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

14.9K
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...
14.9K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

20.2K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
20.2K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

2.9K
2.9K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

65.7K
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,...
65.7K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

19.7K
19.7K
Entropy02:39

Entropy

36.9K
Salt particles that have dissolved in water never spontaneously come back together in solution to reform solid particles. Moreover, a gas that has expanded in a vacuum remains dispersed and never spontaneously reassembles. The unidirectional nature of these phenomena is the result of a thermodynamic state function called entropy (S). Entropy is the measure of the extent to which the energy is dispersed throughout a system, or in other words, it is proportional to the degree of disorder of a...
36.9K

You might also read

Related Articles

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

Sort by
Same author

Physical interactions within the SIR heterochromatin complex potentiate inter-subunit communication and gene repression.

Cell reports·2026
Same author

EZH2 Serine 21 Phosphorylation Restrains Compact-State PRC2 Activation and H3K27me3 Propagation.

bioRxiv : the preprint server for biology·2026
Same author

Structure of the human HIRA histone chaperone with a nucleosome suggests a stepwise nucleosome assembly mechanism.

bioRxiv : the preprint server for biology·2026
Same author

Harmonizing Peak Matching Between Multidimensional NMR Spectra.

bioRxiv : the preprint server for biology·2026
Same author

RNA-induced PRC2 inhibition depends on the sequence of bound RNA.

Nature communications·2026
Same author

RNA-induced PRC2 inhibition depends on the sequence of bound RNA.

Research square·2025

Related Experiment Video

Updated: Mar 1, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

9.4K

Entropy in molecular recognition by proteins.

José A Caro1, Kyle W Harpole1, Vignesh Kasinath1

  • 1Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059.

Proceedings of the National Academy of Sciences of the United States of America
|June 7, 2017
PubMed
Summary
This summary is machine-generated.

Understanding protein-ligand interactions is key in molecular biology. This study reveals a quantitative link between protein dynamics and conformational entropy, crucial for high-affinity molecular recognition.

Keywords:
NMR relaxationbinding thermodynamicsentropymolecular recognitionprotein dynamics

More Related Videos

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.9K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K

Related Experiment Videos

Last Updated: Mar 1, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

9.4K
Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.9K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Molecular recognition by proteins is central to biological processes.
  • Quantifying entropic contributions to protein-ligand binding affinity remains challenging.
  • Previous NMR studies suggested a dynamical proxy for conformational entropy, but its broad applicability was unproven.

Purpose of the Study:

  • To establish a quantitative relationship between protein side-chain dynamics and conformational entropy in protein-ligand complexes.
  • To investigate the role and variability of conformational entropy in modulating binding affinity.
  • To refine the understanding of entropic contributions, including solvent and rotational-translational entropy, and water-protein interactions.

Main Methods:

  • Analysis of 28 diverse protein-ligand complexes.
  • Utilizing Nuclear Magnetic Resonance (NMR) relaxation measurements to probe fast side-chain motions.
  • Developing and applying a dynamical proxy (entropy meter) for conformational entropy.

Main Results:

  • A robust quantitative correlation was demonstrated between measures of fast side-chain motion and conformational entropy.
  • Conformational entropy can exert both favorable and unfavorable influences on binding affinity.
  • In a significant portion of cases, conformational entropy is essential for biologically relevant binding affinity.
  • The dynamical proxy refined estimations of solvent and rotational-translational entropy, and provided insights into specific water-protein interactions.

Conclusions:

  • Fast protein dynamics serve as a reliable proxy for quantifying conformational entropy in protein-ligand recognition.
  • Conformational entropy plays a critical and variable role in determining the affinity of protein-ligand interactions.
  • This work offers a unified perspective on the general importance of entropy in high-affinity molecular recognition.