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Related Concept Videos

Protein Networks02:26

Protein Networks

4.0K
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-protein Interfaces02:04

Protein-protein Interfaces

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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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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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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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Overview of Protein Sorting and Transport01:45

Overview of Protein Sorting and Transport

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Eukaryotic cells have different membrane-bound organelles with distinct protein requirements. The process by which proteins are targeted to a specific organelle is called protein sorting.
Protein sorting can be of two types: signal-based sorting and vesicle-based trafficking. In signal-based sorting, specific amino acid sequences called sorting signals target proteins to the proper location inside the cell either via gated transport or by protein translocation.  In gated transport, folded...
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
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Hubs and Bottlenecks in Protein-Protein Interaction Networks.

Chandramohan Nithya1, Manjari Kiran2, Hampapathalu Adimurthy Nagarajaram3

  • 1Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.

Methods in Molecular Biology (Clifton, N.J.)
|October 6, 2023
PubMed
Summary

Protein-protein interaction networks (PPINs) reveal critical cellular roles. Hubs and bottlenecks, identified by centrality measures like degree and betweenness, are essential proteins vital for network structure and function.

Keywords:
BetweennessBottlenecksCentrality measuresDegreeHubsProtein-protein interaction

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Area of Science:

  • Systems Biology
  • Network Biology
  • Computational Biology

Background:

  • Protein-protein interaction networks (PPINs) are fundamental to cellular processes.
  • Centrality measures are key to identifying crucial proteins within these networks.
  • Hubs and bottlenecks represent topologically and functionally significant proteins in PPINs.

Purpose of the Study:

  • To review the literature on hubs and bottlenecks in PPINs.
  • To elucidate the properties and functions of these essential proteins.
  • To highlight their importance in network structure and cellular processes.

Main Methods:

  • Review of existing scientific literature on protein-protein interaction networks.
  • Analysis of centrality measures, specifically degree and betweenness centrality.
  • Identification and characterization of hub and bottleneck proteins based on network topology.

Main Results:

  • Hubs (high degree centrality) and bottlenecks (high betweenness centrality) are critical nodes in PPINs.
  • These proteins play vital roles in signal transduction, metabolic regulation, and gene expression.
  • Understanding hubs and bottlenecks is essential for comprehending network organization and function.

Conclusions:

  • Hubs and bottlenecks are indispensable for maintaining the integrity and function of cellular networks.
  • Their identification through centrality measures provides insights into protein essentiality.
  • This review consolidates knowledge on these key proteins, aiding further research in systems biology.