1m6f
From Proteopedia
(New page: 200px<br /><applet load="1m6f" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m6f, resolution 1.78Å" /> '''Strong Binding in th...) |
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| - | [[Image:1m6f.gif|left|200px]]<br /><applet load="1m6f" size=" | + | [[Image:1m6f.gif|left|200px]]<br /><applet load="1m6f" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1m6f, resolution 1.78Å" /> | caption="1m6f, resolution 1.78Å" /> | ||
'''Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove'''<br /> | '''Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove'''<br /> | ||
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| + | ==Overview== | ||
| + | A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA. | ||
==About this Structure== | ==About this Structure== | ||
| - | 1M6F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CGQ and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1M6F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CGQ:'>CGQ</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M6F OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Hamelberg, D.]] | [[Category: Hamelberg, D.]] | ||
[[Category: Joubert, A.]] | [[Category: Joubert, A.]] | ||
| - | [[Category: Lee, M | + | [[Category: Lee, M P.H.]] |
[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
[[Category: Nguyen, B.]] | [[Category: Nguyen, B.]] | ||
| - | [[Category: Wilson, W | + | [[Category: Wilson, W D.]] |
[[Category: CGQ]] | [[Category: CGQ]] | ||
[[Category: MG]] | [[Category: MG]] | ||
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[[Category: nucleic acids]] | [[Category: nucleic acids]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:52:00 2008'' |
Revision as of 11:52, 21 February 2008
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Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove
Overview
A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.
About this Structure
1M6F is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove., Nguyen B, Lee MP, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD, J Am Chem Soc. 2002 Nov 20;124(46):13680-1. PMID:12431090
Page seeded by OCA on Thu Feb 21 13:52:00 2008
Categories: Protein complex | Bailly, C. | Brun, R. | Hamelberg, D. | Joubert, A. | Lee, M P.H. | Neidle, S. | Nguyen, B. | Wilson, W D. | CGQ | MG | Dna-drug complex | Double helix | Minor groove binder | Nucleic acids
