Sandbox Reserved 802 - Revision history

Student: /* The Ligands and Ligand Contacts */

2013-10-17T18:17:35Z

The Ligands and Ligand Contacts

←Older revision		Revision as of 18:17, 17 October 2013
Line 14:		Line 14:
	The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.		The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.
	==The Ligands and Ligand Contacts==		==The Ligands and Ligand Contacts==
-	The <scene name='56/563214/A2_ligand_new/1'>ligand binding site</scene> for chain A is observed in blue. The actual substrate is in red. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/A2_ligand_substrates_new/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, the substrate is in mint, and the entire binding site is in blue). These residues (red) interact with and stabilize the substrate (mint).	+	The <scene name='56/563214/A2_ligand_new/1'>ligand binding site</scene> for chain A is observed in blue. The actual substrate (1,3-dihydroxyacetonephosphate [C3H7O6P], which is a glyceraldehyde 3-phosphate analog) is in red. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/A2_ligand_substrates_new/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, the substrate is in mint, and the entire binding site is in blue). These residues (red) interact with and stabilize the substrate (mint) within the active site.

	==Catalytic Residues==		==Catalytic Residues==

Student at 18:13, 17 October 2013

2013-10-17T18:13:28Z

←Older revision		Revision as of 18:13, 17 October 2013
Line 14:		Line 14:
	The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.		The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.
	==The Ligands and Ligand Contacts==		==The Ligands and Ligand Contacts==
-	The <scene name='56/563214/A2_ligand_new/1'>ligand binding site</scene> for chain A is observed in blue. The actual substrate is in red. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/~~A2_ligand_substrates~~/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, ~~while~~ the entire binding site is in blue). These residues interact with and stabilize the ~~ligand~~.	+	The <scene name='56/563214/A2_ligand_new/1'>ligand binding site</scene> for chain A is observed in blue. The actual substrate is in red. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/A2_ligand_substrates_new/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, the substrate is in mint, and the entire binding site is in blue). These residues (red) interact with and stabilize the substrate (mint).

	==Catalytic Residues==		==Catalytic Residues==

Student at 18:03, 17 October 2013

2013-10-17T18:03:24Z

←Older revision		Revision as of 18:03, 17 October 2013
Line 14:		Line 14:
	The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.		The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.
	==The Ligands and Ligand Contacts==		==The Ligands and Ligand Contacts==
-	The <scene name='56/563214/~~A2_ligand~~/1'>~~1,3-Dihydroxyacetonephosphate~~ ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/A2_ligand_substrates/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, while the entire binding site is in blue). These residues interact with and stabilize the ligand.	+	The <scene name='56/563214/A2_ligand_new/1'>ligand binding site</scene> for chain A is observed in blue. The actual substrate is in red. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/A2_ligand_substrates/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, while the entire binding site is in blue). These residues interact with and stabilize the ligand.

	==Catalytic Residues==		==Catalytic Residues==

Student at 18:00, 17 October 2013

2013-10-17T18:00:54Z

←Older revision		Revision as of 18:00, 17 October 2013
Line 4:		Line 4:
	<Structure load='3dfo' size='500' frame='true' align='right' caption='Aldolase' scene='Insert optional scene name here' />		<Structure load='3dfo' size='500' frame='true' align='right' caption='Aldolase' scene='Insert optional scene name here' />
	==Introduction and General Structure==		==Introduction and General Structure==
-	<scene name='56/563214/Aldolase/1'>Fructose-1,6-bisphosphate aldolase</scene> can be observed. Aldolase is an enzyme that is active during glycolysis, which is an overall series of reactions that produces cellular energy (ATP). Specifically, aldolase catalyzes an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate. It is a tetrameter (four subunits)composed of alpha helices and beta sheets (<scene name='56/563214/A2_-_helices_and_sheets/1'>secondary structure</scene>). Please note that alpha helices are observed in blue, and beta sheets are in yellow. The majority of the helices are located on the surface (outside) of the enzyme, where as most of the sheets are found in the interior (inside). Most likely, polar amino acids are located on the peripheral helices, while hydrophobic or paired-polar amino acids are found within the beta sheets.	+	<scene name='56/563214/Aldolase/1'>Fructose-1,6-bisphosphate aldolase</scene> can be observed. Aldolase is an enzyme that is active during glycolysis, which is an overall series of reactions that produces cellular energy (ATP). Specifically, aldolase catalyzes an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and glycerone phosphate. Aldolase is a tetrameter (four subunits)composed of alpha helices and beta sheets (<scene name='56/563214/A2_-_helices_and_sheets/1'>secondary structure</scene>). Please note that alpha helices are observed in blue, and beta sheets are in yellow. The majority of the helices are located on the surface (outside) of the enzyme, where as most of the sheets are found in the interior (inside). Most likely, polar amino acids are located on the peripheral helices, while hydrophobic or paired-polar amino acids are found within the beta sheets.

