brown. We can see that the hydrophobic residues are mostly located on the interior~~ of ~~the protein while the hydrophilic residues are mostly interacting with the protein's exterior~~.	+
-		+
-	Water is often crystallized with the protein, and we can show portions of	+
-	<scene name='56/563203/Water_interactions_chain_a/1'>chain A</scene> where water molecules (light blue) interacts with the chain. We can also analyze the presence of ligand molecules at <scene name='56/563203/Waterandsolv_inter_chain_a/1'>specific</scene> sites, where CoA (fuchsia), phosphate (green) and glycerol (indigo) bind.	+

	We can also see the same effects for the other chains:		We can also see the same effects for the other chains:

Student at 04:07, 17 October 2013

Student — Thu, 17 Oct 2013 04:07:52 GMT

←Older revision		Revision as of 04:07, 17 October 2013
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	<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />		<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />

-	<scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> is a key enzyme in the citric acid cycle of cellular metabolism. Its main role is to ~~form~~ succinate from succinyl-CoA. First, the succinyl-CoA complex undergoes nucleophilic attack by a phosphate molecule, releasing CoA in the process. This phospho-succinate complex then reacts with a histidine group on the enzyme to release succinate (the key compound required for the next step of the citric acid cycle). The phospho group on the histidine subsequently reacts with ADP to form ATP.	+	<scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> is a key enzyme in the citric acid cycle of cellular metabolism. Its main role is to catalyze the formation of succinate from succinyl-CoA. First, the succinyl-CoA complex undergoes nucleophilic attack by a phosphate molecule, releasing CoA in the process. This phospho-succinate complex then reacts with a histidine group on the enzyme to release succinate (the key compound required for the next step of the citric acid cycle). The phospho group on the histidine subsequently reacts with ADP to form ATP.
	This specific crystal structure of succinyl CoA synthetase was synthesized by Frazer et al. (Acta Cryst. (2007). D63, 876–884) and given the PDB code 2NU8.		This specific crystal structure of succinyl CoA synthetase was synthesized by Frazer et al. (Acta Cryst. (2007). D63, 876–884) and given the PDB code 2NU8.
	The form isolated is doubly dimeric protein with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.		The form isolated is doubly dimeric protein with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.

-	~~To get~~ a better picture of the Van der Waal radii and packing of the side chains, it is ~~quite useful~~ to ~~view~~ the <scene name='56/563203/~~Scs_space-filling~~/1'>~~space-filling~~</scene> ~~model, as shown~~	+	As much as we like the ribbon model of proteins, we also need to visualize succinyl CoA synthetase in its <scene name='56/563203/Scs_space-filling/1'>space filling form</scene>. This model gives us a better picture of the Van der Waal radii and packing of the side chains, details usually not obtained by the use of the ribbon model. However, with the ribbon model, it is often easier to visualize the <scene name='56/563203/Hydrogen_bond/1'>hydrogen bonding</scene> present in the enzyme's secondary structure. Here we observe the presence of <scene name='56/563203/Alpha_helices/2'>alpha helices</scene> and <scene name='56/563203/Beta_sheet/3'>beta sheets</scene>. In the beta sheet structure, we observe
-		+
-	~~This~~ <scene name='56/563203/~~Hydrogen_bond~~/1'>~~picture~~</scene> ~~depicts the hydrogen bonding present in the backbone for the protein.~~	+
-		+
-	~~The~~ <scene name='56/563203/Beta_sheet/2'>~~Beta~~ sheets</scene> ~~are represented here~~	+
-		+
	Here's some <scene name='56/563203/H-bond_beta_sheet/1'>hydrogen bonding</scene> for the beta sheet.		Here's some <scene name='56/563203/H-bond_beta_sheet/1'>hydrogen bonding</scene> for the beta sheet.

-	Here are the ~~<scene name='56/563203/Alpha_helices/1'>Alpha helices</scene>~~	+	Here are the

	We can see the <scene name='56/563203/Hydrophilics/1'>hydrophilic residues in ribbon form</scene> here while the <scene name='56/563203/Hydrophobics/2'>hydrophobic residues in ribbon form</scene> are visible as well.		We can see the <scene name='56/563203/Hydrophilics/1'>hydrophilic residues in ribbon form</scene> here while the <scene name='56/563203/Hydrophobics/2'>hydrophobic residues in ribbon form</scene> are visible as well.

