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Related Concept Videos

Entropy02:39

Entropy

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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.
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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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Molecular Chaperones and Protein Folding03:00

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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Entropy and Solvation02:05

Entropy and Solvation

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The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ...
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Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis
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Measuring Entropy in Molecular Recognition by Proteins.

A Joshua Wand1, Kim A Sharp1

  • 1Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; email: wand@pennmedicine.upenn.edu , sharpk@pennmedicine.upenn.edu.

Annual Review of Biophysics
|January 19, 2018
PubMed
Summary

Understanding protein-ligand interactions is key in biology. This study uses a dynamical proxy, or "entropy meter," to measure conformational entropy, revealing its significant impact on molecular recognition and protein function.

Keywords:
NMR relaxationconformational entropymolecular recognitionprotein dynamicsrotational–translational entropysolvation entropy

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Area of Science:

  • Biophysics
  • Structural Biology
  • Biochemistry

Background:

  • Molecular recognition by proteins is central to biological processes.
  • Quantifying the thermodynamic landscape of protein-ligand interactions, especially entropic contributions, remains a significant challenge.

Purpose of the Study:

  • To review the relationship between fast side-chain motion and conformational entropy in proteins.
  • To explore the utility of a dynamical proxy, termed the "entropy meter," for assessing entropic contributions to molecular recognition.

Main Methods:

  • Utilizing Nuclear Magnetic Resonance (NMR) relaxation measurements.
  • Employing theoretical calculations and molecular dynamics simulations.
  • Analyzing the correlation between side-chain dynamics and conformational entropy.

Main Results:

  • Fast side-chain motion serves as a reliable dynamical proxy for conformational entropy.
  • Conformational entropy can significantly influence protein-ligand interactions, ranging from favorable to unfavorable.
  • The "entropy meter" refines understanding of solvent entropy and quantifies the loss of rotational-translational entropy in complexes.

Conclusions:

  • Measurable dynamical properties can quantify entropic roles in protein function.
  • The dynamical "entropy meter" provides a powerful tool for dissecting thermodynamic contributions to protein-ligand binding.
  • This approach promises to enhance our understanding of how entropy modulates protein function.