Globular Proteins: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, Alexander Berchansky

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 * <scene name='Globular_Proteins/Snap2/2'>SNAP-25</scene> - Domain N2 of synaptosomal-associated protein 25 (blue) from human bound to botulinum neurotoxin type A light chain (botox) from ''C. botulinum''. <scene name='Globular_Proteins/Snap/2'>Domain N2</scene> shown unbound but having the same conformation as the bound peptide.
 * <scene name='Globular_Proteins/Sara_sbd2/1'>SARA SBD</scene> - SMAD Anchor for Receptor Activation SMAD-Binding Domain bound to SMAD2 MH2 domain. SARA SBD is the domain of the receptor that binds SMAD, and thereby activates the transforming growth factor-beta signaling pathway.   <scene name='Globular_Proteins/Sara_sbd/2'>SMAD-binding domain</scene> shown unbound and displayed as cartoon but having the same conformation as the bound peptide.
-* <scene name='Globular_Proteins/Hif-1alpha2/2'>HIF-1alpha</scene> - Hypoxia-inducing factor 1α (C-terminal activation domain) bound to transcription activation zinc finger domain of CREB-binding protein. <scene name='Globular_Proteins/Hif-1alpha/2'>HIF</scene> shown unbound and displayed as cartoon but having the same conformation as the bound peptide.  The data of this model was generated NMR analysis of an aqueous solution of the peptides, and the analysis is rapid enough to distinguish the vibrations of the peptides so that more than one model is produced.  It is possible to animate these multiple model and simulate the vibrations of the peptides.  Notice that the vibrations are the greatest in the molecules where the attractive forces are the weakest.  Animate peptides: Unbound <scene name='Globular_Proteins/Hif-1alpha/1'>HIF</scene>; Bound <scene name='Globular_Proteins/Hif-1alpha2/1'>HIF</scene>
+* <scene name='Globular_Proteins/Hif-1alpha2/2'>HIF-1alpha</scene> - Hypoxia-inducing factor 1α (C-terminal activation domain) bound to transcription activation zinc finger domain of CREB-binding protein. <scene name='Globular_Proteins/Hif-1alpha/2'>HIF</scene> shown unbound and displayed as cartoon but having the same conformation as the bound peptide.  The data of this model was generated by NMR analysis of an aqueous solution of the peptides, and the analysis is rapid enough to distinguish the vibrations of the peptides so that more than one model is produced.  It is possible to animate these multiple model and simulate the vibrations of the peptides.  Notice that the vibrations are the greatest in the molecules where the attractive forces are the weakest.  Animate peptides: Unbound <scene name='Globular_Proteins/Hif-1alpha/1'>HIF</scene>; Bound <scene name='Globular_Proteins/Hif-1alpha2/1'>HIF</scene>
 * <scene name='Globular_Proteins/P27-cdk2/1'>p27-Cdk2-Cyclin A</scene> - Cyclin-dependent kinase 2 bound to its activator cyclin A and both bound with a fragment (blue) of p27 which is a kinase inhibitor.  Cyclin-dependent kinases have an important role in moving the cell from one phase of the cell cycle to another. <scene name='Globular_Proteins/P27-cdk2-2/2'>p27</scene> shown unbound but having the same conformation as the bound peptide.
 * <scene name='Globular_Proteins/P27_30-35/1'>p27 (30-35)-Cdk2-Cyclin A</scene> - different data file than the one above containing a smaller fragment of p27 bound to complex. <scene name='Globular_Proteins/P27_30-35-2/1'>p27</scene> shown unbound but having the same conformation as the bound peptide.  Compare the conformation of this small fragment to that of the yellow colored fragment shown unbound above.  Since the binding site is the same in both models when the peptides bind, regardless of the length, the peptides generate the same conformation.