ArticleThe journal of physical chemistry letters2015
Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes.
Article in The journal of physical chemistry letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- The role of zinc finger linkers in zinc finger protein binding to DNA.Journal of computer-aided molecular design · 2021Article
- Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6.Physical chemistry chemical physics : PCCP · 2021Article
- Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.Biophysical chemistry · 2021Review
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes.Journal of biomolecular NMR · 2020Article
- Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family.Cell reports · 2020Article
- NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups.The journal of physical chemistry. B · 2020Article
- Detecting Counterion Dynamics in DNA-Protein Association.Angewandte Chemie (International ed. in English) · 2020Article
- Experimental Evidence of Solvent-Separated Ion Pairs as Metastable States in Electrostatic Interactions of Biological Macromolecules.The journal of physical chemistry letters · 2019Article
- Mobility of Histidine Side Chains Analyzed withThe journal of physical chemistry. B · 2019Article
- Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments.Physical chemistry chemical physics : PCCP · 2019Article
- NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics.Methods in enzymology · 2019Review
- NMR-based investigations into target DNA search processes of proteins.Methods (San Diego, Calif.) · 2018Review
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations.Journal of computer-aided molecular design · 2018Article
- Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States.Biochemistry · 2017Article
- A Unique and Simple Approach to Improve Sensitivity inMolecules (Basel, Switzerland) · 2017Article
- Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins.Nucleic acids research · 2017Article
- Article
- Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA.Biochemistry · 2016Article
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6 authors.
Funding
Abstract
Intermolecular ion pairs (salt bridges) are crucial for protein-DNA association. For two protein-DNA complexes, we demonstrate that the ion pairs of protein side-chain NH3+ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-μs molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP-SIP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins.
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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.