ArticleProceedings of the National Academy of Sciences of the United States of America2009
Dissection of the high rate constant for the binding of a ribotoxin to the ribosome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
- Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design.Computational and structural biotechnology journal · 2020Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Rate Constants and Mechanisms of Protein-Ligand Binding.Annual review of biophysics · 2017Review
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
- Modeling protein association mechanisms and kinetics.Current opinion in structural biology · 2013Review
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
- PIBiophysical reviews · 2013Article
- Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?Communications in computational physics · 2013Article
- A method for computing association rate constants of atomistically represented proteins under macromolecular crowding.Physical biology · 2012Article
- Prediction and dissection of widely-varying association rate constants of actin-binding proteins.PLoS computational biology · 2012Article
- Charged and hydrophobic surfaces on the a chain of shiga-like toxin 1 recognize the C-terminal domain of ribosomal stalk proteins.PloS one · 2012Article
- A common model for cytokine receptor activation: combined scissor-like rotation and self-rotation of receptor dimer induced by class I cytokine.PLoS computational biology · 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
- Review
- A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.Journal of chemical theory and computation · 2011Article
- Diffusion and association processes in biological systems: theory, computation and experiment.BMC biophysics · 2011Article
- Rate theories for biologists.Quarterly reviews of biophysics · 2010Review
- Darwinian biophysics: electrostatics and evolution in the kinetics of molecular binding.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Restrictocin belongs to a family of site-specific ribonucleases that kill cells by inactivating the ribosome. The restrictocin-ribosome binding rate constant was observed to exceed 10(10) M(-1) s(-1). We have developed a transient-complex theory to model the binding rates of protein-protein and protein-RNA complexes. The theory predicts the rate constant as k(a) = k(a0) exp(-DeltaG(el)*/k(B)T), where k(a0) is the basal rate constant for reaching the transient complex, located at the outer boundary of the bound state, by random diffusion, and DeltaG(el)* is the average electrostatic interaction free energy of the transient complex. Here, we applied the transient-complex theory to dissect the high restrictocin-ribosome binding rate constant. We found that the binding rate of restrictocin to the isolated sarcin/ricin loop is electrostatically enhanced by approximately 300-fold, similar to results found in other protein-protein and protein-RNA complexes. The ribosome provides an additional 10,000-fold rate enhancement because of two synergistic mechanisms afforded by the distal regions of the ribosome. First, they provide additional electrostatic attraction with restrictocin. Second, they reposition the transient complex into a region where local electrostatic interactions of restrictocin with the sarcin/ricin loop are particularly favorable. Our calculations rationalize a host of experimental observations and identify a strategy for designing proteins that bind their targets with high speed.
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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.