1fmn
From Proteopedia
(New page: 200px<br /><applet load="1fmn" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fmn" /> '''SOLUTION STRUCTURE OF FMN-RNA APTAMER COMPLE...) |
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'''SOLUTION STRUCTURE OF FMN-RNA APTAMER COMPLEX, NMR, 5 STRUCTURES'''<br /> | '''SOLUTION STRUCTURE OF FMN-RNA APTAMER COMPLEX, NMR, 5 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We report on a combined NMR-molecular dynamics calculation approach that | + | We report on a combined NMR-molecular dynamics calculation approach that has solved the solution structure of the complex of flavin mononucleotide (FMN) bound to the conserved internal loop segment of a 35 nucleotide RNA aptamer identified through in vitro selection. The FMN-RNA aptamer complex exhibits exceptionally well-resolved NMR spectra that have been assigned following application of two, three and four-dimensional heteronuclear NMR techniques on samples containing uniformly 13C, 15N-labeled RNA aptamer in the complex. The assignments were aided by a new through-bond NMR technique for assignment of guanine imino and adenine amino protons in RNA loop segments. The conserved internal loop zippers up through the formation of base-pair mismatches and a base-triple on complex formation with the isoalloxazine ring of FMN intercalating into the helix between a G.G mismatch and a G.U.A base-triple. The recognition specificity is associated with hydrogen bonding of the uracil like edge of the isoalloxazine ring of FMN to the Hoogsteen edge of an adenine at the intercalation site. There is significant overlap between the intercalated isoalloxazine ring and its adjacent base-triple platform in the complex. The remaining conserved residues in the internal loop participate in two G.A mismatches in the complex. The zippered-up internal loop and flanking stem regions form a continuous helix with a regular sugar-phosphate backbone except at a non-conserved adenine, which loops out of the helix to facilitate base-triple formation. Our solution structure of the FMN-RNA aptamer complex is to our knowledge the first structure of an RNA aptamer complex and outlines folding principles that are common to other RNA internal and hairpin loops, and molecular recognition principles common to model self-replication systems in chemical biology. |
==About this Structure== | ==About this Structure== | ||
| - | 1FMN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with FMN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1FMN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=FMN:'>FMN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FMN OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Fiala, R.]] | [[Category: Fiala, R.]] | ||
[[Category: Live, D.]] | [[Category: Live, D.]] | ||
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
| - | [[Category: Suri, A | + | [[Category: Suri, A K.]] |
[[Category: FMN]] | [[Category: FMN]] | ||
[[Category: base pair mismatches]] | [[Category: base pair mismatches]] | ||
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[[Category: fmn-rna complex]] | [[Category: fmn-rna complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:40:16 2008'' |
Revision as of 10:40, 21 February 2008
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SOLUTION STRUCTURE OF FMN-RNA APTAMER COMPLEX, NMR, 5 STRUCTURES
Overview
We report on a combined NMR-molecular dynamics calculation approach that has solved the solution structure of the complex of flavin mononucleotide (FMN) bound to the conserved internal loop segment of a 35 nucleotide RNA aptamer identified through in vitro selection. The FMN-RNA aptamer complex exhibits exceptionally well-resolved NMR spectra that have been assigned following application of two, three and four-dimensional heteronuclear NMR techniques on samples containing uniformly 13C, 15N-labeled RNA aptamer in the complex. The assignments were aided by a new through-bond NMR technique for assignment of guanine imino and adenine amino protons in RNA loop segments. The conserved internal loop zippers up through the formation of base-pair mismatches and a base-triple on complex formation with the isoalloxazine ring of FMN intercalating into the helix between a G.G mismatch and a G.U.A base-triple. The recognition specificity is associated with hydrogen bonding of the uracil like edge of the isoalloxazine ring of FMN to the Hoogsteen edge of an adenine at the intercalation site. There is significant overlap between the intercalated isoalloxazine ring and its adjacent base-triple platform in the complex. The remaining conserved residues in the internal loop participate in two G.A mismatches in the complex. The zippered-up internal loop and flanking stem regions form a continuous helix with a regular sugar-phosphate backbone except at a non-conserved adenine, which loops out of the helix to facilitate base-triple formation. Our solution structure of the FMN-RNA aptamer complex is to our knowledge the first structure of an RNA aptamer complex and outlines folding principles that are common to other RNA internal and hairpin loops, and molecular recognition principles common to model self-replication systems in chemical biology.
About this Structure
1FMN is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Molecular recognition in the FMN-RNA aptamer complex., Fan P, Suri AK, Fiala R, Live D, Patel DJ, J Mol Biol. 1996 May 10;258(3):480-500. PMID:8642604
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