	==Hydrogen and Disulfide Bonds==		==Hydrogen and Disulfide Bonds==
-	The <scene name='56/563214/A3_hydrogen_and_disulfide_bond/1'>hydrogen and disulfide bonds</scene> for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets, which indicates that interaction.	+	The <scene name='56/563214/A3_hydrogen_and_disulfide_bond/1'>hydrogen and disulfide bonds</scene> for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets, which indicates that specific type of interaction.

	==Hydrophobic and Hydrophilic Residues==		==Hydrophobic and Hydrophilic Residues==
Line 14:		Line 14:
	The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.		The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.
	==The Ligands and Ligand Contacts==		==The Ligands and Ligand Contacts==
-	The <scene name='56/563214/A2_ligand/1'>1,3-Dihydroxyacetonephosphate ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that ~~is involved in~~ the aldol reaction catalyzed by aldolase. ~~The main chain nitrogens found within the Ser271~~ and ~~Gly272 residues hold~~ the 1-phosphate ~~group~~ in ~~position~~, while the ~~6-phosphate group~~ is ~~held~~ in ~~position by Lys41, Arg42 and Arg303~~ residues.	+	The <scene name='56/563214/A2_ligand/1'>1,3-Dihydroxyacetonephosphate ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The <scene name='56/563214/A2_ligand_substrates/1'>glyceraldehyde 3-phosphate specific binding residues</scene> are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, while the entire binding site is in blue). These residues interact with and stabilize the ligand.

	==Catalytic Residues==		==Catalytic Residues==

Student: /* Catalytic Residues */

2013-10-17T02:44:34Z

Catalytic Residues

←Older revision		Revision as of 02:44, 17 October 2013
Line 17:		Line 17:

	==Catalytic Residues==		==Catalytic Residues==
-	The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229, all of which help catalyze an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glycerone phosphate and glyceraldehyde 3-phosphate. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks ~~a carbon found within~~ the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).	+	The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229, all of which help catalyze an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glycerone phosphate and glyceraldehyde 3-phosphate. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks the substrate to begin aldol catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).

	==References==		==References==

Student: /* The Ligands and Ligand Contacts */

2013-10-17T02:43:25Z

The Ligands and Ligand Contacts

←Older revision		Revision as of 02:43, 17 October 2013
Line 14:		Line 14:
	The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.		The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.
	==The Ligands and Ligand Contacts==		==The Ligands and Ligand Contacts==
-	The <scene name='56/563214/A2_ligand/1'>1,3-Dihydroxyacetonephosphate ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that is involved in the aldol reaction catalyzed by aldolase The main chain nitrogens found within the Ser271 and Gly272 residues hold the 1-phosphate group in position, while the 6-phosphate group is held in position by Lys41, Arg42 and Arg303 residues.	+	The <scene name='56/563214/A2_ligand/1'>1,3-Dihydroxyacetonephosphate ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that is involved in the aldol reaction catalyzed by aldolase. The main chain nitrogens found within the Ser271 and Gly272 residues hold the 1-phosphate group in position, while the 6-phosphate group is held in position by Lys41, Arg42 and Arg303 residues.
		+
	==Catalytic Residues==		==Catalytic Residues==
	The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229, all of which help catalyze an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glycerone phosphate and glyceraldehyde 3-phosphate. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks a carbon found within the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).		The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229, all of which help catalyze an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glycerone phosphate and glyceraldehyde 3-phosphate. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks a carbon found within the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).

Student: /* Hydrogen and Disulfide Bonds */

2013-10-17T02:34:17Z

Hydrogen and Disulfide Bonds

←Older revision		Revision as of 02:34, 17 October 2013
Line 7:		Line 7:

	==Hydrogen and Disulfide Bonds==		==Hydrogen and Disulfide Bonds==
-	The <scene name='56/563214/A3_hydrogen_and_disulfide_bond/1'>hydrogen and disulfide bonds</scene> for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets.	+	The <scene name='56/563214/A3_hydrogen_and_disulfide_bond/1'>hydrogen and disulfide bonds</scene> for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets, which indicates that interaction.
		+
	==Hydrophobic and Hydrophilic Residues==		==Hydrophobic and Hydrophilic Residues==
	The <scene name='56/563214/A3_hydrophobic/1'>hydrophobic residues</scene> are observed in grey. These residues are mostly observed in the interior of the enzyme (possibly on the beta sheets). Thus, they are hidden from the aqueous solvent. The <scene name='56/563214/A3_hydrophilic/1'>hydrophilic residues</scene> are observed in red. Notice that the majority of the hydrophilic amino acids are located on the alpha helices that are on the outside of this enzyme. Thus, these residues must interact with the solvent, which is aqueous. Plus, notice that there are about equal amounts of hydrophobic and hydrophilic residues.		The <scene name='56/563214/A3_hydrophobic/1'>hydrophobic residues</scene> are observed in grey. These residues are mostly observed in the interior of the enzyme (possibly on the beta sheets). Thus, they are hidden from the aqueous solvent. The <scene name='56/563214/A3_hydrophilic/1'>hydrophilic residues</scene> are observed in red. Notice that the majority of the hydrophilic amino acids are located on the alpha helices that are on the outside of this enzyme. Thus, these residues must interact with the solvent, which is aqueous. Plus, notice that there are about equal amounts of hydrophobic and hydrophilic residues.

