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

Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

556
Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be...
556
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.7K
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...
14.7K
Drug Distribution: Plasma Protein Binding01:29

Drug Distribution: Plasma Protein Binding

8.8K
Drugs predominantly attach to plasma proteins, with only a small percentage remaining unbound. The unbound portion can be calculated as one minus the bound fraction. Acidic drugs form large, inactive complexes by reversibly binding to plasma albumin, which prevents them from diffusing across biological barriers. These drug-protein complexes act as reservoirs for the drugs. As the concentration of unbound drugs decreases, these complexes quickly dissociate to release the free drug, maintaining...
8.8K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

648
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
648
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

16.7K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
16.7K
Protein-Drug Binding: Mechanism and Kinetics01:16

Protein-Drug Binding: Mechanism and Kinetics

1.8K
Protein-drug binding refers to the interaction between drugs and proteins within the body. This binding process can occur intracellularly, involving drug interactions with enzymes or receptors within cells, or extracellularly, involving plasma proteins in the blood.
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...
1.8K

You might also read

Related Articles

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

Sort by
Same author

Conservation of Human IgSF Proteins Throughout Eukaryotic Evolution.

Genome biology and evolution·2026
Same author

Inhibition of HDAC7 reprograms the histone H3.3 landscape to induce heterochromatin spreading and DNA replication defects in cancer cells.

The Journal of biological chemistry·2025
Same author

Optimization of a sarbecovirus llama nanobody-antigen binding interface via a combined computational and phage display protein engineering approach.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

GliaTrap is a biodegradable, non-swelling and non-inflammatory hydrogel with tuned release of CXCL12 to attract migrating glioblastoma cells.

Scientific reports·2025
Same author

Artificial intelligence based assessment of clinical reasoning documentation: an observational study of the impact of the clinical learning environment on resident documentation quality.

BMC medical education·2025
Same author

Socioecological factors linked to co-occurring early childhood sleep health disparities and developmental outcomes: protocol for the sleep in preschoolers cross-sectional study.

BMJ open·2025
Same journal

Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics research.

PLoS computational biology·2026
Same journal

Mobility data resolution needed to inform predictive models of spatial epidemic spread from mobile phone data.

PLoS computational biology·2026
Same journal

DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.

PLoS computational biology·2026
Same journal

Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.

PLoS computational biology·2026
Same journal

Optimized phenotype definitions boost GWAS power.

PLoS computational biology·2026
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: Jan 31, 2026

Pull-down of Calmodulin-binding Proteins
07:51

Pull-down of Calmodulin-binding Proteins

Published on: January 23, 2012

25.9K

Protein-protein binding supersites.

Raji Viswanathan1, Eduardo Fajardo2, Gabriel Steinberg1

  • 1Department of Chemistry, Yeshiva University, New York, NY, United States of America.

Plos Computational Biology
|January 8, 2019
PubMed
Summary
This summary is machine-generated.

Protein interaction sites are not random; non-cognate proteins preferentially bind to specific binding sites. This finding aids in understanding protein interactions and developing new therapeutics.

More Related Videos

Measuring Protein Binding to F-actin by Co-sedimentation
06:17

Measuring Protein Binding to F-actin by Co-sedimentation

Published on: May 18, 2017

17.2K
Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli
08:46

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

Published on: January 6, 2015

33.6K

Related Experiment Videos

Last Updated: Jan 31, 2026

Pull-down of Calmodulin-binding Proteins
07:51

Pull-down of Calmodulin-binding Proteins

Published on: January 23, 2012

25.9K
Measuring Protein Binding to F-actin by Co-sedimentation
06:17

Measuring Protein Binding to F-actin by Co-sedimentation

Published on: May 18, 2017

17.2K
Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli
08:46

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

Published on: January 6, 2015

33.6K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Understanding protein-protein interactions (PPIs) is crucial for identifying binding partners and elucidating regulatory mechanisms.
  • Knowledge of PPIs is essential for developing targeted reagents and therapeutics.
  • Past research on small-molecule binding sites suggests potential for generic binding properties.

Purpose of the Study:

  • To investigate whether protein interaction sites act as generic binding sites for non-cognate protein ligands.
  • To test the hypothesis that protein binding interfaces exhibit promiscuity similar to small-molecule binding sites.

Main Methods:

  • Computational docking experiments were performed on a dataset of 241 protein complexes.
  • Extensive simulations explored various docking programs, non-cognate protein probes, and binding site characteristics.
  • A prediction algorithm was developed based on the frequency of non-cognate probe interactions with binding interfaces.

Main Results:

  • A strong preference was observed for non-cognate protein ligands to bind to the cognate binding site of a receptor.
  • This binding preference remained robust across different docking programs, probe types, and complex sizes.
  • The accuracy of docking scoring functions influenced the correct site identification.
  • A developed prediction algorithm demonstrated competitive accuracy with existing state-of-the-art methods.

Conclusions:

  • Protein interaction sites exhibit a degree of specificity, with a preference for cognate binding.
  • The findings support the hypothesis of generic binding site behavior in protein interactions.
  • The developed prediction algorithm shows promise for advancing PPI analysis and drug discovery.