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Related Concept Videos

Protein Networks02:26

Protein Networks

4.1K
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,...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

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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.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Protein Folding01:22

Protein Folding

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Overview
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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Mapping Function from Dynamics: Future Challenges for Network-Based Models of Protein Structures.

Lorenza Pacini1,2, Rodrigo Dorantes-Gilardi2,3, Laurent Vuillon3

  • 1Ecole Centrale de Lyon, Ampère, UMR5005, Univ. Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.

Frontiers in Molecular Biosciences
|October 28, 2021
PubMed
Summary
This summary is machine-generated.

Protein function is encoded by atomic motions, not just sequence or structure. Network models analyzing protein structures can help identify these dynamic patterns and their relation to biological roles.

Keywords:
network-based modelsprotein dynamicsprotein functionprotein structurespace occupancy

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Proteins perform functions via dynamic atomic motions.
  • Neither amino acid sequence nor unique structure solely encodes protein function.
  • A set of atomic motions, adaptable across sequences and structures, likely encodes function.

Purpose of the Study:

  • Investigate the link between protein dynamics and function.
  • Explore network models for analyzing protein structural data.
  • Identify network measures relevant to functional dynamics.

Main Methods:

  • Utilizing atomic coordinates from the Protein Data Bank.
  • Applying network models to protein structures.
  • Integrating network analysis with experimental data or Molecular Dynamics (MD) simulations.

Main Results:

  • Network models can analyze protein features from structural data.
  • Combining network analysis with experimental or simulation data aids in deciphering protein dynamics.
  • Static structure analysis can reveal network measures relevant to dynamics.

Conclusions:

  • Protein function is intrinsically linked to a set of dynamic atomic motions.
  • Network-based approaches offer a powerful framework for studying protein functional dynamics.
  • Further research can leverage these methods to classify functionally robust, adaptable, or faulty protein dynamics.