ArticleProceedings of the National Academy of Sciences of the United States of America2008
DEAD-box proteins can completely separate an RNA duplex using a single ATP.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 140 citations in OpenAlex.
- Key Points to Consider When Studying RNA Remodeling by Proteins.Methods in molecular biology (Clifton, N.J.) · 2027Review
- RNase E resolves toxic condensates by counteracting phase separation of Type II RhlB helicases.Nucleic acids research · 2026Article
- DEAD-box helicase intrinsically disordered domains and structural dynamics of HIV-1 RNA are required to reveal DDX3X catalytic efficiency.Nucleic acids research · 2025Article
- Role of DEAD/DEAH-box helicases in immunity, infection and cancers.Cell communication and signaling : CCS · 2025Review
- RNA Helicase DDX3 Interacts with the Capsid Protein of Hepatitis E Virus and Plays a Vital Role in the Viral Replication.Pathogens (Basel, Switzerland) · 2025Article
- High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p.Nature communications · 2025Article
- Specific catalytically impaired DDX3X mutants form sexually dimorphic hollow condensates.Nature communications · 2024Article
- NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity.Nature communications · 2024Article
- Regulation and mechanisms of action of RNA helicases.RNA biology · 2024Review
- Cellular functions of eukaryotic RNA helicases and their links to human diseases.Nature reviews. Molecular cell biology · 2023Review
- Measuring the impact of cofactors on RNA helicase activities.Methods (San Diego, Calif.) · 2022Article
- The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.Cell reports · 2022Article
- Attacking a DEAD problem: The role of DEAD-box ATPases in ribosome assembly and beyond.Methods in enzymology · 2022Article
- Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins.Methods in enzymology · 2022Article
- RNA folding and functions of RNA helicases in ribosome biogenesis.RNA biology · 2022Review
- DDX3X structural analysis: Implications in the pharmacology and innate immunity.Current research in immunology · 2022Review
- Article
- Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- DEAD-box RNA Helicase DDX3: Functional Properties and Development of DDX3 Inhibitors as Antiviral and Anticancer Drugs.Molecules (Basel, Switzerland) · 2020Review
- Approaches for measuring the dynamics of RNA-protein interactions.Wiley interdisciplinary reviews. RNA · 2020Review
28 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
DEAD-box proteins are ubiquitous in RNA metabolism and use ATP to mediate RNA conformational changes. These proteins have been suggested to use a fundamentally different mechanism from the related DNA and RNA helicases, generating local strand separation while remaining tethered through additional interactions with structured RNAs and RNA-protein (RNP) complexes. Here, we provide a critical test of this model by measuring the number of ATP molecules hydrolyzed by DEAD-box proteins as they separate short RNA helices characteristic of structured RNAs (6-11 bp). We show that the DEAD-box protein CYT-19 can achieve complete strand separation using a single ATP, and that 2 related proteins, Mss116p and Ded1p, display similar behavior. Under some conditions, considerably <1 ATP is hydrolyzed per separation event, even though strand separation is strongly dependent on ATP and is not supported by the nucleotide analog AMP-PNP. Thus, ATP strongly enhances strand separation activity even without being hydrolyzed, most likely by eliciting or stabilizing a protein conformation that promotes strand separation, and AMP-PNP does not mimic ATP in this regard. Together, our results show that DEAD-box proteins can disrupt short duplexes by using a single cycle of ATP-dependent conformational changes, strongly supporting and extending models in which DEAD-box proteins perform local rearrangements while remaining tethered to their target RNAs or RNP complexes. This mechanism may underlie the functions of DEAD-box proteins by allowing them to generate local rearrangements without disrupting the global structures of their targets.
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