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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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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 Complex Assembly02:41

Protein Complex Assembly

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.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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High-resolution protein complexes from integrating genomic information with molecular simulation.

Alexander Schug1, Martin Weigt, José N Onuchic

  • 1Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA.

Proceedings of the National Academy of Sciences of the United States of America
|December 19, 2009
PubMed
Summary

This study presents a novel computational method to model transient protein complexes in bacterial two-component signal transduction systems (TCS). The approach accurately predicts structures, enabling insights into cellular signaling pathways.

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Area of Science:

  • Microbiology
  • Structural Biology
  • Biochemistry

Background:

  • Bacteria utilize two-component signal transduction systems (TCS) for environmental sensing and response.
  • These systems involve a sensor histidine kinase (SK) and a response regulator (RR), forming transient complexes that are difficult to study structurally.
  • Existing structural data for homologs like Spo0B/Spo0F provide a basis for computational modeling.

Purpose of the Study:

  • To develop and validate a computational method for generating accurate structural models of transient SK/RR protein complexes.
  • To apply this method to predict the structure of a specific TCS, TM0853/TM0468.

Main Methods:

  • Integration of bioinformatically derived contact residue information with molecular dynamics simulations.
  • Utilizing existing structures of individual proteins to guide complex formation.
  • Validation against crystallographic data of a known SK/RR system (Spo0B/Spo0F).

Main Results:

  • The method achieved crystal resolution accuracy when applied to the Spo0B/Spo0F system.
  • A novel complex structure for the TM0853/TM0468 TCS was successfully generated.
  • The predicted TM0853/TM0468 structure is consistent with available experimental data.

Conclusions:

  • The developed computational approach is effective for modeling transient protein-protein interactions in TCS.
  • This method facilitates structural studies of challenging protein complexes, advancing our understanding of bacterial signaling.
  • The predicted structure of TM0853/TM0468 provides valuable insights into this specific bacterial signaling pathway.