ArticleThe journal of physical chemistry. B2012
Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Disassembly of unstable RNA structures by an E. coli DEAD-box chaperone accelerates ribosome assembly.Nucleic acids research · 2025Article
- Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Exploration of nucleoprotein α-MoRE and XD interactions of Nipah and Hendra viruses.Journal of molecular modeling · 2018Article
- Article
- Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly.Biophysical journal · 2015Article
- Exploring the balance between folding and functional dynamics in proteins and RNA.International journal of molecular sciences · 2015Article
- Article
- Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.Biophysical journal · 2014Article
- Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Simulating movement of tRNA through the ribosome during hybrid-state formation.The Journal of chemical physics · 2013Article
- Specific contacts between protein S4 and ribosomal RNA are required at multiple stages of ribosome assembly.RNA (New York, N.Y.) · 2013Article
- Article
- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Assembly of the bacterial ribosomal small subunit (SSU) begins with the folding of the five-way junction upon interaction with the primary binding protein S4. This complex contains the largest contiguous molecular signature, which is a conserved feature in all bacterial 16S rRNAs. In a previous study, we used all-atom molecular dynamics simulations to demonstrate that the co-evolving signature in the N-terminus of S4 is intrinsically disordered and capable of accelerating the binding process through a fly casting mechanism. In this paper, comparisons between the all-atom MD simulations and FRET experiments identify multiple metastable conformations of the naked five-way junction without the presence of S4. Furthermore, we capture the simultaneous folding and binding of the five-way junction and r-protein S4 by use of a structure-based Gō potential implemented within the framework of the all-atom molecular dynamics CHARMM force field. Different folding pathways are observed for the refolding of the five-way junction upon partial binding of S4. Our simulations illustrate the complex nature of RNA folding in the presence of a protein binding partner and provide insight into the role of population shift and the induced fit mechanisms in the protein:RNA folding and binding process.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.