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Related Concept Videos

Protein Networks02:26

Protein Networks

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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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Dynamic Modulus of Elasticity of Concrete01:16

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The dynamic modulus of elasticity assesses how a concrete structure deforms under impact or dynamic loads. It is typically higher than the static modulus of elasticity, measured under slow, steady loading conditions.
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Elastic collision of a system demands conservation of both momentum and kinetic energy. To solve problems involving one-dimensional elastic collisions between two objects, the equations for conservation of momentum and conservation of internal kinetic energy can be used. For the two objects, the sum of momentum before the collision equals the total momentum after the collision. An elastic collision conserves internal kinetic energy, and so the sum of kinetic energies before the collision equals...
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Shape and Texture of Coarse Aggregate01:25

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Aggregate shape is classified based on the relative sharpness or roundness of the edges and corners. This classification includes categories like rounded, angular, elongated, and flaky, each with specific characteristics. Rounded aggregates, fully shaped by attrition, are typical of river or seashore gravel, while angular aggregates, such as crushed rock, have well-defined edges. Aggregates that are elongated and flaky are less desirable, as they can reduce the workability and strength of...
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Elasticity01:12

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Elasticity is the ability of an object to withstand the effects of distortion and to return to its original size and shape once the forces causing deformation are removed. When an elastic material deforms under the action of an external force, it experiences internal resistance to the deformation. However, if no external force is applied, it returns to its original state.
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Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.

Yuichi Togashi1,2,3, Holger Flechsig4

  • 1Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan. togashi@hiroshima-u.ac.jp.

International Journal of Molecular Sciences
|December 20, 2018
PubMed
Summary
This summary is machine-generated.

Elastic network models offer a computationally efficient way to study protein dynamics. These simplified models provide insights into large-scale movements and are useful for comparing multiple protein structures.

Keywords:
allosterycoarse-grained modelelastic networkmolecular dynamicsmolecular machinenonlinearitynormal mode analysisprotein

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Elastic network models (ENMs) are simplified representations of proteins, utilizing particles and springs.
  • They are effective for analyzing protein dynamics and structural changes.
  • ENMs offer a computational advantage over all-atom models.

Purpose of the Study:

  • To review coarse-grained molecular dynamics studies using ENMs.
  • To highlight nonlinear phenomena in protein dynamics.
  • To discuss the application of ENMs to large macromolecular assemblies.

Main Methods:

  • Linear normal mode analysis around a reference structure.
  • Dynamic simulations using elastic network models.
  • Comparative studies between multiple protein structures.

Main Results:

  • ENMs facilitate the study of slow structural dynamics in proteins.
  • Dynamic simulations with ENMs provide novel insights into protein behavior.
  • ENMs are cost-effective for comparative analyses of protein structures.

Conclusions:

  • Elastic network models are valuable tools for understanding protein dynamics.
  • These models are applicable to the study of large-scale macromolecular assemblies.
  • Focus on nonlinear phenomena reveals complex behaviors in protein structures.