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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 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.
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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,...
Protein Organization01:24

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.

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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs.

Gozde Kar1, Ozlem Keskin, Ruth Nussinov

  • 1Center for Computational Biology and Bioinformatics and College of Engineering, Koc University , Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.

Journal of Proteome Research
|December 14, 2011
PubMed
Summary

Ubiquitin ligase E3s select specific ubiquitin-conjugating enzymes (E2s) through critical interactions. This study models these E2-E3 interactions, revealing key binding sites and informing drug discovery for E3-related diseases.

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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:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Ubiquitination is a vital post-translational modification regulating protein degradation, DNA repair, transcription, and signaling.
  • The ubiquitination cascade involves E1, E2, and E3 enzymes, with E3 ligases conferring substrate specificity.
  • Understanding E3-E2 interactions is crucial for deciphering ubiquitination pathway regulation.

Purpose of the Study:

  • To model proteome-scale E3-E2 interactions in the human ubiquitination pathway.
  • To identify specific E3 and E2 protein partners and elucidate their interaction mechanisms.
  • To uncover the principles governing E2 selection by E3 ligases.

Main Methods:

  • Proteome-scale modeling of E3-E2 protein interactions.
  • Analysis of interface structural motifs between E2 and E3 proteins.
  • Identification of critical residues and loops involved in E2-E3 binding.

Main Results:

  • Loop L1 of E2s is identified as a critical binding interface for E3 ligases.
  • A specific residue at the sixth position in E2 loop L1 acts as a key interaction hotspot.
  • Distinct E3 types (HECT vs. RING) show differential interactions with E2 loop L1 residues, indicating specificity determinants.

Conclusions:

  • Structural modeling reveals specific E2-E3 binding mechanisms driven by interface motifs.
  • Sequence variations in E2 loop L1 residues contribute to specificity in E3 binding.
  • These findings have implications for developing targeted therapies against E3 ligases implicated in diseases.