ArticleProceedings of the National Academy of Sciences of the United States of America2003
The RNA-protein complex: direct probing of the interfacial recognition dynamics and its correlation with biological functions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation.Journal of molecular biology · 2017Article
- NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.The journal of physical chemistry letters · 2016Article
- HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N.Journal of bacteriology · 2015Article
- Native state conformational heterogeneity of HP35 revealed by time-resolved FRET.The journal of physical chemistry. B · 2012Article
- Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.RNA (New York, N.Y.) · 2010Article
- The Universal Plausibility Metric (UPM) & Principle (UPP).Theoretical biology & medical modelling · 2009Article
- Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.Nucleic acids research · 2009Article
- Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence.Biochemistry · 2007Article
- RNA-protein recognition: single-residue ultrafast dynamical control of structural specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Recognition modes of RNA tetraloops and tetraloop-like motifs by RNA-binding proteins.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
6 authors.
Funding
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Abstract
The N protein from bacteriophage lambda is a key regulator of transcription antitermination. It specifically recognizes a nascent mRNA stem loop termed boxB, enabling RNA polymerase to read through downstream terminators processively. The stacking interaction between Trp-18 of WT N protein and A7 of boxB RNA is crucial for efficient antitermination. Here, we report on the direct probing of the dynamics for this interfacial binding and the correlation of the dynamics with biological functions. Specifically, we examined the influence of structural changes in four peptides on the femtosecond dynamics of boxB RNA (2-aminopurine labeled in different positions), through mutations of critical residues of N peptide (residues 1-22). We then compare their in vivo (Escherichia coli) transcription antitermination activities with the dynamics. The results demonstrate that the RNA-peptide complexes adopt essentially two dynamical conformations with the time scale for interfacial interaction in the two structures being vastly different, 1 ps for the stacked structure and nanosecond for the unstacked one; only the weighted average of the two is detected in NMR by nuclear Overhauser effect experiments. Strikingly, the amplitude of the observed ultrafast dynamics depends on the identity of the amino acid residues that are one helical turn away from Trp-18 in the peptides and is correlated with the level of biological function of their respective full-length proteins.
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