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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...

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...

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:

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

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,...

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Related Experiment Video

Updated: Jun 17, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Locuaz: an in silico platform for protein binders optimization.

German P Barletta^1,2, Rika Tandiana¹, Miguel Soler^1,3

¹CONCEPT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83 Genova Liguria 16152, Italy.

Bioinformatics (Oxford, England)

|August 6, 2024

Summary

This study introduces a computational platform to optimize protein binders, accelerating the design of high-affinity binders. The platform efficiently explores mutations and evaluates binding affinity, reducing experimental screening time and costs.

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Area of Science:

Biochemistry
Computational Biology
Protein Engineering

Background:

Engineering high-affinity protein binders for specific targets is experimentally intensive.
Computational methods offer potential for accelerating binder optimization but require broad applicability and efficiency.

Purpose of the Study:

To introduce a novel computational platform for optimizing protein binders.
To enhance the efficiency and reduce the cost of designing high-affinity binders.

Main Methods:

A modular computational platform for protein binder optimization.
Includes modules for mutation selection, molecular dynamics simulations, and affinity scoring.
Supports parallel processing for in silico high-throughput screening on High Performance Computing (HPC) systems.

Main Results:

The platform enables efficient exploration of mutations and affinity evaluation.
Facilitates parallel exploration of mutation pathways for accelerated screening.
Offers a customizable framework for implementing user-defined protocols.

Conclusions:

The developed platform significantly accelerates the optimization of protein binders.
Reduces the need for extensive experimental screening in binder design.
Provides a flexible and efficient computational tool for protein engineering.