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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 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,...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

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.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...

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Related Experiment Video

Updated: May 11, 2026

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient
08:06

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient

Published on: September 3, 2014

Predicting protein-protein interactions in the post synaptic density.

Ossnat Bar-shira1, Gal Chechik

  • 1The Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel.

Molecular and Cellular Neurosciences
|May 1, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a computational framework to map the protein network of the postsynaptic density (PSD), improving our understanding of synaptic plasticity, learning, and memory. It predicts novel protein interactions crucial for brain function.

Keywords:
ClassificationComputational biologyNetwork reconstructionPostsynaptic densityProtein–protein interactions

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

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Last Updated: May 11, 2026

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient
08:06

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Published on: September 3, 2014

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

  • Neuroscience
  • Computational Biology
  • Proteomics

Background:

  • The postsynaptic density (PSD) is a critical protein complex at neuronal synapses, essential for synaptic plasticity, learning, and memory.
  • Current knowledge of the PSD proteome and interactome is incomplete and contains inaccuracies, hindering a full understanding of its function.

Purpose of the Study:

  • To develop and present a computational framework for enhancing the reconstruction of the PSD protein-protein interaction network.
  • To identify novel protein interactions within the PSD to elucidate mechanisms of synaptic plasticity and related neurological disorders.

Main Methods:

  • A computational approach was employed, learning interaction patterns from known PSD protein interactions.
  • The framework integrated data from large-scale repositories to expand the interaction set.
  • Novel protein interactions were predicted for proteins suspected to be part of the PSD.

Main Results:

  • The study successfully predicted thirty novel protein interactions within the PSD network.
  • Over half of the predicted interactions were supported by existing literature evidence.
  • Two specific interactions, Lrrtm1 with PSD-95 and Src with Capg, were discussed in detail for their potential roles.

Conclusions:

  • The developed computational framework effectively improves the reconstruction of the PSD interactome.
  • Predicted interactions, such as Lrrtm1-PSD-95 and Src-Capg, offer new insights into synaptic function, glutamatergic dysfunction in schizophrenia, and dendritic spine maturation.