Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch

Noeske, J.; Buck, Janina; Fürtig, Boris; Nasiri, Hamid R.; Schwalbe, Harald; Wöhnert, Jens

doi:10.1093/nar/gkl1094

Cited by 152 publications

(211 citation statements)

References 39 publications

(71 reference statements)

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“…In addition, the line widths of the same hydrogens were determined for hypoxanthine in the presence of the adeninesensing riboswitch aptamer domain (ASR apt ) of B. subtilis pbuEmRNA. The ASR apt is similar to GSR apt , both in sequence and tertiary structure (19,31). However, ASR apt contains a U residue at position 74, but the same position is occupied by a C residue in GSR apt .…”

Section: A Low-affinity Ligand-binding Event Precedes the Folding Towmentioning

confidence: 93%

“…In contrast, the loop-loop interactions between L2 and L3 (Fig. 2) are present in the ligand-free state (31). However, small chemical shift changes of the nucleotides that form the loops indicate variations in the vicinity of this structural element on ligand binding.…”

Section: A Low-affinity Ligand-binding Event Precedes the Folding Towmentioning

confidence: 94%

“…The photolabile protecting group blocks the Watson-Crick site of the purine ligand known to be essential for ligand recognition and binding to the RNA. Based on the imino proton assignment of GSR apt (31), the 1 H-NMR spectrum of the RNA in the presence of DMNPE-hypoxanthine before photolysis indicated that formation of the RNA-ligand complex is completely suppressed. In contrast, in the time series of NMR spectra recorded after laser irradiation, imino proton signals appeared with increasing intensity representing the ligand-bound state after folding of the RNA, whereas signals corresponding to the ligand-free state decreased ( Fig.…”

Section: Two-mentioning

confidence: 99%

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Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Buck

Fürtig²,

Noeske³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

131

140

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spectroscopy ͉ riboswitches ͉ dynamics ͉ purine ͉ caged compound S tructural transitions of proteins and RNA constitute an important aspect of cellular function and information transfer. In proteins, the kinetics of these structural transitions, mainly from an unfolded ensemble to a single unique folded state, can be investigated by hydrogen exchange experiments monitored by NMR spectroscopy (1). Such studies have profoundly influenced our understanding of protein-folding pathways. In hydrogen exchange experiments, labile hydrogen atoms become protected against exchange with the bulk solvent during folding. This acquired exchange protection indicates formation of a persistent structure at atomic resolution. Incorporation of structural information derived from exchange experiments into molecular dynamics (MD) simulations (2), including data from methods exhibiting time and atomic resolution together with -value analysis (3) derived from mutational work, has provided detailed structural information of intermediates populated during folding.RNA molecules can adopt a variety of secondary and tertiary conformations (4, 5). In general, the energetic difference between alternate RNA conformations is very small, and the equilibrium distribution is strongly affected through the binding of proteins (6), ions (7), or small metabolites (8-10), or by structural modifications (11). Alternate RNA structures are stabilized by different Watson-Crick base-pairing interactions (12). To date, RNA folding has been investigated by using x-ray footprinting (13), oligonucleotide hybridization, and classical biochemical methods in conjunction with mutational data (14). Although hydrogen exchange rates can be used as reporters of RNA ground-state dynamics and stability (15-17), RNA hydrogen exchange experiments conducted in a pulse-chase manner fail in most cases because of the high intrinsic exchange rates observed even in folded RNA structures.Here, we report on ligand-induced conformational changes of an RNA at atomic resolution by using real-time NMR methods. We investigated the hypoxanthine-induced folding of the guanine-sensing riboswitch aptamer domain (GSR apt ) of the Bacillus subtilis xpt-pbuX operon (18). Riboswitch RNAs have emerged as an important example of macromolecular structural transitions that lead to transcriptional or translational regulation of protein expression induced through the specific binding of a metabolite (reviewed in refs. 19 and 20). Riboswitches are located in the 5Ј-untranslated region (5Ј-UTR) of bacterial mRNA and consist of a highly specific metabolite receptor region (aptamer domain) coupled to a 3Ј-downstream sequence (expression platform). Gene expression is thought to be modulated in response to conformational differences between the ligand-bound and ligand-free conformations of the aptamer domain (21). Crystal structures of the ligand-bound aptamer domains belonging to the class of purine riboswitches (guanineand adenine-sensing riboswitches) have revealed the presence of complex tertiary stru...

