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Related Concept Videos

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

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 Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the translocon complex.
Protein-protein Interfaces02:04

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 polypeptide...
Protein-Protein Interfaces02:04

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 polypeptide...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
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Published on: August 21, 2019

Dynamical networks in tRNA:protein complexes.

Anurag Sethi1, John Eargle, Alexis A Black

  • 1Department of Chemistry,University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Proceedings of the National Academy of Sciences of the United States of America
|April 9, 2009
PubMed
Summary
This summary is machine-generated.

Network analysis reveals conserved allosteric signaling pathways in aminoacyl-tRNA synthetases (aaRS) despite diverse molecular interactions. Key residues and nucleotides are crucial for efficient signal transmission in these essential protein:RNA complexes.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Class I aminoacyl-tRNA synthetases (aaRS) are crucial enzymes for protein synthesis.
  • Bacterial glutamyl-tRNA synthetase (GluRS):tRNA(Glu) and archaeal leucyl-tRNA synthetase (LeuRS):tRNA(Leu) complexes represent distinct aaRS systems.
  • Understanding allosteric signaling in these complexes is key to deciphering enzyme regulation.

Purpose of the Study:

  • To identify and compare allosteric signaling pathways in bacterial GluRS:tRNA(Glu) and archaeal LeuRS:tRNA(Leu) complexes.
  • To investigate the conserved mechanisms of tRNA aminoacylation regulation.
  • To pinpoint critical residues and nucleotides involved in inter-community communication.

Main Methods:

  • Community network analysis applied to molecular dynamics simulations.
  • Construction of dynamic contact maps to represent physical interaction networks.
  • Identification of highly interconnected communities and critical communication pathways within aaRS:tRNA complexes.

Main Results:

  • Despite different molecular interactions, conserved similarities exist in the allosteric networks for tRNA charging.
  • Network topology reveals distinct communities with numerous internal communication pathways.
  • Signal transmission between communities relies on a limited set of critical interactions.
  • Evolutionarily conserved residues and nucleotides are enriched in inter-community signaling pathways.

Conclusions:

  • Allosteric signaling in class I aaRS:tRNA complexes exhibits conserved features despite evolutionary divergence.
  • Specific residues and nucleotides play pivotal roles in mediating communication across the network.
  • These findings provide insights into the regulatory mechanisms of protein synthesis and potential drug targets.