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Related Concept Videos

Protein Networks02:26

Protein Networks

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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.
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Protein Networks02:26

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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Protein Complex Assembly02:41

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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Protein Complexes with Interchangeable Parts01:57

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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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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species.

Jianliang Gao1, Bo Song2, Xiaohua Hu2

  • 1School of Information Science and Engineering, Central South University, Changsha, 410083, China. gaojianliang@csu.edu.cn.

BMC Bioinformatics
|October 28, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces ConnectedAlign, a novel bioinformatics method for identifying conserved protein complexes across multiple species. It enhances evolutionary conserved substructure discovery by prioritizing network connectivity.

Keywords:
Big dataGraph data analysisNetwork alignment

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Network alignment in bioinformatics aids in discovering evolutionary conserved substructures within protein-protein interaction (PPI) networks.
  • Existing methods often prioritize pairwise network similarity over the connectivity features of substructures like protein complexes.

Purpose of the Study:

  • To address the limitations of current network alignment methods by focusing on conserved protein complexes.
  • To develop an efficient algorithm that considers the connectivity of aligned proteins within PPI networks.

Main Methods:

  • Propose ConnectedAlign, an efficient method for identifying conserved protein complexes.
  • Incorporate the feature of connectivity into network alignment algorithms for PPI networks.
  • Apply the method to multiple PPI networks from different species.

Main Results:

  • ConnectedAlign significantly improves the coverage of conserved protein complexes.
  • The method maintains consistency in aligned results while prioritizing connectivity.
  • Successfully extends knowledge of protein complexes from well-studied to poorly-studied species.

Conclusions:

  • Extensive experiments on human, yeast, fruit fly, and worm PPI networks validate ConnectedAlign's effectiveness.
  • The proposed method demonstrates superior performance in identifying cross-species protein complexes.
  • ConnectedAlign offers a robust approach for comparative network biology and functional inference.