https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Noam+Gonen 2026-09-16T06:13:16Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348630 2015-01-17T16:25:12Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical &lt;scene name='Sandbox-test/Avidin_b-barrels/1'&gt;beta-barrel&lt;/scene&gt;. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer. <br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348629 2015-01-17T16:15:17Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer. <br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348626 2015-01-17T16:09:20Z

<p>Noam Gonen: Undo revision 2348624 by Noam Gonen (Talk)</p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer.<br /> <br /> '''Hydrophilic interactions in the binding site of avidin''' <br /> <br /> Ureido oxygen of the biotin molecule forms three hydrogen bonds with the side chains of Asn-12, Ser-16, and Tyr-33 of avidin forming a tetrahedral oxyanion. In addition, each of the two ureido nitrogens participates in a single hydrogen-bond interaction with Thr-35 and Asn-118. The biotin sulfur may interact with Thr-77. <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348624 2015-01-17T16:06:51Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer.<br /> <br /> '''Hydrophilic interactions in the binding site of avidin''' <br /> <br /> Ureido oxygen of the biotin molecule forms three hydrogen bonds with the side chains of Asn-12, Ser-16, and Tyr-33 of avidin forming a tetrahedral oxyanion. In addition, each of the two ureido nitrogens participates in a single hydrogen-bond interaction with Thr-35 and Asn-118. The biotin sulfur may interact with Thr-77. <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348623 2015-01-17T16:06:25Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer.<br /> <br /> '''Hydrophilic interactions in the binding site of avidin''' <br /> <br /> Ureido oxygen of the biotin molecule forms three hydrogen bonds with the side chains of Asn-12, Ser-16, and Tyr-33 of avidin forming a tetrahedral oxyanion. In addition, each of the two ureido nitrogens participates in a single hydrogen-bond interaction with Thr-35 and Asn-118. The biotin sulfur may interact with Thr-77. <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348622 2015-01-17T16:05:48Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer.<br /> <br /> '''Hydrophilic interactions in the binding site of avidin''' <br /> <br /> Ureido oxygen of the biotin molecule forms three hydrogen bonds with the side chains of Asn-12, Ser-16, and Tyr-33 of avidin forming a tetrahedral oxyanion. In addition, each of the two ureido nitrogens participates in a single hydrogen-bond interaction with Thr-35 and Asn-118. The biotin sulfur may interact with Thr-77. <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348621 2015-01-17T16:03:10Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> '''Hydrophobic residues in the binding site of avidin'''<br /> <br /> These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer. <br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348619 2015-01-17T16:00:49Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> ==Biotin binding ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348618 2015-01-17T15:59:03Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ &lt;math&gt;10−15 &lt;/math&gt; M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348617 2015-01-17T15:57:28Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ &lt;math&gt;10^-15&lt;/math&gt; M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348616 2015-01-17T15:55:57Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> '''Interaction 1-2'''<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> <br /> '''Interaction 1-3'''<br /> <br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348615 2015-01-17T15:55:21Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> '''Interaction 1-2''' <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> '''Interaction 1-3'''<br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> <br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348613 2015-01-17T15:54:13Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> == '''Interaction 1-2''' ==<br /> <br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> '''Interaction 1-3'''<br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348611 2015-01-17T15:53:31Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> <br /> ----<br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> '''Interaction 1-3'''<br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348610 2015-01-17T15:51:54Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> '''Interaction 1-3'''<br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> '''Interaction 1-4'''<br /> Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348609 2015-01-17T15:50:05Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> '''Interaction 1-3'''<br /> Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348608 2015-01-17T15:35:01Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> '''Interaction 1-3'''<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348607 2015-01-17T15:33:20Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> '''Interaction 1-2'''<br /> Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348605 2015-01-17T15:31:56Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Monomer- monomer interaction ==<br /> '''Interaction 1-2'''<br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348604 2015-01-17T15:29:07Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel. <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348603 2015-01-17T15:28:15Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. <br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Structure ==<br /> The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds.[2]<br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348588 2015-01-17T10:36:11Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds.[2]<br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> <br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348587 2015-01-17T10:33:17Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds.[2]<br /> &lt;StructureSection load='2avi' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Noam Gonen/Avidin'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348586 2015-01-17T10:24:45Z

