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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-Protein Interfaces

Protein-Protein Interfaces

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,...

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....

Ligand Binding Sites

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...

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...

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Related Experiment Video

Updated: Mar 31, 2026

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

Drug leads for interactive protein targets with unknown structure.

Ariel Fernández¹, L Ridgway Scott²

¹Argentine Institute of Mathematics (IAM), National Research Council (CONICET), Buenos Aires 1083, Argentina; AF Innovation, Avenida del Libertador 1092, Buenos Aires 1112, Argentina.

Drug Discovery Today

|October 21, 2015

Summary

A new drug discovery technology identifies drug leads by analyzing protein sequences and phosphorylation sites, bypassing the need for target protein structures. This approach successfully targets protein-protein interactions (PPIs) and is exemplified by a heart failure treatment.

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

Published on: January 26, 2024

Area of Science:

Biochemistry and Drug Discovery
Computational Biology and Bioinformatics

Background:

Disrupting protein-protein interfaces (PPIs) is crucial for drug discovery but challenging, especially with unknown protein structures.
Phosphorylation-susceptible sites within PPIs add complexity to targeting these interactions.
Current structure-based methods have limitations when target protein structures are unavailable.

Purpose of the Study:

To introduce a novel technology for identifying drug leads that inhibit protein associations.
To demonstrate the capability of this technology to function without requiring target protein structures.
To contrast this sequence-based approach with existing structure-based drug discovery methods.

Main Methods:

Utilizes protein sequence data and information on phosphorylation-susceptible sites within PPIs.
Develops drug leads based solely on sequence and phosphorylation site analysis.
Compares the novel method against traditional structure-based drug discovery techniques.

Main Results:

Successfully identified drug leads capable of inhibiting protein associations using only sequence information.
Illustrated the technology's application through a patented invention for heart failure treatment.
Demonstrated the feasibility of generating effective drug leads without prior knowledge of target protein structure.

Conclusions:

A novel, sequence-based technology can effectively identify drug leads for inhibiting PPIs.
This approach overcomes the limitations of structure-based methods, particularly when target structures are unknown.
The successful development of a heart failure therapeutic validates the potential of this innovative drug discovery strategy.