Sandbox Reserved 1563 - Revision history

Garrett Leibow at 05:55, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 05:55:20 GMT

←Older revision		Revision as of 05:55, 9 December 2019
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	<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. The hydrophilic residues interact with the outside enviornment. They contain amino acid residues that can hydrogen bond and are used to maintain structure for the active binding site. The hydrophobic region (Gly 361 and Gly 383) interacts with the phosphate chain. This will allow for more movement of the cations.		<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. The hydrophilic residues interact with the outside enviornment. They contain amino acid residues that can hydrogen bond and are used to maintain structure for the active binding site. The hydrophobic region (Gly 361 and Gly 383) interacts with the phosphate chain. This will allow for more movement of the cations.

-	<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this ~~view the black structures are the ACT molecules~~. ~~These are the~~ ligands of the ~~IMPDH protein~~.	+	<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. Ligands for this structure include GDP and G5P ions. The ligands of NAD, G5P, and GDP will form hydrogen and hydrophobic bonds between each other. When cations pass through they will interact with the phosphates.

	<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cysteine more reactive, which in turn induces binding.		<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cysteine more reactive, which in turn induces binding.

Garrett Leibow at 05:51, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 05:51:15 GMT

←Older revision		Revision as of 05:51, 9 December 2019
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	The <scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene> is important to get a more accurate representation of the amount of space the protein would take up. It better shows the interactions in the structure. In the image the light blue is the amino acid residues. The red dots represent water molecules. The orange is phosphorus. Lastly the blue is nitrogen.		The <scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene> is important to get a more accurate representation of the amount of space the protein would take up. It better shows the interactions in the structure. In the image the light blue is the amino acid residues. The red dots represent water molecules. The orange is phosphorus. Lastly the blue is nitrogen.

-	<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. ~~For this image purple represent polar molecules~~ and ~~grey represents~~ hydrophobic ~~molecules~~.	+	<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. The hydrophilic residues interact with the outside enviornment. They contain amino acid residues that can hydrogen bond and are used to maintain structure for the active binding site. The hydrophobic region (Gly 361 and Gly 383) interacts with the phosphate chain. This will allow for more movement of the cations.

	<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.		<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.
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	<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.		<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.

-	<scene name='82/823087/Impdh_composition/2'>IMPDH composition</scene>. ~~Brown represents a protein~~. ~~Red~~ represents ~~a RNA~~. ~~Green represents ligands~~.	+	<scene name='82/823087/Impdh_composition/2'>IMPDH composition</scene>. G5P and GDP ligands are shown in Pink. The green represents the anions that, during the intermediate step, function as ligands. Cations will travel through an active IMPDH.
-		+
	== '''Energy Transformation''' ==		== '''Energy Transformation''' ==

Garrett Leibow at 05:41, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 05:41:00 GMT

←Older revision		Revision as of 05:41, 9 December 2019
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	<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of <scene name='82/823087/Impdh_tertiary_structure/1'>tertiary structures</scene>. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.		<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of <scene name='82/823087/Impdh_tertiary_structure/1'>tertiary structures</scene>. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.

-	<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>~~. In the space filled view we can see~~ a ~~better~~ representation of ~~how much~~ space the protein would ~~actually~~ take up. In the image the ~~white~~ is the ~~protein as a whole and the~~ red dots represent ~~hydrogen bonds~~.	+	The <scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene> is important to get a more accurate representation of the amount of space the protein would take up. It better shows the interactions in the structure. In the image the light blue is the amino acid residues. The red dots represent water molecules. The orange is phosphorus. Lastly the blue is nitrogen.

	<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. For this image purple represent polar molecules and grey represents hydrophobic molecules.		<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. For this image purple represent polar molecules and grey represents hydrophobic molecules.
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	<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.		<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.

-	<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes ~~cystine~~ more reactive, which in turn induces binding.	+	<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cysteine more reactive, which in turn induces binding.

-	<scene name='82/823087/Impdh_triad_active_binding/5'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes ~~cystine~~ more reactive and binding is induced. In the image the ~~cystines~~ are in white. This is where binding would occur.	+	<scene name='82/823087/Impdh_triad_active_binding/5'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cysteine more reactive and binding is induced. In the image the cysteines are in white. This is where binding would occur. So for this image the cysteines that are made more reactive are shown in light green. Asp 259 (shown in red in this image) hydrogen bonds to ribose hydroxyls and Ser 315 (also shown in red) hydrogen bonds to ribose phosphate. Gly 383 (Shown in Light blue) interacts with NAD through hydrophobic interactions. Gly 361 (also light blue) binds to NAD through hydrophobic interactions as well.

	<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.		<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.

Garrett Leibow at 05:24, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 05:24:01 GMT

←Older revision		Revision as of 05:24, 9 December 2019
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	== '''Structural highlights and structure-function relationships''' ==		== '''Structural highlights and structure-function relationships''' ==

-	<scene name='82/823087/Impdh_secondary_structures/4'>IMPDH secondary structures</scene>.	+	In the <scene name='82/823087/Impdh_secondary_structures/4'>IMPDH secondary structures</scene>. Alpha and beta sheets are shown. The active site of the protein is located on the C-terminus end in the TIM barrel. This contains 8 beta sheets and 8 alpha helices.

