1d0u
From Proteopedia
(New page: 200px<br /><applet load="1d0u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d0u" /> '''SOLUTION STRUCTURE OF AN RNA BINDING SITE FO...) |
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| - | [[Image:1d0u.gif|left|200px]]<br /><applet load="1d0u" size=" | + | [[Image:1d0u.gif|left|200px]]<br /><applet load="1d0u" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d0u" /> | caption="1d0u" /> | ||
'''SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN'''<br /> | '''SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Phosphorothioate substitution-interference experiments, routinely used to | + | Phosphorothioate substitution-interference experiments, routinely used to stereospecifically identify phosphoryl oxygen sites that participate in RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on the untested assumption that substitution does not alter the conformation of the modified molecule from its biologically active state. Using NMR spectroscopy, we have tested this assumption by determining the structural effect of stereospecific phosphorothioate substitution at five positions in an RNA hairpin containing the binding site for bacteriophage MS2 capsid protein. At most sites, substitution has little or no effect, causing minor perturbations in the phosphate backbone and increasing the stacking among nucleotides in the hairpin loop. At one site, however, phosphorothioate substitution causes an unpaired adenine necessary for formation of the capsid protein-RNA complex to loop out of the RNA helix into the major groove. These results indicate that phosphorothioate substitution can substantially alter the conformation of RNA at positions of irregular secondary structure, complicating the use of substitution-interference experiments to study RNA structure and function. |
==About this Structure== | ==About this Structure== | ||
| - | 1D0U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1D0U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D0U OCA]. |
==Reference== | ==Reference== | ||
Phosphorothioate substitution can substantially alter RNA conformation., Smith JS, Nikonowicz EP, Biochemistry. 2000 May 16;39(19):5642-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10801314 10801314] | Phosphorothioate substitution can substantially alter RNA conformation., Smith JS, Nikonowicz EP, Biochemistry. 2000 May 16;39(19):5642-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10801314 10801314] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Nikonowicz, E | + | [[Category: Nikonowicz, E P.]] |
| - | [[Category: Smith, J | + | [[Category: Smith, J S.]] |
[[Category: bulged base]] | [[Category: bulged base]] | ||
[[Category: rna hairpin]] | [[Category: rna hairpin]] | ||
[[Category: stem-loop]] | [[Category: stem-loop]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:11:42 2008'' |
Revision as of 10:11, 21 February 2008
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SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
Overview
Phosphorothioate substitution-interference experiments, routinely used to stereospecifically identify phosphoryl oxygen sites that participate in RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on the untested assumption that substitution does not alter the conformation of the modified molecule from its biologically active state. Using NMR spectroscopy, we have tested this assumption by determining the structural effect of stereospecific phosphorothioate substitution at five positions in an RNA hairpin containing the binding site for bacteriophage MS2 capsid protein. At most sites, substitution has little or no effect, causing minor perturbations in the phosphate backbone and increasing the stacking among nucleotides in the hairpin loop. At one site, however, phosphorothioate substitution causes an unpaired adenine necessary for formation of the capsid protein-RNA complex to loop out of the RNA helix into the major groove. These results indicate that phosphorothioate substitution can substantially alter the conformation of RNA at positions of irregular secondary structure, complicating the use of substitution-interference experiments to study RNA structure and function.
About this Structure
1D0U is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Phosphorothioate substitution can substantially alter RNA conformation., Smith JS, Nikonowicz EP, Biochemistry. 2000 May 16;39(19):5642-52. PMID:10801314
Page seeded by OCA on Thu Feb 21 12:11:42 2008
