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Related Concept Videos

Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
Gibbs Free Energy02:39

Gibbs Free Energy

One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
An Introduction to Free Energy01:05

An Introduction to Free Energy

How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. According to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy...
Gibbs Free Energy and Thermodynamic Favorability02:23

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:
Free Energy and Equilibrium00:55

Free Energy and Equilibrium

The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔG is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
The reaction quotient, Q, is a convenient measure of the status of an...

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Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System
12:30

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Published on: February 9, 2017

Free energy surfaces from single-distance information.

Philipp Schuetz1, René Wuttke, Benjamin Schuler

  • 1Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.

The Journal of Physical Chemistry. B
|October 23, 2010
PubMed
Summary

We developed a network-based method to map protein folding landscapes using a single distance measurement. This approach accurately identifies protein states and folding barriers from molecular dynamics simulations and single-molecule FRET experiments.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Statistical Mechanics

Background:

  • Complex free energy surfaces, like protein folding landscapes, are challenging to characterize.
  • Traditional methods often require extensive data or multiple reaction coordinates.

Purpose of the Study:

  • To develop a novel network-based method for determining free energy landscapes from limited data.
  • To accurately identify protein basins and barriers using a single intramolecular distance time series.

Main Methods:

  • Constructing a transition network by clustering time series data based on short-time distributions.
  • Utilizing a minimum-cut-based free energy profile for barrier-preserving dimensionality reduction.
  • Applying the method to molecular dynamics (MD) simulations and emulated single-molecule Förster resonance energy transfer (FRET) data.

Main Results:

  • Accurate determination of the native state and unfolding barrier (approx. 10 kJ/mol) for a β-sheet peptide using a single C(β)-C(β) distance from MD simulations.
  • Identification of non-native conformers by analyzing long-time distance distributions.
  • Successful application to emulated FRET data and real single-molecule FRET measurements, correctly identifying folded and unfolded populations.

Conclusions:

  • The network-based method provides an accurate and efficient approach to characterizing complex free energy landscapes.
  • This method is applicable to both simulation data and experimental measurements like single-molecule FRET.
  • It offers a powerful tool for understanding protein folding dynamics with minimal input data.