-	<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of tertiary structures. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.	+	<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of <scene name='82/823087/Impdh_tertiary_structure/1'>tertiary structures</scene>. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.
-		+
-	~~<scene name='82/823087/Impdh_tertiary_structure/1'>IMPDH Tertiary strucure</scene>.~~	+

	<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>. In the space filled view we can see a better representation of how much space the protein would actually take up. In the image the white is the protein as a whole and the red dots represent hydrogen bonds.		<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>. In the space filled view we can see a better representation of how much space the protein would actually take up. In the image the white is the protein as a whole and the red dots represent hydrogen bonds.

Garrett Leibow at 05:13, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 05:13:54 GMT

←Older revision		Revision as of 05:13, 9 December 2019
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	<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of tertiary structures. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.		<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of tertiary structures. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.

-	IMPDH Tertiary strucure.	+	<scene name='82/823087/Impdh_tertiary_structure/1'>IMPDH Tertiary strucure</scene>.

	<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>. In the space filled view we can see a better representation of how much space the protein would actually take up. In the image the white is the protein as a whole and the red dots represent hydrogen bonds.		<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>. In the space filled view we can see a better representation of how much space the protein would actually take up. In the image the white is the protein as a whole and the red dots represent hydrogen bonds.

Garrett Leibow at 04:45, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 04:45:10 GMT

←Older revision		Revision as of 04:45, 9 December 2019
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	<scene name='82/823087/Impdh_secondary_structures/4'>IMPDH secondary structures</scene>.		<scene name='82/823087/Impdh_secondary_structures/4'>IMPDH secondary structures</scene>.

-	<scene name='82/823087/~~Impdh_quaternary_structure~~/2'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of tertiary structures. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.	+	<scene name='82/823087/Impdh_quat_structure/1'>IMPDH quaternary structure</scene>. These quaternary structures include tetramers, compacted and extended octamers, and multiunit complexes. These are created through multiple subunits of tertiary structures. They are formed and reinforced through hydrogen bonding, disulfide bonds, and hydrophobic interactions.
		+
		+	IMPDH Tertiary strucure.

	<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>. In the space filled view we can see a better representation of how much space the protein would actually take up. In the image the white is the protein as a whole and the red dots represent hydrogen bonds.		<scene name='82/823087/Impdh_space_fill/1'>IMPDH space filled</scene>. In the space filled view we can see a better representation of how much space the protein would actually take up. In the image the white is the protein as a whole and the red dots represent hydrogen bonds.

Garrett Leibow at 04:26, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 04:26:37 GMT

←Older revision		Revision as of 04:26, 9 December 2019
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	<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.		<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.

-	<scene name='82/823087/Impdh_triad_active_binding/4'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cystine more reactive and binding is induced. In the image the cystines are in white. This is where binding would occur.	+	<scene name='82/823087/Impdh_triad_active_binding/5'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cystine more reactive and binding is induced. In the image the cystines are in white. This is where binding would occur.

	<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.		<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.

Garrett Leibow at 03:28, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 03:28:07 GMT

←Older revision		Revision as of 03:28, 9 December 2019
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	<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.		<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.

-	<scene name='82/823087/Impdh_triad_active_binding/2'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cystine more reactive and binding is induced. In the image the cystines are in white. This is where binding would occur.	+	<scene name='82/823087/Impdh_triad_active_binding/4'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cystine more reactive and binding is induced. In the image the cystines are in white. This is where binding would occur.

	<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.		<scene name='82/823087/Impdh_charge/2'>IMPDH charge</scene>. IMPDH has no significant charge since it is found in physiological environments. Positively and negatively charged amino acids play a part in intermediate covalent binding steps<ref>PMID: 31416831</ref>.

Garrett Leibow at 03:12, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 03:12:48 GMT

←Older revision		Revision as of 03:12, 9 December 2019
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	<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.		<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.

-	<scene name='82/823087/Impdh_triad/5'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.	+	<scene name='82/823087/Impdh_triad/6'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.

	<scene name='82/823087/Impdh_triad_active_binding/2'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cystine more reactive and binding is induced. In the image the cystines are in white. This is where binding would occur.		<scene name='82/823087/Impdh_triad_active_binding/2'>IMPDH active binding site</scene>. The active binding cite is where the binding takes place after the catalytic triad makes cystine more reactive and binding is induced. In the image the cystines are in white. This is where binding would occur.

Garrett Leibow at 02:41, 9 December 2019

Garrett Leibow — Mon, 09 Dec 2019 02:41:17 GMT

←Older revision		Revision as of 02:41, 9 December 2019
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	<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. For this image purple represent polar molecules and grey represents hydrophobic molecules.		<scene name='82/823087/Impdh_hydrophobicity/4'>IMPDH hydrophobicity view</scene>. For this image purple represent polar molecules and grey represents hydrophobic molecules.

-	<scene name='82/823087/Impdh_ligand_view/4'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.	+	<scene name='82/823087/Impdh_ligand_view/5'>IMPDH ligand view</scene>. In this view the black structures are the ACT molecules. These are the ligands of the IMPDH protein.

	<scene name='82/823087/Impdh_triad/5'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.		<scene name='82/823087/Impdh_triad/5'>IMPDH triad</scene>. The IMPDH triad includes Arg (320), Asn (306), and Asp (272). This is represented by the solid black structures in the image. This triad is important as it makes cystine more reactive, which in turn induces binding.