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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...
Protein Networks02:26

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,...
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...
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...
Protein-Drug Binding: Mechanism and Kinetics01:16

Protein-Drug Binding: Mechanism and Kinetics

Protein-drug binding refers to the interaction between drugs and proteins within the body. This binding process can occur intracellularly, involving drug interactions with enzymes or receptors within cells, or extracellularly, involving plasma proteins in the blood.
Various forces drive these interactions, including hydrogen bonds, hydrophobic interactions, ionic bonds, electrostatic interactions, and van der Waals forces. These bonds enable drugs to bind to specific sites on proteins,...

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Protein interactions in 3D: from interface evolution to drug discovery.

Christof Winter1, Andreas Henschel, Anne Tuukkanen

  • 1Biotechnology Center, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany.

Journal of Structural Biology
|May 19, 2012
PubMed
Summary

Understanding protein interaction interfaces and their evolution is crucial for drug discovery. This review covers algorithms, databases, and applications in predicting and analyzing these interfaces.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Evolutionary biology

Background:

  • Protein interactions are fundamental to cellular processes.
  • Understanding protein interaction interfaces is key to deciphering biological mechanisms.
  • Evolutionary analysis of interfaces offers insights into functional convergence.

Purpose of the Study:

  • To review algorithms and databases for analyzing 3D protein interactions.
  • To discuss the role of interface evolution in understanding binding partners.
  • To highlight applications in drug discovery and interface prediction.

Main Methods:

  • Review of existing literature on protein interaction algorithms and databases.
  • Analysis of studies focusing on the evolution of protein interaction interfaces.
  • Discussion of computational approaches for interface prediction.

Main Results:

  • Identification of key residues in convergently evolved interfaces.
  • Elucidation of evolutionary relationships between unrelated interfaces.
  • Demonstration of the utility of interface analysis in drug discovery.

Conclusions:

  • Interface evolution provides a basis for identifying convergent evolution and common binding partners.
  • Knowledge of protein interaction interfaces is vital for pharmaceutical applications.
  • Algorithms and databases for 3D protein interactions support advancements in drug discovery and prediction.