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Protein-protein Interfaces

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...

Protein Networks

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 Sites

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

Detection and Analysis of Short Linear Motif-Based Protein-Protein Interactions with SLiMAn2 Web Server.

Alexandre Mezghrani¹, Juliette Simon¹, Victor Reys²

¹Centre de Biologie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier, France.

Methods in Molecular Biology (Clifton, N.J.)

|July 12, 2024

Summary

Interactomics yields vast protein-protein interaction (PPI) data, but identifying specific molecular interfaces is challenging. The SLiMAn webserver aids in analyzing short linear motif (SLiM)-based PPIs within protein networks.

Keywords:

Comparative modeling Interactomes Protein sequence Proteome annotations

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Molecular Biology
Bioinformatics
Structural Biology

Background:

Interactomics generates extensive protein-protein interaction (PPI) data crucial for cellular processes.
Current data often lacks precise molecular interface information, hindering network understanding and modulation.
Many PPIs involve short linear motifs (SLiMs) or domain-domain interactions, with functional SLiMs often obscured by spurious ones.

Purpose of the Study:

To address the challenge of identifying direct molecular contacts within complex interactomes.
To introduce a user-friendly bioinformatics tool for analyzing SLiM-based PPIs.
To facilitate rapid molecular and structural analysis of SLiM-mediated interactions in protein networks.

Main Methods:

Development and application of the SLiMAn webserver.
Interactive analysis of SLiM-based protein-protein interactions.
Focus on distinguishing functional SLiMs from spurious ones within interactome data.

Main Results:

SLiMAn provides a method for deeper analysis of interactomes.
The tool facilitates the identification of actual contacts and direct interactions.
Enables interactive exploration of SLiM-based PPIs.

Conclusions:

User-friendly bioinformatics tools are essential for advancing interactomics research.
SLiMAn offers a practical solution for analyzing SLiM-based PPIs.
The webserver aids in understanding molecular interfaces and modulating protein networks.