ArticleJournal of the American Chemical Society2006
Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex.
Article in Journal of the American Chemical Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 55 citations in OpenAlex.
- Design, Synthesis, Antitumor Activity Evaluation, and Molecular Dynamics Simulation of Some 2-aminopyrazine Derivatives.Current computer-aided drug design · 2025Article
- Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM.Nucleic acids research · 2022Article
- High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants.Biomolecules · 2022Article
- Role of Position K+4 in the Phosphorylation and Dephosphorylation Reaction Kinetics of the CheY Response Regulator.Biochemistry · 2021Article
- Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding.International journal of molecular sciences · 2019Article
- Understanding the binding specificities of mRNA targets by the mammalian Quaking protein.Nucleic acids research · 2019Article
- Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.Scientific reports · 2017Article
- Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods.RNA biology · 2016Article
- Importance of the Linker Region in Matrix Metalloproteinase-1 Domain Interactions.RSC advances · 2016Article
- Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase.Protein science : a publication of the Protein Society · 2015Article
- A compare-and-contrast NMR dynamics study of two related RRMs: U1A and SNF.Biophysical journal · 2014Article
- Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 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
- Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.Biochemistry · 2011Article
- Induced fit or conformational selection for RNA/U1A folding.RNA (New York, N.Y.) · 2010Article
- Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.Nucleic acids research · 2009Article
- 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
- Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.Biophysical journal · 2007Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A complete understanding of gene expression relies on a comprehensive understanding of the protein-RNA recognition process. However, the study of protein-RNA recognition is complicated by many factors that contribute to both binding affinity and specificity, including structure, energetics, dynamical motions, and cooperative interactions. Several recent studies have suggested that energetic coupling between residues contributes to formation of the complex between the U1A protein and stem loop 2 of U1 snRNA as a consequence of a cooperative network of interactions. We have performed molecular dynamics simulations on the U1A-RNA complex, including explicit water and counterions, and analyzed the results based on the calculated positional cross-correlations of atomic fluctuations. The results indicate that cross-correlations calculated on a per residue basis agree well with the observed inter-residue cooperativity and predict that the networks identified to date may also be coupled into an extensive hyper-network that reflects the intrinsic rigidity of the RNA recognition motif. In addition, we report a comparison of the MD calculated correlations with the results of a positional covariance analysis based on the sequences of 330 RNA recognition motifs, including U1A. The calculated inter-residue cross-correlations agree very well with the results of the sites exhibiting positional covariance. Collectively, these results strongly support the hypothesis that collective fluctuations contribute to cooperativity and the corresponding observed thermodynamic coupling. Predictions of additional sites in U1A that may be involved in cooperative networks are advanced.
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