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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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

Updated: May 20, 2026

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
13:37

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Published on: June 20, 2014

Comprehensive peptidomimetic libraries targeting protein-protein interactions.

Landon R Whitby1, Dale L Boger

  • 1Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States.

Accounts of Chemical Research
|July 18, 2012
PubMed
Summary

Researchers developed novel small molecule libraries that mimic protein secondary structures to discover drugs targeting protein-protein interactions (PPIs). These libraries successfully identified high-affinity modulators for HIV-1 gp41 and opioid receptors, advancing drug discovery for PPIs.

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Identifying Protein-protein Interaction Sites Using Peptide Arrays
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Identifying Protein-protein Interaction Sites Using Peptide Arrays

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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Related Experiment Videos

Last Updated: May 20, 2026

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
13:37

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Published on: June 20, 2014

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Medicinal Chemistry
  • Chemical Biology
  • Drug Discovery

Background:

  • Transient protein-protein interactions (PPIs) are crucial in cellular signaling, viral infections, and immune responses, representing key targets for drug discovery.
  • Current strategies for identifying small molecule modulators of PPIs are often limited to targets with known structures.
  • A gap exists in screening libraries for molecules that mimic peptide secondary structures involved in PPIs.

Purpose of the Study:

  • To design, synthesize, and validate comprehensive small molecule libraries that mimic the three major recognition motifs of PPIs: α-helix, β-turn, and β-strand.
  • To create libraries capable of mimicking key interaction residues for a wide range of targetable PPIs.
  • To provide tools for discovering lead compounds and understanding the recognition motifs and key residues in PPIs.

Main Methods:

  • Development of molecular scaffolds designed to mimic peptide secondary structures (α-helix, β-turn).
  • Synthesis of an 8000-member α-helix mimetic library and a 4200-member β-turn mimetic library, incorporating diverse amino acid side chain combinations.
  • Screening of these libraries against known PPI targets, including p53/MDM2, HIV-1 gp41, and opioid receptors.

Main Results:

  • Discovery of high-affinity α-helix mimetics (K(i) = 0.7 μM) targeting HIV-1 gp41.
  • Identification of high-affinity and selective β-turn mimetics (K(i) = 80 nM) for the κ-opioid receptor.
  • Demonstration that these libraries can identify lead compounds and elucidate PPI recognition mechanisms even for uncharacterized interactions.

Conclusions:

  • Comprehensive libraries of peptide secondary structure mimetics are powerful tools for interrogating PPIs.
  • These mimetics offer a viable strategy for discovering small molecule modulators of PPI networks.
  • The approach facilitates therapeutic target validation, lead compound discovery, and the identification of modulators for biological processes.