ArticleThe journal of physical chemistry. B2008
Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.
Article in The journal of physical chemistry. B, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 23 citations in OpenAlex.
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Electrostatic effects on the folding stability of FKBP12.Protein engineering, design & selection : PEDS · 2016Article
- Computational support for a scaffolding mechanism of centriole assembly.Scientific reports · 2016Article
- Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex.Protein science : a publication of the Protein Society · 2015Article
- PIBiophysical reviews · 2013Article
- Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?Communications in computational physics · 2013Article
- Intrinsic disorder: signaling via highly specific but short-lived association.Trends in biochemical sciences · 2012Article
- Automated prediction of protein association rate constants.Structure (London, England : 1993) · 2011Article
- Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines.Biophysical journal · 2011Article
- U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.Biopolymers · 2011Article
- Rate theories for biologists.Quarterly reviews of biophysics · 2010Review
- pH-dependent association of proteins. The test case of monoclonal antibody HyHEL-5 and its antigen hen egg white lysozyme.The journal of physical chemistry. B · 2009Article
- Dissection of the high rate constant for the binding of a ribotoxin to the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Fundamental aspects of protein-protein association kinetics.Chemical reviews · 2009Review
- Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method.Journal of chemical theory and computation · 2008Article
- On the Dielectric Boundary in Poisson-Boltzmann Calculations.Journal of chemical theory and computation · 2008Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We have developed a computational approach for predicting protein-protein association rates (Alsallaq and Zhou, Structure 2007, 15, 215). Here we expand the range of applicability of this approach to protein-RNA binding and report the first results for protein-RNA binding rates predicted from atomistic modeling. The system studied is the U1A protein and stem/loop II of the U1 small nuclear RNA. Experimentally it was observed that the binding rate is significantly reduced by increasing salt concentration while the dissociation changes little with salt concentration, and charges distant from the binding site make marginal contribution to the binding rate. These observations are rationalized. Moreover, predicted effects of salt and charge mutations are found to be in quantitative agreement with experimental results.
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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.