Student: /* Introduction and General Structure */

2013-10-17T02:32:48Z

Introduction and General Structure

←Older revision		Revision as of 02:32, 17 October 2013
Line 4:		Line 4:
	<Structure load='3dfo' size='500' frame='true' align='right' caption='Aldolase' scene='Insert optional scene name here' />		<Structure load='3dfo' size='500' frame='true' align='right' caption='Aldolase' scene='Insert optional scene name here' />
	==Introduction and General Structure==		==Introduction and General Structure==
-	<scene name='56/563214/Aldolase/1'>Fructose-1,6-bisphosphate aldolase</scene> can be observed. Aldolase is an enzyme that is active during glycolysis, which is an overall series of reactions that produces cellular energy (ATP). Specifically, aldolase catalyzes an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate. It is a tetrameter (four subunits)composed of alpha helices and beta sheets (<scene name='56/563214/A2_-_helices_and_sheets/1'>secondary structure</scene>). Please note that alpha helices are observed in blue, and beta sheets are in yellow. The majority of the helices are located on the surface (outside) of the enzyme, where as most of the sheets are found in the interior. Most likely, polar amino acids are located on the peripheral helices, while hydrophobic or paired-polar amino acids are found within the beta ~~sheet~~.	+	<scene name='56/563214/Aldolase/1'>Fructose-1,6-bisphosphate aldolase</scene> can be observed. Aldolase is an enzyme that is active during glycolysis, which is an overall series of reactions that produces cellular energy (ATP). Specifically, aldolase catalyzes an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate. It is a tetrameter (four subunits)composed of alpha helices and beta sheets (<scene name='56/563214/A2_-_helices_and_sheets/1'>secondary structure</scene>). Please note that alpha helices are observed in blue, and beta sheets are in yellow. The majority of the helices are located on the surface (outside) of the enzyme, where as most of the sheets are found in the interior (inside). Most likely, polar amino acids are located on the peripheral helices, while hydrophobic or paired-polar amino acids are found within the beta sheets.
		+
	==Hydrogen and Disulfide Bonds==		==Hydrogen and Disulfide Bonds==
	The <scene name='56/563214/A3_hydrogen_and_disulfide_bond/1'>hydrogen and disulfide bonds</scene> for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets.		The <scene name='56/563214/A3_hydrogen_and_disulfide_bond/1'>hydrogen and disulfide bonds</scene> for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets.

Student at 02:31, 17 October 2013

2013-10-17T02:31:02Z

←Older revision		Revision as of 02:31, 17 October 2013
Line 12:		Line 12:
	The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.		The <scene name='56/563214/A2_water_space_fill/1'>water molecules</scene> that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.
	==The Ligands and Ligand Contacts==		==The Ligands and Ligand Contacts==
-	The <scene name='56/563214/A2_ligand/1'>ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). ~~There are no cofactors present~~ in ~~this enzyme.~~ The main chain nitrogens found within the Ser271 and Gly272 residues hold the 1-phosphate group in position, while the 6-phosphate group is held in position by Lys41, Arg42 and Arg303 residues.	+	The <scene name='56/563214/A2_ligand/1'>1,3-Dihydroxyacetonephosphate ligand binding site</scene> for chain A is observed in blue. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that is involved in the aldol reaction catalyzed by aldolase The main chain nitrogens found within the Ser271 and Gly272 residues hold the 1-phosphate group in position, while the 6-phosphate group is held in position by Lys41, Arg42 and Arg303 residues.
	==Catalytic Residues==		==Catalytic Residues==
-	The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks a carbon found within the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).	+	The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229, all of which help catalyze an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glycerone phosphate and glyceraldehyde 3-phosphate. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks a carbon found within the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).
-		+

	==References==		==References==
		+	1. M.St-Jean et al. (2009). Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase. Biochemistry, 48, 4528-4537. PubMed id: 19354220 DOI: 10.1021/bi8021558
		+
		+	2. http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
		+
		+	3. http://www.rcsb.org/pdb/explore/explore.do?structureId=3DFO

Student at 05:30, 15 October 2013

2013-10-15T05:30:07Z

←Older revision		Revision as of 05:30, 15 October 2013
Line 16:		Line 16:
	The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks a carbon found within the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).		The <scene name='56/563214/A2_catalytic_residues/1'>catalytic residues</scene> are displayed in red. They are Asn33, Glu187, and Lys229. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks a carbon found within the substrate to begin catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).

-	==Ligands==
-
-	==Catalytic Residues==

	==References==		==References==