<p>Noam Gonen: </p> <hr /> <div>== INTRODUCTION ==<br /> Avidin is a tetrameric or dimeric[1] biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds.[2]<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Noam Gonen/Avidin'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348585 2015-01-17T10:23:56Z

<p>Noam Gonen: </p> <hr /> <div><br /> == INTRODUCTION ==<br /> <br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Noam Gonen/Avidin'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348584 2015-01-17T10:23:19Z

<p>Noam Gonen: </p> <hr /> <div>'''INTRODUCTION'''<br /> == <br /> ----<br /> Headline text ==<br /> <br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Noam Gonen/Avidin'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=User:Noam_Gonen/Avidin&diff=2348583 2015-01-17T10:22:57Z

<p>Noam Gonen: New page: INTRODUCTION &lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&gt; This is a default text for your page &#039;&#039;&#039;Noam Gonen/Avidin&#039;&#039;&#039;. Click above ...</p> <hr /> <div>INTRODUCTION<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Noam Gonen/Avidin'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340849 2015-01-13T20:46:49Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1ema' size='340' side='right' caption='GFP(PDB entry [[1ema]]'<br /> <br /> <br /> <br /> == Introduction ==<br /> <br /> <br /> Green fluorescent protein ('''GFP'''), originally isolated from the jellyfish Aequorea victoria (PDB entry [[1ema]]), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340848 2015-01-13T20:42:38Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> <br /> == Introduction ==<br /> <br /> <br /> Green fluorescent protein ('''GFP'''), originally isolated from the jellyfish Aequorea victoria (PDB entry [[1ema]]), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340847 2015-01-13T20:41:22Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> <br /> == Introduction ==<br /> <br /> <br /> Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> <br /> <br /> <br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340846 2015-01-13T20:40:27Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> <br /> == Introduction ==<br /> <br /> <br /> Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> <br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340845 2015-01-13T20:39:46Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> <br /> == Introduction ==<br /> <br /> <br /> Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340844 2015-01-13T20:35:28Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> Exploring the Structure<br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Elizeu/sandbox/citocromo_c&diff=2340843 2015-01-13T20:34:18Z

<p>Noam Gonen: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.<br /> Exploring the Structure<br /> <br /> GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]<br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066048 2014-11-22T14:40:28Z

<p>Noam Gonen: </p> <hr /> <div>==example page for haemoglobin ==<br /> <br /> ==Cooperative binding of oxygen by haemoglobin==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/3'&gt;heme&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state. ‘&lt;ref&gt;PMID:9521756&lt;/ref&gt;’.<br /> &lt;/structuresction&gt;<br /> =references==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066047 2014-11-22T14:39:17Z

<p>Noam Gonen: </p> <hr /> <div>==example page for haemoglobin ==<br /> <br /> ==Cooperative binding of oxygen by haemoglobin==<br /> &lt;StructureSection load='1a00' size='200' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/3'&gt;heme&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state. ‘&lt;ref&gt;PMID:8703075&lt;/ref&gt;’.<br /> &lt;/structuresction&gt;<br /> =references==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066046 2014-11-22T14:38:27Z

<p>Noam Gonen: </p> <hr /> <div>==example page for haemoglobin ==<br /> <br /> ==Cooperative binding of oxygen by haemoglobin==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/3'&gt;heme&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state. ‘&lt;ref&gt;PMID:8703075&lt;/ref&gt;’.<br /> &lt;/structuresction&gt;<br /> =references==<br /> &lt;references/&gt;</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066045 2014-11-22T14:33:10Z

