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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 Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview

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Related Experiment Video

Updated: May 22, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Elastic network normal modes provide a basis for protein structure refinement.

Pawel Gniewek1, Andrzej Kolinski, Robert L Jernigan

  • 1Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.

The Journal of Chemical Physics
|May 23, 2012
PubMed
Summary
This summary is machine-generated.

Elastic network models (ENMs) capture protein thermal motions. Analyzing non-native states reveals that protein thermal motions overlap with deformations needed for native structure refinement, especially for mobile residues.

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Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

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Last Updated: May 22, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Elastic Network Models (ENMs), like the anisotropic network model (ANM), accurately represent protein native state thermal motions.
  • ENMs model protein dynamics as interconnected nodes with harmonic springs, explaining conformational changes crucial for functions like ligand binding.

Purpose of the Study:

  • To investigate protein structure refinement by analyzing thermal motions in non-native states.
  • To explore the relationship between thermal fluctuations and conformational changes required for reaching the native state.

Main Methods:

  • Utilized I-TASSER server for template-free modeling to generate protein decoys representing conformational space near the native state.
  • Employed hierarchical structure clustering to select relevant protein substates.
  • Analyzed thermal motions within these substates and compared them to necessary deformations for native structure.

Main Results:

  • Significant overlap was observed between thermal motions in certain substates and the deformations required to achieve the native state.
  • More mobile residues exhibited higher overlap with necessary deformations compared to less mobile residues.

Conclusions:

  • Protein thermal motions in non-native states contain information relevant to structure refinement.
  • Reducing conformational space to dominant normal modes can enhance the refinement of poorly resolved protein models.