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Related Concept Videos

Protein Networks02:26

Protein Networks

4.1K
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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Electron Transport Chain Components01:29

Electron Transport Chain Components

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The electron transport chain (ETC) is a crucial metabolic pathway that facilitates energy conversion in prokaryotic and eukaryotic cells. In eukaryotes, the ETC comprises four membrane-associated protein complexes in the inner mitochondrial membrane. In prokaryotes, the ETC in the plasma membrane can vary in composition, with fewer or different complexes depending on the organism and environmental conditions. These complexes transfer electrons from electron donors, such as NADH and FADH2, to...
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The Supercomplexes in the Crista Membrane01:41

The Supercomplexes in the Crista Membrane

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The mitochondrial cristae membrane is the primary site for the oxidative phosphorylation (OXPHOS) process of energy conversion mediated through respiratory complexes I to V. These complexes have been widely studied for decades, and it has been proven that they form supramolecular structures called respiratory supercomplexes (SC). These higher-order complexes may be crucial in maintaining the biochemical structure and improving the physiological activity of the individual complexes while...
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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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Electron Transport Chain: Complex III and IV01:43

Electron Transport Chain: Complex III and IV

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During the electron transport chain, electrons from NADH and FADH2 are first transferred to complexes I and II, respectively. These two complexes then transfer the electrons to ubiquinol, which carries them further to complex III. Complex III passes the electrons across the intermembrane space to Cyt c, which carries them further to complex IV. Complex IV donates electrons to oxygen and reduces it to water. As electrons pass through complexes I, III, and IV, the energy released aids the pumping...
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Electron Transport Chains01:28

Electron Transport Chains

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The final stage of cellular respiration is oxidative phosphorylation that consists of two steps: the electron transport chain and chemiosmosis. The electron transport chain is a set of proteins found in the inner mitochondrial membrane in eukaryotic cells. Its primary function is to establish a proton gradient that can be used during chemiosmosis to produce ATP and generate electron carriers, such as NAD+ and FAD, that are used in glycolysis and the citric acid cycle.
The ETC is comprised of...
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Related Experiment Video

Updated: Sep 18, 2025

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

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Active Protein Network Analysis Reveals Coordinated Modules and Critical Proteins Involving Extracellular Electron

Dewu Ding1, Wei Wang1, Meineng Wang2

  • 1School of Mathematics and Computer Science, Yichun University, Yichun 336000, China.

Genes
|June 26, 2025
PubMed
Summary

This study reveals how electroactive bacteria like Shewanella oneidensis MR-1 dynamically reorganize protein networks. Key proteins SO_0225 and SO_2402 coordinate interactions, optimizing extracellular electron transfer (EET) pathways under changing conditions.

Keywords:
active networkscoordinated modulescritical proteinsextracellular electron transferprotein networks

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High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis
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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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Area of Science:

  • Microbiology
  • Systems Biology
  • Bioinformatics

Background:

  • Traditional gene expression analysis overlooks dynamic protein interactions at constant expression levels.
  • Investigating active protein networks offers a more nuanced understanding of cellular processes.

Purpose of the Study:

  • To explore protein interaction dynamics in Shewanella oneidensis MR-1 under varying extracellular electron transfer (EET) conditions.
  • To identify key proteins and pathways involved in coordinating these interactions.

Main Methods:

  • Construction of condition-specific and time-course active protein networks.
  • Integration of gene expression and protein interaction data from S. oneidensis MR-1.

Main Results:

  • Identified coordinated functional modules active under different EET conditions.
  • Discovered SO_0225 and SO_2402 as central proteins coordinating interaction dynamics, especially under oxygen limitation.
  • Elucidated activation stages of the Mtr pathway through time-course network analysis.

Conclusions:

  • Shewanella oneidensis MR-1 exhibits dynamic protein network reorganization in response to varying EET conditions.
  • This dynamic regulation is crucial for optimizing electron transfer pathways.
  • Findings offer insights into the adaptability of electroactive bacteria.