2juk
From Proteopedia
(New page: 200px<br /><applet load="2juk" size="350" color="white" frame="true" align="right" spinBox="true" caption="2juk" /> '''guanidino neomycin B recognition of an HIV-1...) |
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==Overview== | ==Overview== | ||
| - | Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The | + | Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site. |
==About this Structure== | ==About this Structure== | ||
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Guanidinoneomycin B recognition of an HIV-1 RNA helix., Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE, Chembiochem. 2008 Jan 4;9(1):93-102. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18058789 18058789] | Guanidinoneomycin B recognition of an HIV-1 RNA helix., Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE, Chembiochem. 2008 Jan 4;9(1):93-102. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18058789 18058789] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Butcher, S | + | [[Category: Butcher, S E.]] |
[[Category: Elson-Schwab, L.]] | [[Category: Elson-Schwab, L.]] | ||
[[Category: Niccolai, N.]] | [[Category: Niccolai, N.]] | ||
| - | [[Category: Staple, D | + | [[Category: Staple, D W.]] |
[[Category: Tor, Y.]] | [[Category: Tor, Y.]] | ||
[[Category: Venditti, V.]] | [[Category: Venditti, V.]] | ||
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[[Category: rna-ligand interactions]] | [[Category: rna-ligand interactions]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:05:56 2008'' |
Revision as of 16:05, 21 February 2008
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guanidino neomycin B recognition of an HIV-1 RNA helix
Overview
Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.
About this Structure
2JUK is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Guanidinoneomycin B recognition of an HIV-1 RNA helix., Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE, Chembiochem. 2008 Jan 4;9(1):93-102. PMID:18058789
Page seeded by OCA on Thu Feb 21 18:05:56 2008
