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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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Post-translational Translocation of Proteins to the RER01:27

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A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...
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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Protein Modifications in the RER01:26

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Initiation of Translation02:33

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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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Identification of Post-translational Modifications of Plant Protein Complexes
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Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle.

Aidan P Tay1, Angelita Liang1, Marc R Wilkins1

  • 1Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.

Current Protocols in Bioinformatics
|January 18, 2019
PubMed
Summary
This summary is machine-generated.

PTMOracle is a Cytoscape app that visualizes post-translational modifications (PTMs) within protein-protein interaction (PPI) networks. It aids in exploring PTMs

Keywords:
Cytoscapedata integrationnetwork visualizationpost-translational modificationprotein-protein interaction

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Post-translational modifications (PTMs) are crucial for regulating protein activity and protein-protein interactions (PPIs).
  • Investigating the functional interplay between PTMs and PPIs presents significant challenges.
  • Understanding these relationships is key to deciphering complex cellular signaling pathways.

Purpose of the Study:

  • To introduce PTMOracle, a Cytoscape application designed for the co-visualization and co-analysis of PTMs within PPI networks.
  • To demonstrate protocols for systematically exploring PTM-associated relationships and their impact on PPIs.
  • To facilitate hypothesis generation regarding the regulatory roles of PTMs in PPIs.

Main Methods:

  • PTMOracle integrates and co-analyzes extensive data, considering domains, motifs, and disordered regions.
  • Utilizes OraclePainter for visualizing proteins colored by their modifications within networks.
  • Employs OracleTools for cross-matching PTMs with sequence features and OracleResults for detailed protein-specific PTM analysis.

Main Results:

  • PTMOracle enables comprehensive network exploration and visualization of PTMs in the context of PPIs.
  • Facilitates the identification of complex PTM-associated regulatory mechanisms.
  • Provides tools for analyzing PTMs in relation to protein sequences and network structures.

Conclusions:

  • PTMOracle offers a systematic approach to investigate the functional significance of PTMs in PPI networks.
  • The application aids researchers in generating testable hypotheses about PTM regulation.
  • Enhances understanding of how PTMs modulate protein interactions and cellular functions.