193d: Difference between revisions

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[[Image:193d.gif|left|200px]]<br /><applet load="193d" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:193d.gif|left|200px]]<br /><applet load="193d" size="350" color="white" frame="true" align="right" spinBox="true"

caption="193d" />

'''SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX'''<br />

==Overview==

The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical, structure related to the antibiotic echinomycin which is known to, bisintercalate into DNA. Common features among these antibiotics include, two heterocyclic aromatic ring systems propagating from a cross-bridged, cyclic octadepsipeptide scaffold. We report on the solution structure of, the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex), based on a combined NMR-molecular dynamics study including intensity-based, refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the, duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6, and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are, wedge-shaped and unwound, with significant unwinding also observed at the, (C4-C5).(C4-G5) step bracketed between the intercalation sites. The, cross-bridged cyclic octadepsipeptide is positioned in the minor groove, with the methyl groups on its Ala and NMe-MCp residues directed towards, and making van der Waals contacts with the minor groove edge of the, duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala, backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e, to Ala-CO) account for the sequence specificity associated with complex, formation. The solution structure of the QN-DNA oligomer complex, which, contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA, oligomer complex, which contains Hoogsteen base-pairs on either side of, the bisintercalation site.

The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular dynamics study including intensity-based refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6 and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are wedge-shaped and unwound, with significant unwinding also observed at the (C4-C5).(C4-G5) step bracketed between the intercalation sites. The cross-bridged cyclic octadepsipeptide is positioned in the minor groove with the methyl groups on its Ala and NMe-MCp residues directed towards and making van der Waals contacts with the minor groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e to Ala-CO) account for the sequence specificity associated with complex formation. The solution structure of the QN-DNA oligomer complex, which contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA oligomer complex, which contains Hoogsteen base-pairs on either side of the bisintercalation site.

==About this Structure==

193D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CH3 and NBU as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].

193D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CH3:'>CH3</scene> and <scene name='pdbligand=NBU:'>NBU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].

==Reference==

Line 13:

[[Category: Protein complex]]

[[Category: Chen, H.]]

[[Category: Patel, D.J.]]

[[Category: Patel, D J.]]

[[Category: CH3]]

[[Category: NBU]]

Line 21:

[[Category: quinomycin]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:39:13 2008''

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-[[Image:193d.gif|left|200px]]<br /><applet load="193d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:193d.gif|left|200px]]<br /><applet load="193d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="193d" />
 '''SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX'''<br />
 ==Overview==
-The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical, structure related to the antibiotic echinomycin which is known to, bisintercalate into DNA. Common features among these antibiotics include, two heterocyclic aromatic ring systems propagating from a cross-bridged, cyclic octadepsipeptide scaffold. We report on the solution structure of, the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex), based on a combined NMR-molecular dynamics study including intensity-based, refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the, duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6, and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are, wedge-shaped and unwound, with significant unwinding also observed at the, (C4-C5).(C4-G5) step bracketed between the intercalation sites. The, cross-bridged cyclic octadepsipeptide is positioned in the minor groove, with the methyl groups on its Ala and NMe-MCp residues directed towards, and making van der Waals contacts with the minor groove edge of the, duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala, backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e, to Ala-CO) account for the sequence specificity associated with complex, formation. The solution structure of the QN-DNA oligomer complex, which, contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA, oligomer complex, which contains Hoogsteen base-pairs on either side of, the bisintercalation site.
+The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular dynamics study including intensity-based refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6 and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are wedge-shaped and unwound, with significant unwinding also observed at the (C4-C5).(C4-G5) step bracketed between the intercalation sites. The cross-bridged cyclic octadepsipeptide is positioned in the minor groove with the methyl groups on its Ala and NMe-MCp residues directed towards and making van der Waals contacts with the minor groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e to Ala-CO) account for the sequence specificity associated with complex formation. The solution structure of the QN-DNA oligomer complex, which contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA oligomer complex, which contains Hoogsteen base-pairs on either side of the bisintercalation site.
 ==About this Structure==
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CH3 and NBU as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].
+D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CH3:'>CH3</scene> and <scene name='pdbligand=NBU:'>NBU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Protein complex]]
 [[Category: Chen, H.]]
-[[Category: Patel, D.J.]]
+[[Category: Patel, D J.]]
 [[Category: CH3]]
 [[Category: NBU]]
@@ Line 21: / Line 21: @@
 [[Category: quinomycin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:12:08 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:39:13 2008''