Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein-Drug Binding: Determination Methods

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...

States of Water

States of Water

Water exists in any one of the three classical states: solid (ice), liquid (water), and gas (steam or water vapor). The state of water depends on i) the intermolecular forces that draw molecules together and ii) the kinetic energy that leads to movements that pull them apart.
Water freezes when the intermolecular forces are greater than the kinetic energy. Unlike most other substances, water is less dense in its solid state than in its liquid state. This is because each water molecule can form...

Protein-protein Interfaces

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...

Factors Affecting Protein-Drug Binding: Drug Interactions

Factors Affecting Protein-Drug Binding: Drug Interactions

Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

Water and Mineral Acquisition

Water and Mineral Acquisition

Specialized tissues in plant roots have evolved to capture water, minerals, and some ions from the soil. Roots exhibit a variety of branching patterns that facilitate this process. The outermost root cells have specialized structures called root hairs that increase the root surface, thus increasing soil contact. Water can passively cross into roots, as the concentration of water in the soil is higher than that of the root tissue. Minerals, in contrast, are actively transported into root cells.

You might also read

Related Articles

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

Sort by

Same author

Deciphering the Anticancer Potential of Bifidobacterium longum MB BBLM15 Derived Postbiotic Metabolites in Cervical Cancer: In Vitro, In Silico, and Synergy Studies.

Probiotics and antimicrobial proteins·2026

Same author

In silico characterization of acetyl-CoA carboxylase from Staphylococcus aureus and Escherichia coli: A comparative analysis.

Computational biology and chemistry·2026

Same author

Exploring Bakuchiol as an HSP90-Targeting Lead Against Triple-Negative Breast Cancer: Evidence from In Silico, In Vitro, and Synergy Studies.

Journal of computer-aided molecular design·2026

Same author

Designing potent and immunogenic epitope based peptide vaccine against all serotypes of DENV via structural, physico-chemical and immunoinformatics-based approaches.

Scientific reports·2026

Same author

Higher racial diversity in US business and law schools is linked to higher graduate salaries.

Nature·2026

Same author

Racial diversity in higher education is associated with higher student salaries.

Nature·2026

Search research articles

Related Experiment Video

Updated: Jan 23, 2026

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

POWAINDv1.0: A Program for Protein-Water Interactions Determination.

Sahini Banerjee¹, Buddhadev Mondal², Rifat Nawaz Ul Islam³

¹Department of Biological Sciences, ISI, Kolkata, West Bengal, India.

|June 22, 2019

Summary

This study introduces POWAINDv1.0, a novel computational tool for analyzing protein-shell water interactions. It provides detailed insights into how water molecules influence protein structure and binding specificity.

Keywords:

Crystallographic Shell-water atom specific interactions bridge interactions program residue-specific interactions water dynamics

More Related Videos

Luciferase Complementation Imaging Assay in Nicotiana benthamiana Leaves for Transiently Determining Protein-protein Interaction Dynamics

Luciferase Complementation Imaging Assay in Nicotiana benthamiana Leaves for Transiently Determining Protein-protein Interaction Dynamics

Published on: November 20, 2017

Study of Protein-protein Interactions in Autophagy Research

Study of Protein-protein Interactions in Autophagy Research

Published on: September 9, 2017

Related Experiment Videos

Last Updated: Jan 23, 2026

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Luciferase Complementation Imaging Assay in Nicotiana benthamiana Leaves for Transiently Determining Protein-protein Interaction Dynamics

Luciferase Complementation Imaging Assay in Nicotiana benthamiana Leaves for Transiently Determining Protein-protein Interaction Dynamics

Published on: November 20, 2017

Study of Protein-protein Interactions in Autophagy Research

Study of Protein-protein Interactions in Autophagy Research

Published on: September 9, 2017

Area of Science:

Structural Bioinformatics
Biophysics
Computational Biology

Background:

Proteins are crucial biomolecules in cellular aqueous environments, with their structure balancing rigidity and flexibility for binding specificity.
Intramolecular and intermolecular interactions, including those with shell-waters, are vital for maintaining protein tertiary structure stability.
The dynamics of shell-water interactions with protein atom-groups (AGP) and weak forces remain incompletely understood.

Purpose of the Study:

To develop and present a systematic computational procedure for analyzing crystallographic shell-water (CSH) interactions with proteins.
To investigate the dynamics of shell-water interactions with specific residues and atom-groups of proteins (AGP).
To characterize the nature and contribution of CSH-protein interactions to overall protein structure and function.

Main Methods:

Development of a computational procedure named POWAINDv1.0.
Analysis of interactions between crystallographic shell-waters (CSH) and protein atom-groups (AGP) in a residue-specific manner.
Extraction of shell-water and AGP-specific bridge-interactions.
Evaluation of interaction favorability based on van der Waals radii of interacting atoms.

Main Results:

POWAINDv1.0 successfully analyzes CSH-protein interactions, detailing residue and AGP-specific contributions.
The program identifies and characterizes bridge-interactions between shell-waters and AGPs.
Analysis provides insights into the favorable and unfavorable nature of these interactions, aiding in understanding protein stability.

Conclusions:

POWAINDv1.0 offers a detailed method for analyzing CSH-protein interactions, crucial for understanding protein structure and stability.
The tool provides intricate details on shell-water contributions to protein architecture.
This approach has significant applications in structural bioinformatics and understanding biomolecular interactions.