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Title: Stacking interactions in PUF-RNA complexes

Abstract

Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to 'target' versus 'off-target' interactions, and thus be an important consideration in the design of proteins with new specificities.

Authors:
; ; ; ; ; ;  [1];  [2]
  1. NIH
  2. (
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1040892
Resource Type:
Journal Article
Resource Relation:
Journal Name: RNA; Journal Volume: 17; Journal Issue: 2011
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; AFFINITY; AMINO ACIDS; BIOCHEMISTRY; CHAINS; DESIGN; IN VIVO; MUTAGENESIS; PROTEINS; RESIDUES; RNA; SPECIFICITY; TARGETS

Citation Formats

Yiling Koh, Yvonne, Wang, Yeming, Qiu, Chen, Opperman, Laura, Gross, Leah, Tanaka Hall, Traci M, Wickens, Marvin, and UW). Stacking interactions in PUF-RNA complexes. United States: N. p., 2012. Web. doi:10.1261/rna.2540311.
Yiling Koh, Yvonne, Wang, Yeming, Qiu, Chen, Opperman, Laura, Gross, Leah, Tanaka Hall, Traci M, Wickens, Marvin, & UW). Stacking interactions in PUF-RNA complexes. United States. doi:10.1261/rna.2540311.
Yiling Koh, Yvonne, Wang, Yeming, Qiu, Chen, Opperman, Laura, Gross, Leah, Tanaka Hall, Traci M, Wickens, Marvin, and UW). 2012. "Stacking interactions in PUF-RNA complexes". United States. doi:10.1261/rna.2540311.
@article{osti_1040892,
title = {Stacking interactions in PUF-RNA complexes},
author = {Yiling Koh, Yvonne and Wang, Yeming and Qiu, Chen and Opperman, Laura and Gross, Leah and Tanaka Hall, Traci M and Wickens, Marvin and UW)},
abstractNote = {Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to 'target' versus 'off-target' interactions, and thus be an important consideration in the design of proteins with new specificities.},
doi = {10.1261/rna.2540311},
journal = {RNA},
number = 2011,
volume = 17,
place = {United States},
year = 2012,
month = 7
}
  • Seven new Cd(II) complexes consisting of different phenanthroline derivatives and organic acid ligands, formulated as [Cd(PIP){sub 2}(dnba){sub 2}] (1), [Cd(PIP)(ox)].H{sub 2}O (2), [Cd(PIP)(1,4-bdc)(H{sub 2}O)].4H{sub 2}O (3), [Cd(3-PIP){sub 2}(H{sub 2}O){sub 2}].4H{sub 2}O (4), [Cd{sub 2}(3-PIP){sub 4}(4,4'-bpdc)(H{sub 2}O){sub 2}].5H{sub 2}O (5), [Cd(3-PIP)(nip)(H{sub 2}O)].H{sub 2}O (6), [Cd{sub 2}(TIP){sub 4}(4,4'-bpdc)(H{sub 2}O){sub 2}].3H{sub 2}O (7) (PIP=2-phenylimidazo[4,5-f]1,10-phenanthroline, 3-PIP=2-(3-pyridyl)imidazo[4,5-f]1,10-phenanthroline, TIP=2-(2-thienyl)imidazo[4,5-f]1,10-phenanthroline, Hdnba=3,5-dinitrobenzoic acid, H{sub 2}ox=oxalic acid, 1,4-H{sub 2}bdc=benzene-1,4-dicarboxylic acid, 4,4'-H{sub 2}bpdc=biphenyl-4,4'-dicarboxylic acid, H{sub 2}nip=5-nitroisophthalic acid) have been synthesized under hydrothermal conditions. Complexes 1 and 4 possess mononuclear structures; complexes 5 and 7 are isostructural and have dinuclear structures; complexes 2 and 3 feature 1D chain structures; complex 6more » contains 1D double chain, which are further extended to a 3D supramolecular structure by {pi}-{pi} stacking and hydrogen bonding interactions. The N-donor ligands with extended {pi}-system and organic acid ligands play a crucial role in the formation of the final supramolecular frameworks. Moreover, thermal properties and fluorescence of 1-7 are also investigated. -- Graphical abstract: Seven new supramolecular architectures have been successfully isolated under hydrothermal conditions by reactions of different phen derivatives and Cd(II) salts together with organic carboxylate anions auxiliary ligands. Display Omitted Research highlights: {yields} Complexes 1-7 are 0D or 1D polymeric structure, the {pi}-{pi} stacking and H-bonding interactions extend the complexes into 3D supramolecular network. To our knowledge, systematic study on {pi}-{pi} stacking and H-bonding interactions in cadmium(II) complexes are still limited. {yields} The structural differences among the title complexes indicate the importance of N-donor chelating ligands for the creation of molecular architectures. {yields} The thermal and fluorescence properties of title complexes have also been reported.« less
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