ArticleJournal of structural biology2007
A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.
Article in Journal of structural biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 45 citations in OpenAlex.
- Statistical Coupling Analysis Predicts Correlated Motions in Dihydrofolate Reductase.The journal of physical chemistry. B · 2024Article
- "Conformational dynamics of C1r inhibitor proteins from Lyme disease and relapsing fever spirochetes".bioRxiv : the preprint server for biology · 2023Article
- Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction.Molecular diversity · 2023Article
- Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants.Computational and structural biotechnology journal · 2022Article
- Understanding the binding specificities of mRNA targets by the mammalian Quaking protein.Nucleic acids research · 2019Article
- Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.Biophysical journal · 2019Article
- Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.Scientific reports · 2017Article
- Article
- A compare-and-contrast NMR dynamics study of two related RRMs: U1A and SNF.Biophysical journal · 2014Article
- Binding affinity and cooperativity control U2B″/snRNA/U2A' RNP formation.Biochemistry · 2014Article
- Tertiary model of a plant cellulose synthase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Intrinsic flexibility of snRNA hairpin loops facilitates protein binding.RNA (New York, N.Y.) · 2012Article
- The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutSα-DNA complexes.Journal of biomolecular structure & dynamics · 2012Article
- Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation.PloS one · 2012Article
- Dynamical allosterism in the mechanism of action of DNA mismatch repair protein MutS.Biophysical journal · 2011Article
- U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.Biopolymers · 2011Article
- Induced fit or conformational selection for RNA/U1A folding.RNA (New York, N.Y.) · 2010Article
- Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements.The journal of physical chemistry. B · 2008Article
- Molecular dynamics simulations of nucleic acid-protein complexes.Current opinion in structural biology · 2008Review
- Recognition of essential purines by the U1A protein.BMC biochemistry · 2007Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Cooperative interactions play an important role in recognition and binding in macromolecular systems. In this study, we find that cross-correlated atomic fluctuations can be used to identify cooperative networks in a protein-RNA system. The dynamics of the RRM-containing protein U1A-stem loop 2 RNA complex have been calculated theoretically from a 10 ns molecular dynamics (MD) simulation. The simulation was analyzed by calculating the covariance matrix of all atomic fluctuations. These matrix elements are then presented in the form of a two-dimensional grid, which displays fluctuations on a per residue basis. The results indicate the presence of strong, selective cross-correlated fluctuations throughout the RRM in U1A-RNA. The atomic fluctuations correspond well with previous biophysical studies in which a multiplicity of cooperative networks have been reported and indicate that the various networks identified in separate individual experiments are fluctuationally correlated into a hyper-network encompassing most of the RRM. The calculated results also correspond well with independent results from a statistical covariance analysis of 330 aligned RRM sequences. This method has significant implications as a predictive tool regarding cooperativity in the protein-nucleic acid recognition 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.