ArticleNucleic acids research2016
Changes in conformational dynamics of basic side chains upon protein-DNA association.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
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- Transient interactions modulate the affinity of NF-κB transcription factors for DNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular contacts in the Cren7-DNA complex: A quantitative investigation for electrostatic interaction.Biophysical journal · 2023Article
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- Observation of Arginine Side-Chain Motions Coupled to the Global Conformational Exchange Process in Deubiquitinase A.ACS omega · 2022Article
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- Heavy chain-only antibody genes in fish evolved to generate unique CDR3 repertoire.European journal of immunology · 2022Article
- Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA.Angewandte Chemie (International ed. in English) · 2021Article
- Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.Biophysical chemistry · 2021Review
- Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape?The journal of physical chemistry. B · 2020Article
- 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
- NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups.The journal of physical chemistry. B · 2020Article
- Nucleotide Binding Modes in a Motor Protein Revealed byChembiochem : a European journal of chemical biology · 2020Article
- Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges.Frontiers in immunology · 2020Review
- Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription.Biophysical journal · 2019Article
- Mobility of Histidine Side Chains Analyzed withThe journal of physical chemistry. B · 2019Article
- YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis.Nucleic acids research · 2019Article
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6 authors.
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Abstract
Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.
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