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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Networks02:26

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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.
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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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Assembly of Signaling Complexes01:30

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Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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Structural landscapes of PPI interfaces.

Carlos H M Rodrigues1,2,3, Douglas E V Pires1,2,4, Tom L Blundell5

  • 1Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria.

Briefings in Bioinformatics
|June 3, 2022
PubMed
Summary
This summary is machine-generated.

Protein-protein interactions (PPIs) are crucial for biological functions and drug discovery. Our analysis reveals that even flat PPI interfaces contain small, druggable pockets, challenging previous assumptions.

Keywords:
drug designprotein binding siteprotein–protein interfacestructural biology

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Area of Science:

  • Structural biology
  • Biochemistry
  • Drug discovery

Background:

  • Proteins mediate critical biological functions through specific interactions.
  • Protein-protein interfaces (PPIs) were previously thought to be predominantly flat.
  • Recent studies suggest concave binding sites exist at PPIs, similar to small-molecule targets.

Purpose of the Study:

  • To conduct a large-scale analysis of protein-protein interface geometry and properties.
  • To comprehensively review the landscape of protein-protein interfaces.
  • To identify druggable pockets within these interfaces.

Main Methods:

  • Analysis of all protein-protein interfaces in the Protein Data Bank.
  • Characterization of binding geometry and physicochemical properties.
  • Review of structural and thermodynamic data.

Main Results:

  • Protein-protein interfaces exhibit diverse geometries, not exclusively flat.
  • Even large, flat interfaces can harbor small, concave pockets.
  • These pockets share characteristics with traditional drug-binding sites.

Conclusions:

  • The protein-protein interface landscape is more complex than previously understood.
  • Druggable pockets are present even in seemingly flat protein-protein interfaces.
  • This finding has significant implications for structure-based drug design targeting protein interactions.