Student at 02:58, 17 October 2013

Student — Thu, 17 Oct 2013 02:58:40 GMT

←Older revision		Revision as of 02:58, 17 October 2013
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	<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />		<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />

-	Succinyl ~~coenzyme A (~~CoA) synthetase is a key enzyme in the citric acid cycle of cellular metabolism. Its main role is to form succinate from succinyl-CoA. First, the succinyl-CoA complex undergoes nucleophilic attack by a phosphate molecule, releasing CoA in the process. This phospho-succinate complex then reacts with a histidine group on the enzyme to release succinate (the key compound required for the next step of the citric acid cycle). The phospho group on the histidine subsequently reacts with ADP to form ATP.	+	<scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> is a key enzyme in the citric acid cycle of cellular metabolism. Its main role is to form succinate from succinyl-CoA. First, the succinyl-CoA complex undergoes nucleophilic attack by a phosphate molecule, releasing CoA in the process. This phospho-succinate complex then reacts with a histidine group on the enzyme to release succinate (the key compound required for the next step of the citric acid cycle). The phospho group on the histidine subsequently reacts with ADP to form ATP.
-	This specific crystal structure of succinyl CoA synthetase ~~wsa~~ synthesized by Frazer et al. (Acta Cryst. (2007). D63, 876–884)	+	This specific crystal structure of succinyl CoA synthetase was synthesized by Frazer et al. (Acta Cryst. (2007). D63, 876–884) and given the PDB code 2NU8.
-	~~This~~ is a doubly dimeric protein ~~<scene name='56/563203/Succinyl_coa_synthetase/1'>succinyl CoA synthetase</scene>~~ with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.	+	The form isolated is doubly dimeric protein with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.

	To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown		To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown

Student at 02:57, 17 October 2013

Student — Thu, 17 Oct 2013 02:57:10 GMT

←Older revision		Revision as of 02:57, 17 October 2013
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	<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />		<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />

-	This is a ~~tetrameric~~ protein <scene name='56/563203/Succinyl_coa_synthetase/1'>~~Succinyl~~ CoA synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>	+	Succinyl coenzyme A (CoA) synthetase is a key enzyme in the citric acid cycle of cellular metabolism. Its main role is to form succinate from succinyl-CoA. First, the succinyl-CoA complex undergoes nucleophilic attack by a phosphate molecule, releasing CoA in the process. This phospho-succinate complex then reacts with a histidine group on the enzyme to release succinate (the key compound required for the next step of the citric acid cycle). The phospho group on the histidine subsequently reacts with ADP to form ATP.
		+	This specific crystal structure of succinyl CoA synthetase wsa synthesized by Frazer et al. (Acta Cryst. (2007). D63, 876–884)
		+	This is a doubly dimeric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>succinyl CoA synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>, where chains A and D, B and E are dimers.

	To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown		To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown

Student at 22:53, 16 October 2013

Student — Wed, 16 Oct 2013 22:53:05 GMT

←Older revision		Revision as of 22:53, 16 October 2013
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	<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />		<Structure load='2NU8' size='500' frame='true' align='right' caption='C123aT Mutant ''E. coli'' Succinyl CoA synthetase' scene='C123aT Mutant' />

-	This is a tetrameric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/1'>Chain A</scene>, <scene name='56/563203/Chain_b/1'>Chain B</scene>, <scene name='56/563203/Chain_c/1'>Chain D</scene> and <scene name='56/563203/Chain_e/1'>Chain E</scene>	+	This is a tetrameric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/2'>Chain A</scene>, <scene name='56/563203/Chain_b/2'>Chain B</scene>, <scene name='56/563203/Chain_c/2'>Chain D</scene> and <scene name='56/563203/Chain_e/2'>Chain E</scene>

	To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown		To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown

Student at 22:44, 16 October 2013

Student — Wed, 16 Oct 2013 22:44:08 GMT

←Older revision		Revision as of 22:44, 16 October 2013
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	R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352		R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352

-	Its <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on ~~chain~~ A and ~~chain~~ B. On chain A, the glutamic acid residue at position 208 and the histidine residue at position 246 while for chain B (shown in pink), ~~Its~~ catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).	+	Its <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on chains A and B. On <scene name='56/563203/Catalytic_residues_chain_a/1'>chain A</scene>, the glutamic acid residue at position 208 and the histidine residue at position 246 while for <scene name='56/563203/Catalytic_residues_chain_b/1'>chain B</scene> (shown in pink), its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).

