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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...

Protein Networks

Protein Networks

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,...

Conserved Binding Sites

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...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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Related Experiment Video

Updated: May 2, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Protein-Protein Interaction Stabilizers from MD Simulation-Derived Pharmacophores.

Mohd Ibrahim¹, Martin Zacharias¹

¹Physics Department and Center for Functional Protein Assemblies, Technical University of Munich, 85748 Garching, Germany.

Journal of Chemical Information and Modeling

|May 1, 2026

Summary

This summary is machine-generated.

This study introduces PPIS-MDPharma, a novel workflow to discover protein-protein interaction (PPI) stabilizers. It uses molecular dynamics simulations to identify drug candidates for treating diseases caused by disrupted cellular processes.

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Area of Science:

Biochemistry and Structural Biology
Computational Chemistry
Drug Discovery

Background:

Protein-protein interactions (PPIs) are vital for cellular functions.
Dysregulated PPIs are implicated in various diseases.
Stabilizing PPIs with small molecules is a therapeutic strategy.

Purpose of the Study:

To develop an efficient workflow for identifying PPI stabilizers.
To leverage molecular dynamics (MD) simulations and pharmacophore screening.

Main Methods:

Extracting pharmacophore features (hydrogen bonding, electrostatic, hydrophobic, aromatic) from MD simulations.
Rapid pharmacophore screening of a 50-million compound database.
Rescoring candidates using MMGBSA.

Main Results:

Identified numerous PPI stabilizer candidates for seven protein complexes.
Top-ranked ligands showed MMGBSA scores comparable to known stabilizers.
The workflow is computationally efficient compared to docking methods.

Conclusions:

The PPIS-MDPharma workflow effectively identifies PPI stabilizers.
This approach offers a promising, efficient tool for drug discovery targeting PPIs.
Enables development of novel therapeutics for various diseases.