ArticleJournal of molecular biology2007
Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model.
Article in Journal of molecular biology, 2007. 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, 41 citations in OpenAlex.
- 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 salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.International journal of molecular sciences · 2020Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Synthetic RNA recognition motifs that selectively recognize HIV-1 trans-activation response element hairpin RNA.ACS chemical biology · 2014Article
- Investigations of the binding of [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II) to DNA via various cross-linking modes.International journal of molecular sciences · 2013Article
- The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA.Nucleic acids research · 2013Article
- U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.Biopolymers · 2011Article
- Computational reverse-engineering of a spider-venom derived peptide active against Plasmodium falciparum SUB1.PloS one · 2011Article
- Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria.ACS chemical biology · 2009Article
- Conformationally restricted nucleotides as a probe of structure-function relationships in RNA.RNA (New York, N.Y.) · 2008Article
- Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements.The journal of physical chemistry. B · 2008Article
- Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.The journal of physical chemistry. B · 2008Article
- Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
An MM-GBSA computational protocol was used to investigate wild-type U1A-RNA and F56 U1A mutant experimental binding free energies. The trend in mutant binding free energies compared to wild-type is well-reproduced. Following application of a linear-response-like equation to scale the various energy components, the binding free energies agree quantitatively with observed experimental values. Conformational adaptation contributes to the binding free energy for both the protein and the RNA in these systems. Small differences in DeltaGs are the result of different and sometimes quite large relative contributions from various energetic components. Residual free energy decomposition indicates differences not only at the site of mutation, but throughout the entire protein. MM-GBSA and ab initio calculations performed on model systems suggest that stacking interactions may nearly, but not completely, account for observed differences in mutant binding affinities. This study indicates that there may be different underlying causes of ostensibly similar experimentally observed binding affinities of different mutants, and thus recommends caution in the interpretation of binding affinities and specificities purely by inspection.
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