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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

12.6K
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

Protein Networks

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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.
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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Protein Organization01:24

Protein Organization

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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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Protein-Protein Interfaces02:04

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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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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.
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...
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Updated: Aug 20, 2025

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

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Protein interactions: anything new?

Susana Barrera-Vilarmau1, João M C Teixeira1, Monika Fuxreiter1,2

  • 1Department of Biomedical Sciences, University of Padova, Italy.

Essays in Biochemistry
|November 23, 2022
PubMed
Summary
This summary is machine-generated.

Protein interactions are dynamic, adapting to cellular environments through multiple binding modes. The energy landscape framework explains this context-dependent behavior, paving the way for a universal model of protein interactions.

Keywords:
energy landscape frameworkfuzzinesshigher-order assemblyliquid-liquid phase separationprotein-protein interactions

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Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay
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Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay

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Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay
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Area of Science:

  • Biochemistry
  • Biophysics
  • Cell Biology

Background:

  • Understanding protein interactions is crucial for cellular function.
  • Current models struggle to explain interactions in complex cellular environments like biomolecular condensates.
  • Protein interactions range from simple complexes to large, dynamic assemblies.

Purpose of the Study:

  • To propose a universal framework for understanding protein interactions across different scales.
  • To explain how proteins adapt their interactions based on the cellular context.
  • To investigate the role of multiple binding modes in protein-protein interactions.

Main Methods:

  • Reviewing the evolution of protein interaction concepts from rigid structures to conformational ensembles.
  • Applying the energy landscape framework, typically used for protein folding, to protein interactions.
  • Analyzing the phenomenon of multiple binding modes (MBM) in protein interactions.

Main Results:

  • Protein interactions are not static but are context-dependent and involve multiple binding modes (MBM).
  • The energy landscape framework can successfully explain the multiplicity of binding modes observed in proteins.
  • This framework provides a physics-based approach to understanding dynamic protein behaviors.

Conclusions:

  • A universal model for protein interactions can be developed using the energy landscape framework.
  • This approach offers insights into the behavior of proteins within cellular environments, including biomolecular condensates.
  • Understanding dynamic protein interactions is key to deciphering complex cellular processes.