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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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,...
Protein Networks02:26

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Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
Diversity in Cell Signaling Responses01:22

Diversity in Cell Signaling Responses

The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
Graded and Abrupt Responses
Some signaling systems generate...

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

Protein evolution on a human signaling network.

Qinghua Cui1, Enrico O Purisima, Edwin Wang

  • 1Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada. cuiqinghua@bjmu.edu.cn

BMC Systems Biology
|February 20, 2009
PubMed
Summary
This summary is machine-generated.

Cellular network structure constrains protein evolution. Signaling network analysis reveals evolutionary rates decrease along signal flow and neighbor proteins evolve similarly, with physical interactions showing closest rates.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Systems Biology

Background:

  • Cellular network architecture influences protein evolution, posing both opportunities and limitations.
  • Previous studies focused on protein interaction networks, leaving the impact of signaling networks on protein evolution less understood.
  • The reciprocal relationship between signaling networks and protein evolution remains an area requiring further investigation.

Purpose of the Study:

  • To construct a comprehensive human signaling network for evolutionary analysis.
  • To investigate how signaling network topology affects protein evolutionary rates (dN/dS values).
  • To explore the co-evolutionary dynamics between proteins within signaling pathways.

Main Methods:

  • Manual curation of human signaling pathways to build a network of over 1,600 nodes and 5,000 links.
  • Analysis of dN/dS values for human-mouse orthologous proteins mapped onto the signaling network.
  • Examination of evolutionary rate similarities based on network topology, path lengths, and interaction types.

Main Results:

  • Protein evolutionary rates (dN/dS) decrease from the extracellular space towards the nucleus along signal flow.
  • Neighboring proteins in the network exhibit similar evolutionary rates (co-fast or co-slow), with physically interacting pairs showing the most similar rates.
  • Evolutionary rate similarity diminishes with increasing distance along directed shortest paths, but not for neutral paths.

Conclusions:

  • Signaling networks impose significant constraints on protein evolution, consistent with findings in protein interaction networks.
  • Network characteristics demonstrably influence protein evolutionary and co-evolutionary behaviors.
  • Protein evolution dynamically shapes the functional outcomes of signaling networks, offering general principles for understanding these processes.