Sandbox Reserved 433: Difference between revisions

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==Additional Features==

The GSK-3β and '''staurosporine''' complex shows <scene name='48/483890/Additional_feature_v6/5'>~~distint~~ hydrogen bonding (H-bond) interaction</scene>.

There are three kinds of interactions in the GSK-3β and staurosporine complex, including: direct H-bonds, water-mediated polar interactions and hydrophobic interactions .The GSK-3β and '''staurosporine''' complex shows <scene name='48/483890/Additional_feature_v6/5'>distinct hydrogen bonding (H-bond) interaction</scene>.

~~It is observed that there are direct H-bonds, water-mediated polar interactions and hydrophobic interactions in the~~ ~~GSK-3β and staurosporine complex.~~

There are only two direct H-bonds, and they are observed between

* The '''carbonyl oxygen''' of Asp 133 and '''N1 (nitrogen)''' of staurosporine. The length of this hydrogen bond is 2.93 Å.

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Besides direct H-bond, the water-mediated polar interactions are observed between the '''carbonyl oxygen''' of Gln 185 and '''N4 (nitrogen)''' of the glycosidic ring.

The typical hydrogen bond (H-bond) is categorized to be between 2.2 and 4.0 Å <ref name="~~rasmol~~">Jeffrey, George A. An introduction to hydrogen bonding; Oxford University Press: Oxford, 1997</ref>.

The typical hydrogen bond (H-bond) is categorized to be between 2.2 and 4.0 Å <ref name="book">Jeffrey, George A. An introduction to hydrogen bonding; Oxford University Press: Oxford, 1997</ref>.

Since many pdb files lack hydrogen atoms, a significant H-bond can be considered when donor-acceptor distance are probably 3.5 Å.

Since many pdb files lack hydrogen atoms, a significant H-bond can be considered when donor-acceptor distance are probably 3.5 Å <ref name="book" />.

However, the length between between Gln 185 and Strauroporine is 4.47 Å which surpasses typical H-bond distance; therefore, it forms a water mediated polar interaction between these atoms instead of direct H-bond

However, the length between between Gln 185 and Strauroporine is 4.47 Å which surpasses typical H-bond distance; therefore, it forms a water mediated polar interaction between these atoms instead of direct H-bond<ref name="paper">PMID: 14529625</ref>.

This is a unique interaction to the GSK-3β and staurosporine complex, since other protein kinase (e.g. CDK2, Chk1, LCK, PKA) -staurosporine complexes show direct H-bond interaction between two moieties.

There is a significant number of <scene name='48/483890/Additional_feature_v4/2'>hydrophobic interaction</scene> in the GSK-3β and staurosporine complex; to be more specific, this complex buries 891 Å2 surface area. The '''hydrophobic residues''' significantly interact with the fuzed carbazole moiety of saurosporine.

There is a significant number of <scene name='48/483890/Additional_feature_v4/2'>hydrophobic interaction</scene> in the GSK-3β and staurosporine complex; to be more specific, this complex buries 891 Å2 surface area<ref name="paper" />. The '''hydrophobic residues''' significantly interact with the fuzed carbazole moiety of saurosporine.

==Quiz Question 1==

GSK-3 beta has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3 beta complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3 beta complex. This is because, in a GSK-3 beta complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding.

GSK-3 beta has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3 beta complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3 beta complex. This is because, in a GSK-3 beta complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding<ref name="paper" />.

What type of bonding does GSK-3 beta exhibit with staurosporine, and which of its residues form this type of bond? A green screen of the complex as well as a lewis structure of the staurosporine molecule are found below, if needed.

Sandbox Reserved 433: Difference between revisions

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@@ Line 25: / Line 25: @@
 ==Additional Features==
-The GSK-3β and <span style="color:yellow">'''staurosporine'''</span> complex shows <scene name='48/483890/Additional_feature_v6/5'>distint hydrogen bonding (H-bond) interaction</scene>.
+There are three kinds of interactions in the  GSK-3β and staurosporine complex, including: direct H-bonds, water-mediated polar interactions and hydrophobic interactions .The GSK-3β and <span style="color:yellow">'''staurosporine'''</span> complex shows <scene name='48/483890/Additional_feature_v6/5'>distinct hydrogen bonding (H-bond) interaction</scene>.
-It is observed that there are direct H-bonds, water-mediated polar interactions and hydrophobic interactions in the  GSK-3β and staurosporine complex.
 There are only two direct H-bonds, and they are observed between
 * The <span style="color:red">'''carbonyl oxygen'''</span> of Asp 133 and <span style="color:blue">'''N<sup>1</sup> (nitrogen)'''</span> of staurosporine. The length of this hydrogen bond is 2.93 Å.
@@ Line 32: / Line 32: @@
 Besides direct H-bond, the water-mediated polar interactions are observed between the <span style="color:red">'''carbonyl oxygen'''</span> of Gln 185 and <span style="color:blue">'''N<sup>4</sup> (nitrogen)'''</span> of the glycosidic ring.
-The typical hydrogen bond (H-bond) is categorized to be between 2.2 and 4.0 Å <ref name="rasmol">Jeffrey, George A. An introduction to hydrogen bonding; Oxford University Press: Oxford, 1997</ref>.
+The typical hydrogen bond (H-bond) is categorized to be between 2.2 and 4.0 Å <ref name="book">Jeffrey, George A. An introduction to hydrogen bonding; Oxford University Press: Oxford, 1997</ref>.
-Since many pdb files lack hydrogen atoms, a significant H-bond can be considered when donor-acceptor distance are probably 3.5 Å.
+Since many pdb files lack hydrogen atoms, a significant H-bond can be considered when donor-acceptor distance are probably 3.5 Å <ref name="book" />.
-However, the length between between Gln 185 and Strauroporine is 4.47 Å which surpasses typical H-bond distance; therefore, it forms a water mediated polar interaction between these atoms instead of direct H-bond
+However, the length between between Gln 185 and Strauroporine is 4.47 Å which surpasses typical H-bond distance; therefore, it forms a water mediated polar interaction between these atoms instead of direct H-bond<ref name="paper">PMID: 14529625</ref>.
 This is a unique interaction to the GSK-3β and staurosporine complex, since other protein kinase  (e.g. CDK2, Chk1, LCK, PKA) -staurosporine complexes show direct H-bond interaction  between two moieties.
-There is a significant number of  <scene name='48/483890/Additional_feature_v4/2'>hydrophobic interaction</scene> in the GSK-3β and staurosporine complex; to be more specific,  this complex buries  891 Å<sup>2</sup> surface area. The <span style="color:pink">'''hydrophobic residues'''</span> significantly interact with the fuzed carbazole moiety of saurosporine.
+There is a significant number of  <scene name='48/483890/Additional_feature_v4/2'>hydrophobic interaction</scene> in the GSK-3β and staurosporine complex; to be more specific,  this complex buries  891 Å<sup>2</sup> surface area<ref name="paper" />. The <span style="color:pink">'''hydrophobic residues'''</span> significantly interact with the fuzed carbazole moiety of saurosporine.
 ==Quiz Question 1==
-GSK-3 beta has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3 beta complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3 beta complex. This is because, in a GSK-3 beta complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding.
+GSK-3 beta has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3 beta complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3 beta complex. This is because, in a GSK-3 beta complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding<ref name="paper" />.
 What type of bonding does GSK-3 beta exhibit with staurosporine, and which of its residues form this type of bond? A green screen of the complex as well as a lewis structure of the staurosporine molecule are found below, if needed.