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Related Concept Videos

¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
Arrhenius Plots02:34

Arrhenius Plots

The Arrhenius equation relates the activation energy and the rate constant, k, for chemical reactions. In the Arrhenius equation, k = Ae−Ea/RT, R is the ideal gas constant, which has a value of 8.314 J/mol·K, T is the temperature on the kelvin scale, Ea is the activation energy in J/mole, e is the constant 2.7183, and A is a constant called the frequency factor, which is related to the frequency of collisions and the orientation of the reacting molecules.
The Arrhenius equation can be used to...
Energy Diagrams - I01:14

Energy Diagrams - I

The dynamics of a mechanical system can be easily understood by interpreting a potential energy diagram. Since energy is a scalar quantity, the interpretation of the dynamics of the system becomes even simpler.
Take the example of a skater on a parabolic ramp. The potential energy at different points along the ramp will be proportional to the height of the ramp, which varies quadratically with the horizontal position on the ramp. As the skater moves down the ramp from the highest position,...
Energy Diagrams - II01:10

Energy Diagrams - II

Energy diagrams are important to understand the dynamics of a system. The topology of an energy diagram helps illustrate the equilibrium points of the system.
The point in the energy diagram at which the system’s potential energy is the lowest is known as the local minima. The system tends to stay in this position indefinitely unless acted upon by a net force. The slope of the potential energy diagram at the local minima is zero, indicating that zero net force is acting on the system. The slope...
Phase Diagrams02:39

Phase Diagrams

A phase diagram combines plots of pressure versus temperature for the liquid-gas, solid-liquid, and solid-gas phase-transition equilibria of a substance. These diagrams indicate the physical states that exist under specific conditions of pressure and temperature and also provide the pressure dependence of the phase-transition temperatures (melting points, sublimation points, boiling points). Regions or areas labeled solid, liquid, and gas represent single phases, while lines or curves represent...
pV-Diagrams01:18

pV-Diagrams

The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...

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Related Experiment Video

Updated: May 31, 2026

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions
11:22

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Published on: January 30, 2018

Behind the folding funnel diagram.

Martin Karplus1

  • 1Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. marci@tammy.harvard.edu

Nature Chemical Biology
|June 21, 2011
PubMed
Summary
This summary is machine-generated.

This commentary clarifies the protein folding funnel diagram, explaining how decreasing configurational entropy hinders folding. New diagrams offer a clearer representation of protein folding mechanisms than traditional funnel diagrams.

More Related Videos

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
10:09

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Published on: April 28, 2011

Related Experiment Videos

Last Updated: May 31, 2026

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions
11:22

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Published on: January 30, 2018

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
10:09

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Published on: April 28, 2011

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Physical Chemistry

Background:

  • The funnel diagram is widely used to depict protein folding.
  • Understanding protein folding mechanisms is crucial in molecular biology.
  • Historical approaches to protein folding lack clarity.

Purpose of the Study:

  • To clarify the interpretation of the protein folding funnel diagram.
  • To review historical perspectives on protein folding mechanisms.
  • To introduce improved diagrams for representing protein folding.

Main Methods:

  • Review of historical literature on protein folding.
  • Analysis of the role of free energy and entropy in protein folding.
  • Development of alternative graphical representations.

Main Results:

  • The decrease in configurational entropy hinders protein folding.
  • The traditional funnel diagram can be ambiguous.
  • New diagrams provide a less ambiguous representation.

Conclusions:

  • The interpretation of the protein folding funnel diagram needs clarification.
  • Alternative diagrams better represent the factors governing protein folding.
  • Understanding entropy's role is key to protein folding research.