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Related Concept Videos

Entropy02:39

Entropy

35.0K
Salt particles that have dissolved in water never spontaneously come back together in solution to reform solid particles. Moreover, a gas that has expanded in a vacuum remains dispersed and never spontaneously reassembles. The unidirectional nature of these phenomena is the result of a thermodynamic state function called entropy (S). Entropy is the measure of the extent to which the energy is dispersed throughout a system, or in other words, it is proportional to the degree of disorder of a...
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Entropy01:18

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The first law of thermodynamics is quantitatively formulated via an equation relating the internal energy of a system, the heat exchanged by it, and the work done on it. A quantitative formulation of the second law of thermodynamics leads to defining a state function, the entropy.
When an ideal gas expands isothermally, the disorder in the gas increases. From the molecular perspective, the gas molecules have more volume to move around in.
Consider an infinitesimal step in the expansion, which...
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Standard Entropy Change for a Reaction03:00

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Entropy is a state function, so the standard entropy change for a chemical reaction (ΔS°rxn) can be calculated from the difference in standard entropy between the products and the reactants.
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Acid and Bases: Ka, pKa, and Relative Strengths02:35

Acid and Bases: Ka, pKa, and Relative Strengths

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This lesson delves into a critical aspect of the relative strengths of acids and bases. The strength of an acid is evaluated by the acid dissociation into its conjugate base and a hydronium ion in water. The complete dissociation of a strong acid is confirmed with a very high concentration of hydronium ions. As a result, an incomplete dissociation process affirms a weak acid. Therefore, the equilibrium is in the forward direction for strong acids and backward for weak acids in these reactions.
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REDAN: Relative Entropy-Based Dynamical Allosteric Network Model.

Hongyu Zhou1, Peng Tao1

  • 1Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States.

Molecular Physics
|July 30, 2019
PubMed
Summary
This summary is machine-generated.

A new model, the relative entropy-based dynamical allosteric network (REDAN), quantifies protein allosteric responses. This method measures population shifts in protein structures during allosteric transitions, offering insights into cellular signaling.

Keywords:
allosterydistributionnetworkrelative entropy

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Protein allostery is crucial for cellular signaling but lacks accurate quantitative measurement methods.
  • Existing methodologies struggle to precisely measure protein allosteric responses to external perturbations.

Purpose of the Study:

  • To introduce a quantitative model for measuring protein allosteric response.
  • To develop a method for assessing population shifts in protein structures during allosteric transitions.

Main Methods:

  • Introduced the relative entropy concept from information theory as a quantitative metric.
  • Developed the relative entropy-based dynamical allosteric network (REDAN) model.
  • Applied rigorous searching algorithms based on relative entropy to analyze allosteric residues, pathways, and communities.

Main Results:

  • The REDAN model provides a quantitative metric for protein allostery.
  • Allosteric effects can be evaluated at three structural levels: residues, pathways, and communities.
  • Demonstrated metric-based insights into the allostery of the second PDZ domain (PDZ2) in human PTP1E upon peptide binding.

Conclusions:

  • The REDAN model offers a novel approach to quantitatively measure protein allostery.
  • This method enhances understanding of protein dynamics and signaling pathways.
  • Provides valuable insights for drug discovery and protein engineering.