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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Extraction: Partition and Distribution Coefficients01:14

Extraction: Partition and Distribution Coefficients

The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
For extracting a solute from an aqueous phase into an organic...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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 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-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...

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Related Experiment Video

Updated: May 24, 2026

Determination of Plasma Membrane Partitioning for Peripherally-associated Proteins
11:11

Determination of Plasma Membrane Partitioning for Peripherally-associated Proteins

Published on: June 15, 2018

Empirical protein partition functions.

Douglas Poland1

  • 1Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA.

The Journal of Physical Chemistry. B
|March 1, 2012
PubMed
Summary

This study presents a method to calculate a protein's partition function using heat capacity data. This approach allows for the determination of thermodynamic properties and can visually indicate distinct protein states.

Area of Science:

  • Biophysics
  • Statistical Mechanics
  • Thermodynamics

Background:

  • Proteins exhibit complex thermodynamic behavior influenced by their energy landscape.
  • Calculating thermodynamic functions from empirical data is crucial for understanding protein stability and folding.
  • Traditional methods may rely on assumptions about distinct protein states.

Purpose of the Study:

  • To outline a method for constructing a protein's partition function from empirical heat capacity data.
  • To enable the calculation of all thermodynamic functions of a protein as a function of temperature.
  • To provide a graphical method for assessing the validity of assuming distinct protein states (e.g., native and denatured).

Main Methods:

  • Calculating energy moments from the temperature dependence of heat capacity data.

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  • Employing the maximum-entropy method to derive an approximate protein energy distribution.
  • Utilizing the energy distribution to determine energy level degeneracy.
  • Constructing the partition function using degeneracy information.

    • Main Results:

    • A procedure to build the partition function from empirical heat capacity measurements.
    • The ability to compute thermodynamic functions (free energy, energy, entropy, heat capacity) and energy probability distributions.
    • A visualization tool (3D plot) to assess the approximation of distinct protein states.

    Conclusions:

    • Empirical heat capacity data can be used to construct a protein's partition function.
    • This method allows for comprehensive thermodynamic analysis without prior assumptions about protein states.
    • The approach offers insights into protein conformational heterogeneity and stability.