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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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Protein Dynamics in Living Cells01:19

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Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
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Structural Protein Function01:56

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Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
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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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DynOmics: dynamics of structural proteome and beyond.

Hongchun Li1, Yuan-Yu Chang2, Ji Young Lee1

  • 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh PA, 15213, USA.

Nucleic Acids Research
|May 5, 2017
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Summary

DynOmics portal and ENM 1.0 server analyze protein dynamics using elastic network models. They assess functional sites and conformational ensembles considering the molecular environment.

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Bioinformatics

Background:

  • Structural proteomics data is rapidly growing.
  • Understanding protein dynamics is crucial for biological function.
  • Existing methods may not fully capture environmental influences on dynamics.

Purpose of the Study:

  • To develop a portal (DynOmics) and server (ENM 1.0) for analyzing protein dynamics.
  • To integrate and extend elastic network models (ENMs) to include molecular environment.
  • To provide tools for assessing functional sites and conformational changes.

Main Methods:

  • Utilized Gaussian Network Model (GNM) and Anisotropic Network Model (ANM).
  • Extended ENMs to incorporate environmental factors (e.g., lipid bilayers, ligands).
  • Developed a user-friendly portal for PDB structure analysis and visualization.

Main Results:

  • ENM 1.0 efficiently evaluates collective dynamics of proteins and complexes.
  • The server predicts functional sites, allosteric mechanisms, and interaction poses.
  • Generated ensembles of conformers based on predicted motion modes.

Conclusions:

  • DynOmics and ENM 1.0 provide a comprehensive platform for studying protein dynamics.
  • Environmental context significantly influences protein conformational ensembles.
  • The tools facilitate the investigation of structure-function relationships.