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

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 polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding Sites02:40

Ligand Binding Sites

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...
Factors Affecting Protein-Drug Binding: Drug-Related Factors01:18

Factors Affecting Protein-Drug Binding: Drug-Related Factors

Drug binding to proteins is a complex phenomenon influenced by various drug-related factors, each playing a significant role in the interaction between drugs and proteins within the body.
One crucial factor in drug-protein binding is the drug's lipophilicity or its affinity for fat. More lipophilic drugs tend to have higher binding extents. For example, highly lipophilic drugs like cloxacillin exhibit substantial protein binding, with as much as 95% of the drug binding to proteins. In contrast,...
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

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...

You might also read

Related Articles

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

Sort by
Same author

Modeling the bio-nano interactions of polypropylene nanoparticles.

The Journal of chemical physics·2026
Same author

Biophysical Descriptors of Nanoparticle Protein Coronas.

The journal of physical chemistry letters·2025
Same author

Transition State Conformations for IDPs: Application to Human Amylin (hIAPP).

The journal of physical chemistry. B·2025
Same author

Predicting biomolecule adsorption on nanomaterials: a hybrid framework of molecular simulations and machine learning.

Nanoscale·2025
Same author

<i>UANanoDock</i>: A Web-Based <i>UnitedAtom</i> Multiscale Nanodocking Tool for Predicting Protein Adsorption onto Nanoparticles.

Journal of chemical information and modeling·2025
Same author

CELS-3D-Cutting edge light source for exciting fluorescence in microtome-based 3D microscopy and targeted correlative microscopy.

Journal of anatomy·2024
Same journal

The influence of chirality on the macroscopic behavior of multiferroic smectic phases.

The Journal of chemical physics·2026
Same journal

Polaron transformed canonically consistent quantum master equation.

The Journal of chemical physics·2026
Same journal

The x-ray absorption spectrum of the propargyl radical C3H3â—Ź.

The Journal of chemical physics·2026
Same journal

Transient hydroperoxyalkyl intermediates (•QOOH) in isopentane oxidation. I. Conformer- and isomer-resolved infrared spectra.

The Journal of chemical physics·2026
Same journal

Transient hydroperoxyalkyl intermediates (•QOOH) in isopentane oxidation. II. Isomer-resolved unimolecular dynamics.

The Journal of chemical physics·2026
Same journal

Quantum state-to-state dynamics studies of the C(3P) + OH(X2Π) → CO(a3Π) + H(2S) reaction based on a new HCO(12A″) potential energy surface.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: May 16, 2026

Monitoring Protein Adsorption with Solid-state Nanopores
08:51

Monitoring Protein Adsorption with Solid-state Nanopores

Published on: December 2, 2011

Orientation-dependent protein binding at nanoparticle interfaces.

Vigneshwari Karunakaran Annapoorani1,2, Ian Rouse1,2, Vladimir Lobaskin1,2

  • 1School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.

The Journal of Chemical Physics
|May 14, 2026
PubMed
Summary
This summary is machine-generated.

This study presents a new computational framework to quantify protein-nanoparticle interactions. It combines coarse-grained models with molecular docking for better predictive modeling in nanomedicine and drug delivery.

More Related Videos

Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications
14:43

Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications

Published on: September 23, 2013

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers
09:33

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Published on: March 21, 2025

Related Experiment Videos

Last Updated: May 16, 2026

Monitoring Protein Adsorption with Solid-state Nanopores
08:51

Monitoring Protein Adsorption with Solid-state Nanopores

Published on: December 2, 2011

Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications
14:43

Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications

Published on: September 23, 2013

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers
09:33

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Published on: March 21, 2025

Area of Science:

  • Computational chemistry
  • Nanobiotechnology
  • Materials science

Background:

  • Accurate quantification of protein-nanoparticle interactions is crucial for nanobiotechnology, nanomedicine, and drug delivery.
  • Existing computational and experimental methods have limitations in characterizing these interactions.

Purpose of the Study:

  • To develop and validate a computational framework combining coarse-grained united-atom (UA) models with molecular docking.
  • To characterize protein adsorption on silicon dioxide (SiO2) nanoparticles.
  • To provide a quantitative bridge between coarse-grained energetics and docking outputs for protein-nanoparticle interfaces.

Main Methods:

  • Construction of orientation-resolved heatmaps specifying protein-nanoparticle poses using polar and azimuthal angles.
  • Reporting binding propensity via minimum UA adsorption energy or docking score.
  • Analysis of eight birch pollen allergen proteins and quantification of similarity using Jensen-Shannon divergence.

Main Results:

  • The framework successfully characterizes protein adsorption on SiO2 nanoparticles.
  • Encouraging agreement was found between docking scores and UA adsorption energetics for several proteins.
  • Identified limitations and potential improvements, such as optimized angular resolution and parameter refinement.

Conclusions:

  • The developed framework offers a quantitative link between coarse-grained energetics and docking predictions at protein-nanoparticle interfaces.
  • This approach supports improved predictive modeling and mechanistic understanding of protein-nanoparticle binding.
  • The study highlights routes for enhancing the accuracy and applicability of computational models in nanobiotechnology.