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Thermodynamic Potentials

Thermodynamic Potentials

Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Protein Networks

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 Networks

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,...

Gibbs Free Energy and Thermodynamic Favorability

Gibbs Free Energy and Thermodynamic Favorability

The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:

Thermodynamic Systems

Thermodynamic Systems

A thermodynamic system is a set of objects whose thermodynamic properties are of interest. The system is considered to be embedded in its surroundings or the environment. The system and its environment can exchange heat and do work on each other through a boundary that separates them. However, the immediate surroundings of the system interact with it directly and therefore have a much stronger influence on its behavior and properties.
Consider an example of tea boiling in a kettle. The tea and...

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Related Experiment Video

Updated: Jun 15, 2026

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

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

Published on: July 16, 2017

Thermodynamic database for proteins: features and applications.

M Michael Gromiha¹, Akinori Sarai

¹Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

Methods in Molecular Biology (Clifton, N.J.)

|March 12, 2010

Summary

This summary is machine-generated.

ProTherm is a thermodynamic database for protein stability, offering data on proteins and mutants. This resource aids in understanding and predicting protein stability using various analytical methods.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Protein stability is crucial for protein function.
Predicting protein stability is essential for protein engineering and drug design.

Purpose of the Study:

To develop and present ProTherm, a comprehensive thermodynamic database for proteins and mutants.
To analyze the relationships between protein thermodynamics, structure, and function.
To outline methods for predicting protein stability.

Main Methods:

Compilation of thermodynamic data for proteins and mutants.
Development of ProTherm database with search, display, and visualization tools.
Analysis of relationships between amino acid properties and mutant stability, empirical energy functions, and machine learning techniques.

Main Results:

ProTherm database established, containing extensive thermodynamic data, sequence, structure, and experimental information.
Analysis revealed insights into protein thermodynamics, structure, and function.
Various methods for predicting protein stability were explored and documented.

Conclusions:

ProTherm serves as a valuable resource for researchers studying protein stability.
The database facilitates understanding and prediction of protein stability.
Progress in developing predictive methods for protein stability has been made.