Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

14.3K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.3K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.3K
4.3K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

62.3K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
62.3K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

19.0K
19.0K
Ligand Binding Sites02:40

Ligand Binding Sites

14.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.7K
Protein Networks02:26

Protein Networks

4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Cysteine thiol-to-sulfonate oxidation induces unfolding for the functional switching of the extracellular HMGB1 protein.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Improved NMR-based diffusion measurements for inorganic ions.

The Analyst·2026
Same author

Competition between Nucleic Acids and Intrinsically Disordered Regions within Proteins.

Accounts of chemical research·2025
Same author

Effects of Probe-Related Correlations on Local Electrostatic Potentials Around DNA.

Journal of computational chemistry·2025
Same author

Anisotropic Dynamics of Protein Side Chain NH<sub>2</sub> Groups Revealed through Analysis of <sup>2</sup>H and <sup>15</sup>N NMR Relaxation Rates.

The journal of physical chemistry letters·2025
Same author

Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules.

Journal of the American Chemical Society·2024

Related Experiment Video

Updated: Dec 10, 2025

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
08:07

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

2.0K

Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.

Binhan Yu1, B Montgomery Pettitt1, Junji Iwahara1

  • 1Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States.

Accounts of Chemical Research
|August 27, 2020
PubMed
Summary

Protein-nucleic acid binding relies on dynamic ionic interactions. Recent NMR studies reveal counterion release and ion pair transitions, crucial for molecular recognition and biological processes.

More Related Videos

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

377
Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

14.8K

Related Experiment Videos

Last Updated: Dec 10, 2025

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
08:07

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

2.0K
Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

377
Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

14.8K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • Protein-nucleic acid interactions are vital for cellular functions.
  • Electrostatic interactions, including salt bridges and counterion atmospheres, are critical for binding.
  • Limited experimental data existed on ion behavior in these processes until recently.

Purpose of the Study:

  • To investigate the dynamic nature of ionic interactions between proteins and nucleic acids.
  • To quantify counterion release during protein-nucleic acid association.
  • To understand the thermodynamic and kinetic roles of these interactions.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy for direct detection of counterion release.
  • Analysis of salt-concentration dependence of association constants.
  • Theoretical modeling and validation of ion mobility and interactions.

Main Results:

  • Direct detection of counterion release using NMR spectroscopy.
  • Quantification of the entropic impact of counterion release on binding thermodynamics.
  • Observation of rapid picosecond-to-nanosecond transitions in protein-nucleic acid ion pairs.
  • Differential behavior of arginine and lysine side chains at molecular interfaces.

Conclusions:

  • Dynamic ionic interactions, including counterion release and ion pair transitions, are fundamental to protein-nucleic acid recognition.
  • NMR spectroscopy provides quantitative insights into these dynamic processes.
  • Arginine and lysine side chains play distinct roles in mediating these interactions.