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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). Mon . "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 = {Mon Jul 02 00:00:00 EDT 2012},
month = {Mon Jul 02 00:00:00 EDT 2012}
}