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Section: A Low-affinity Ligand-binding Event Precedes the Folding Towmentioning

confidence: 93%

Section: A Low-affinity Ligand-binding Event Precedes the Folding Towmentioning

confidence: 94%

Section: Two-mentioning

confidence: 99%

See 1 more Smart Citation

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Buck

Fürtig²,

Noeske³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

131

140

View full text Add to dashboard Cite

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“…The idea that ligand binding must be accompanied by a large conformational change was supported early on by in-line probing data [9] showing that aptamer domains are significantly less structured in the unbound state. Recent NMR studies have yielded detailed insights into the structure of the more disordered ligand free state of purine sensing aptamer domains [10][11][12]. These studies show that while the long-range loop-loop interactions that stabilize global structure are transiently preformed and reinforced by Mg 2+ binding, the ligand binding pocket is largely disordered in the absence of ligands.…”

Section: Probing Conformational Changes In Aptamer Domainsmentioning

confidence: 99%

RNA dynamics: it is about time

Al‐Hashimi

Walter

2008

Current Opinion in Structural Biology

298

295

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SummaryMany recently discovered RNA functions rely on highly complex multi-step conformational transitions that occur in response to an array of cellular signals. These dynamics accompany and guide, for example, RNA co-transcriptional folding, ligand sensing and signaling, site-specific catalysis in ribozymes, and the hierarchically ordered assembly of ribonucleoproteins. RNA dynamics are encoded by both the inherent properties of RNA structure, spanning many motional modes with a large range of amplitudes and timescales, and external trigger factors, ranging from proteins, nucleic acids, metal ions, metabolites, and vitamins to temperature and even directional RNA biosynthesis itself. Here, we review recent advances in our understanding of RNA dynamics as highlighted by biophysical tools.

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“…Most notably in this regard is an interaction between terminal loops of P2 and P3 helices for guanine and adenine riboswitches [33,39,46]. This is a stable motif, comprised of two base quadruples and a noncanonical base pair, which still adopts its configuration even when removed from the full context of the purine riboswitch [46]. However, despite its ligand-independent formation, it is required for association of the purine ligand to the RNA.…”

Section: Riboswitches Bind Ligands With High Selectivity Utilizing Unmentioning

confidence: 99%

Structural features of metabolite-sensing riboswitches

Wakeman

Winkler

Dann

2007

Trends in Biochemical Sciences

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Riboswitches, metabolite-sensing RNA elements found in untranslated regions of the transcripts they regulate, possess extensive tertiary structure to couple metabolite binding to genetic control. Herein, we discuss recently published structures from four riboswitch classes and compare these natural RNA structures to those of in vitro selected RNA aptamers, which bind similar ligands to those of the riboswitches. Additionally, we examine the glmS riboswitch, the first example of a ribozyme-based riboswitch. This RNA provides the latest twist in the riboswitch field and portends exciting advances in the coming years. Our knowledge of the mechanisms of genetic regulation by riboswitches has increased mightily in recent years and will continue to grow as new riboswitch classes and ligands are discovered and structurally characterized. KeywordsRNA structure; riboswitch; ribozyme; transcription attenuation; noncoding RNAs; posttranscriptional regulation; crystallography; NMR Riboswitches: Remnants of an ancient mode of genetic regulation?The "central dogma" states that information is stored as DNA, transcribed into RNA, and translated into proteins, which are traditionally thought to satisfy most cellular structural and catalytic requirements. Genetic control of these steps is believed to occur primarily through the action of regulatory proteins; however, the importance of noncoding RNAs in these processes has become increasingly appreciated in recent years [1]. In eubacterial organisms, regulatory RNAs can elicit control of gene expression through regulation of transcription attenuation, translation initiation [reviewed in 2,3], or mRNA stability [4]. These eubacterial regulatory RNAs function via diverse intermolecular (trans) or intramolecular (cis) mechanisms to regulate the target mRNA. Trans-acting regulatory RNAs interact with target mRNAs to control translation, mRNA stability, or transcription termination [reviewed in 5,6, 7], whereas others regulate gene expression through specific sequestration of RNA-binding proteins [8]. Cis-acting RNAs, which are the focus of this review, are located within untranslated regions (UTRs) of the mRNA transcript that they regulate. Genetic control by the latter RNA elements can be accomplished either through the sole action of the RNA molecule or in conjunction with recruited protein factors.A classic example of a cis-acting regulatory RNA is the transcription attenuation control of tryptophan biosynthesis genes in certain Gram-negative bacteria [9]. For this mechanism, the kinetics of translation of a short leader peptide dictates the conformational state of the overall 5′-UTR. Under tryptophan-depleted conditions the translating ribosome stalls at tryptophan codons within the leader peptide thereby allowing for formation of an antiterminator helix and [24-26; reviewed in 27,12]. Given their ability to function as sensitive sentinels for intracellular metabolites in a protein-independent manner, these RNAs are likely to require exquisite structural sophistication....

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Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch

Cited by 152 publications

References 39 publications

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

RNA dynamics: it is about time

Structural features of metabolite-sensing riboswitches

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