Student at 22:39, 16 October 2013

Student — Wed, 16 Oct 2013 22:39:36 GMT

←Older revision		Revision as of 22:39, 16 October 2013
Line 6:		Line 6:

	This is a tetrameric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/1'>Chain A</scene>, <scene name='56/563203/Chain_b/1'>Chain B</scene>, <scene name='56/563203/Chain_c/1'>Chain D</scene> and <scene name='56/563203/Chain_e/1'>Chain E</scene>		This is a tetrameric protein <scene name='56/563203/Succinyl_coa_synthetase/1'>Succinyl CoA synthetase</scene> with the known binding ligands present in the protein crystallization. The four chains depicted: <scene name='56/563203/Chain_a/1'>Chain A</scene>, <scene name='56/563203/Chain_b/1'>Chain B</scene>, <scene name='56/563203/Chain_c/1'>Chain D</scene> and <scene name='56/563203/Chain_e/1'>Chain E</scene>
-
-	[[Media:http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetImage.pl?kegg_id=C00008]]

	To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown		To get a better picture of the Van der Waal radii and packing of the side chains, it is quite useful to view the <scene name='56/563203/Scs_space-filling/1'>space-filling</scene> model, as shown
Line 41:		Line 39:
	R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352		R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352

-	Its <scene name='56/563203/Catalytic_residues/1'>catalytic residues</scene> are on chain A and chain B. On chain A, the glutamic acid residue at position 208 and the histidine residue at position 246 while for chain B (shown in pink), Its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).	+	Its <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on chain A and chain B. On chain A, the glutamic acid residue at position 208 and the histidine residue at position 246 while for chain B (shown in pink), Its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).

←Older revision		Revision as of 04:46, 17 October 2013
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	Another important factor in protein analysis is knowing where the hydrophobic and hydrophilic residues are. While the <scene name='56/563203/Hydrophilics/2'>hydrophilic residues</scene> and the <scene name='56/563203/Hydrophobics/3'>hydrophobic residues</scene> in ribbon form are visually appealing, it is usually more useful to approach these residues with a stick/wireframe representation. We can get a clearer picture of the <scene name='56/563203/Hydrophobics_transparency_2/1'>hydrophobic</scene> chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to obtain the <scene name='56/563203/Hydrophilic_transparency_1/1'>hydrophilic chains</scene>, which are shown in light brown. We can see that the hydrophobic residues are mostly located on the interior of the protein while the hydrophilic residues are mostly interacting with the protein's exterior.		Another important factor in protein analysis is knowing where the hydrophobic and hydrophilic residues are. While the <scene name='56/563203/Hydrophilics/2'>hydrophilic residues</scene> and the <scene name='56/563203/Hydrophobics/3'>hydrophobic residues</scene> in ribbon form are visually appealing, it is usually more useful to approach these residues with a stick/wireframe representation. We can get a clearer picture of the <scene name='56/563203/Hydrophobics_transparency_2/1'>hydrophobic</scene> chains as stick and wire models in the presence of the rest of the molecule. The maroon chains represent the hydrophobic residues seen earlier while the transparent part of the protein shows the other residues present. We can invert this image to obtain the <scene name='56/563203/Hydrophilic_transparency_1/1'>hydrophilic chains</scene>, which are shown in light brown. We can see that the hydrophobic residues are mostly located on the interior of the protein while the hydrophilic residues are mostly interacting with the protein's exterior.

