ArticleThe journal of physical chemistry. B2011
Theoretical assessment of the oligolysine model for ionic interactions in protein-DNA complexes.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 33 citations in OpenAlex.
- Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation.Biopolymers · 2024Article
- Sequence Properties of An Intramolecular Interaction That Inhibits p53 DNA Binding.Biomolecules · 2022Article
- Multivalent Ion-Mediated Attraction between Like-Charged Colloidal Particles: Nonmonotonic Dependence on the Particle Charge.ACS omega · 2021Article
- Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins.Biophysical journal · 2021Article
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- Role of Salt Valency in the Switch of H-NS Proteins between DNA-Bridging and DNA-Stiffening Modes.Biophysical journal · 2018Article
- Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AHJournal of the American Chemical Society · 2017Article
- Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs.Nucleic acids research · 2017Article
- The Missing Electrostatic Interactions Between DNA Substrate and Sulfolobus solfataricus DNA Photolyase: What is the Role of Charged Amino Acids in Thermophilic DNA Binding Proteins?The journal of physical chemistry. B · 2016Article
- Physicochemical Properties of Ion Pairs of Biological Macromolecules.Biomolecules · 2015Review
- Problems of robustness in Poisson-Boltzmann binding free energies.Journal of chemical theory and computation · 2015Article
- Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments.The Journal of chemical physics · 2014Article
- Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation.The Journal of chemical physics · 2014Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The observed salt dependence of charged ligand binding to polyelectrolytes, such as proteins to DNA or antithrombin to heparin, is often interpreted by means of the "oligolysine model." We review this model as derived entirely within the framework of the counterion condensation theory of polyelectrolytes with no introduction of outside assumptions. We update its comparison with experimental data on the structurally simple systems for which it was originally intended. We then compute the salt dependence of the binding free energy for a variety of protein-DNA complexes with nonlinear Poisson-Boltzmann (NLPB) simulation methods. The results of the NLPB calculations confirm the central prediction of the oligolysine model that the net charge density of DNA remains invariant to protein binding. Specifically, when a cationic protein residue penetrates the layer of counterions condensed on DNA, a counterion is released to bulk solution, and when an anionic protein residue penetrates the condensed counterion layer, an additional counterion is condensed from bulk solution. We also conclude, however, that the cumulative effect of charged protein residues distant from the binding interface makes a significant contribution to the salt dependence of binding, an observation not accommodated by the oligolysine model.
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