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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,...

Protein Networks

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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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...

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Proteome-Scale Human Interactomics.

Katja Luck¹, Gloria M Sheynkman¹, Ivy Zhang¹

¹Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

Trends in Biochemical Sciences

|March 13, 2017

Summary

This summary is machine-generated.

New human protein-protein interaction (PPI) maps offer a breakthrough in understanding cellular organization. These interactome data provide a roadmap for future research in human interactomics and cellular life.

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Area of Science:

Molecular Biology
Systems Biology
Bioinformatics

Background:

Cellular functions rely on complex networks of molecular interactions.
Understanding these interactomes is crucial for modeling cellular organization at the proteome scale.

Purpose of the Study:

To analyze systematically generated human protein-protein interaction (PPI) data.
To provide insights into the challenges and opportunities in interactomics.
To establish a roadmap for creating a reference human interactome.

Main Methods:

Analysis of four recently published human PPI maps.
Integration of interactome data with complementary studies.

Main Results:

The publication of human PPI maps marks a significant advancement in interactomics.
Systematic analysis reveals opportunities and challenges in handling large-scale interactome data.
A clear roadmap for generating a reference human interactome has been defined.

Conclusions:

These interactome maps herald a new era of proteome-scale human interactomics.
The findings offer new perspectives on the organization of cellular life.
Further research can build upon these resources to deepen our understanding of cellular processes.