-	Another important factor to consider the solvent accessibility of solvent molecules. Water is often crystallized with the protein, and we can show portions of <scene name='56/563203/Water_interactions_chain_a/1'>chain A</scene> where water molecules (light blue) interacts with the chain. We can also analyze the presence of ligand molecules at <scene name='56/563203/Waterandsolv_inter_chain_a/1'>specific</scene> sites, where CoA (fuchsia), phosphate (green) and glycerol (indigo) bind.	+	Another important factor to consider the solvent accessibility of solvent molecules. Water is often crystallized with the protein, and we can show portions of <scene name='56/563203/Water_interactions_chain_a/1'>chain A</scene> where water molecules (light blue) interacts with the chain. We can also analyze the presence of ligand molecules at <scene name='56/563203/Waterandsolv_inter_chain_a/1'>specific</scene> sites, where CoA (fuchsia), phosphate (green) and glycerol (indigo) bind. We can also observe the same effects for the other chains:
-		+
-	We can also ~~see~~ the same effects for the other chains:	+
	<scene name='56/563203/Water_interactions_chain_b/1'>Chain B</scene>'s water interactions (in red) are depicted and its <scene name='56/563203/Waterandsolv_inter_chain_b/1'>ligand</scene> sites are also observed (CoA (fuchsia), sulfate (purple)).		<scene name='56/563203/Water_interactions_chain_b/1'>Chain B</scene>'s water interactions (in red) are depicted and its <scene name='56/563203/Waterandsolv_inter_chain_b/1'>ligand</scene> sites are also observed (CoA (fuchsia), sulfate (purple)).
-	<scene name='56/563203/Water_interactions_chain_c/1'>Chain D</scene>'s water (in red) are depicted. Its <scene name='56/563203/Waterandsolv_inter_chain_d/1'>ligand </scene> binding sites are also observed (CoA (fuchsia), glycerol (indigo).	+	<scene name='56/563203/Water_interactions_chain_c/1'>Chain D</scene>'s water interactions (in red) are depicted. Its <scene name='56/563203/Waterandsolv_inter_chain_d/1'>ligand </scene> binding sites are also observed (CoA (fuchsia), glycerol (indigo).
	<scene name='56/563203/Water_interactions_chain_e/1'>Chain E</scene>'s water interactions (in red) are depicted and its		<scene name='56/563203/Water_interactions_chain_e/1'>Chain E</scene>'s water interactions (in red) are depicted and its
-	<scene name='56/563203/Waterandsolv_inter_chain_e/1'>ligand</scene> binding sites are also observed (CoA (fuchsia), sulfate (purple).	+	<scene name='56/563203/Waterandsolv_inter_chain_e/1'>ligand</scene> binding sites are also observed (CoA (fuchsia), sulfate (purple). We exercise caution her in noting what we consider to be the ligands. Sulfate and phosphate are typically solvents located in the crystal structure of the protein, so they are not the true ligands that we are interested in. On the other hand, we are interested in CoA and glycerol as they are the true ligands that are bound to the enzyme to facilitate the catalysis. Noting this caveat, we can also observe the <scene name='56/563203/Ligand_binding_sites/2'>side chain contacts</scene> with the ligands. The color of the ligands are coded as such:
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-	We can also ~~see~~ the <scene name='56/563203/Ligand_binding_sites/2'>side chain contacts</scene> with the ligands. The color of the ligands are coded as such:	+
	CoA (fuchsia), phosphate (green), sulfate (purple) and glycerol (indigo). The sulfate and phosphate molecules are not particularly important as they are more of solvent molecules rather than ligands. The major species here are the CoA and glycerol molecules. The glycerol molecule is surrounded by hydrophobic residues (depicted by the white-colored side chains) whereas the CoA molecule has hydrophilic residues (Lys) stabilizing the negatively charged phosphate groups while hydrophobic residues (e.g. Ile, Pro,) stabilize the rest of the CoA.		CoA (fuchsia), phosphate (green), sulfate (purple) and glycerol (indigo). The sulfate and phosphate molecules are not particularly important as they are more of solvent molecules rather than ligands. The major species here are the CoA and glycerol molecules. The glycerol molecule is surrounded by hydrophobic residues (depicted by the white-colored side chains) whereas the CoA molecule has hydrophilic residues (Lys) stabilizing the negatively charged phosphate groups while hydrophobic residues (e.g. Ile, Pro,) stabilize the rest of the CoA.
		+
	For chains A and D, the glycerol binds to sites		For chains A and D, the glycerol binds to sites
	I221, V225, T226, K227, P228, V229, A228, G269 and V270		I221, V225, T226, K227, P228, V229, A228, G269 and V270
	CoA binds to these sites		CoA binds to these sites
	G14, T16, G17, S18, Q19, V38, T39, P40, K42, Y71, V72, P73, F76, S80, I95, T96, E97, N122, T123, P124, I136		G14, T16, G17, S18, Q19, V38, T39, P40, K42, Y71, V72, P73, F76, S80, I95, T96, E97, N122, T123, P124, I136
		+
	For chains B and E, CoA binds to these sites		For chains B and E, CoA binds to these sites
	R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352		R29, E33, S36, K66, G265, A266, G267, G320, G321, V323, R324, C325, I328, L349, E350, G351, N352

	Its <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on chains A and B. On <scene name='56/563203/Catalytic_residues_chain_a/1'>chain A</scene>, the glutamic acid residue at position 208 and the histidine residue at position 246 while for <scene name='56/563203/Catalytic_residues_chain_b/1'>chain B</scene> (shown in pink), its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).		Its <scene name='56/563203/Catalytic_residues/3'>catalytic residues</scene> are on chains A and B. On <scene name='56/563203/Catalytic_residues_chain_a/1'>chain A</scene>, the glutamic acid residue at position 208 and the histidine residue at position 246 while for <scene name='56/563203/Catalytic_residues_chain_b/1'>chain B</scene> (shown in pink), its catalytic residues are the tyrosine residue at position 109 and the glutamic acid residue at position 197 (shown in blue).