<p>Noam Gonen: </p> <hr /> <div>==example page for haemoglobin ==<br /> <br /> ==Cooperative binding of oxygen by haemoglobin==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/3'&gt;heme&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066024 2014-11-22T10:35:55Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> ==example page for haemoglobin==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/3'&gt;heme&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066021 2014-11-22T10:31:12Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> ==example page for haemoglobin==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/2'&gt;ligand&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066020 2014-11-22T10:28:37Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on &lt;scene name='60/609833/1/2'&gt;ligand&lt;/scene&gt; in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066019 2014-11-22T10:01:57Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1a00' size='300' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066018 2014-11-22T10:00:53Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1a00' size='350' side='right' caption='HUMAN BETA GLOBIN (PDB entry [[1a00]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066017 2014-11-22T09:58:31Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1a00' size='350' side='right' caption=' (PDB entry [[3rec]])' scene=''&gt;&lt;/StructureSection&gt;<br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066016 2014-11-22T09:56:02Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1a00]]) results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066015 2014-11-22T09:54:44Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1ema]]) results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066014 2014-11-22T09:53:46Z

<p>Noam Gonen: </p> <hr /> <div>== Cooperative binding of oxygen by haemoglobin ==<br /> <br /> The cooperative binding of oxygen by '''haemoglobin''' (pdb entry [[1GZX]]) results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066013 2014-11-22T09:51:03Z

<p>Noam Gonen: </p> <hr /> <div><br /> == Cooperative binding of oxygen by haemoglobin ==<br /> <br /> The cooperative binding of oxygen by haemoglobin results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066009 2014-11-22T09:47:45Z

<p>Noam Gonen: </p> <hr /> <div>The cooperative binding of oxygen by haemoglobin results from restraints on ligand binding in the T state. The unfavourable interactions made by the ligands at the haems destabilise the T state and favour the high affinity R state. The T &lt;==&gt; R equilibrium leads, in the presence of a ligand, to a rapid increase in the R state population and therefore generates cooperative binding. There is now considerable understanding of this phenomenon, but the interactions that reduce ligand affinity in the T state have not yet been fully explored, owing to the difficulties in preparing T state haemoglobin crystals in which all the subunits are oxygenated. A protocol has been developed to oxygenate deoxy T state adult human haemoglobin (HbA) crystals in air at 4 C at all four haems without significant loss of crystalline order. The X-ray crystal structure, determined to 2.1 A spacing, shows significant changes in the alpha and beta haem pockets as well as changes at the alpha(1)beta(2) interface in the direction of the R quaternary structure. Most of the shifts and deviations from deoxy T state HbA are similar to, but larger than, those previously observed in the T state met and other partially liganded T state forms. They provide clear evidence of haem-haem interaction in the T state.</div>

Noam Gonen https://proteopedia.org/index.php?title=Sandbox_888&diff=2066007 2014-11-22T09:44:29Z

<p>Noam Gonen: New page: ==Your Heading Here (maybe something like &#039;Structure&#039;)== &lt;StructureSection load=&#039;1stp&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Caption for this structure&#039; scene=&#039;&#039;&gt; This is a default text for you...</p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''&gt;<br /> This is a default text for your page '''Sandbox 888'''. Click above on '''edit this page''' to modify. Be careful with the &amp;lt; and &amp;gt; signs.<br /> You may include any references to papers as in: the use of JSmol in Proteopedia &lt;ref&gt;DOI 10.1002/ijch.201300024&lt;/ref&gt; or to the article describing Jmol &lt;ref&gt;PMID:21638687&lt;/ref&gt; to the rescue.<br /> <br /> == Function ==<br /> <br /> == Disease ==<br /> <br /> == Relevance ==<br /> <br /> == Structural highlights ==<br /> <br /> This is a sample scene created with SAT to &lt;scene name=&quot;/12/3456/Sample/1&quot;&gt;color&lt;/scene&gt; by Group, and another to make &lt;scene name=&quot;/12/3456/Sample/2&quot;&gt;a transparent representation&lt;/scene&gt; of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br /> <br /> &lt;/StructureSection&gt;<br /> == References ==<br /> &lt;references/&gt;</div>

Noam Gonen