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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
Free Energy01:21

Free Energy

Free energy—abbreviated as G for the scientist Gibbs who discovered it—is a measurement of useful energy that can be extracted from a reaction to do work. It is the energy in a chemical reaction that is available after entropy is accounted for. Reactions that take in energy are considered endergonic and reactions that release energy are exergonic. Plants carry out endergonic reactions by taking in sunlight and carbon dioxide to produce glucose and oxygen. Animals, in turn, break down the...
One-Degree-of-Freedom System01:24

One-Degree-of-Freedom System

In mechanical engineering, one-degree-of-freedom systems form the basis of a wide range of electrical and mechanical components. Using these models, engineers can predict the behavior of various parts in a larger system, which gives them insight into how different forces interact with each other.
A one-degree-of-freedom system is defined by an independent variable that determines its state and behavior. One example of a one-degree-of-freedom system is a simple harmonic oscillator, such as a...
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Force and Potential Energy in Three Dimensions01:04

Force and Potential Energy in Three Dimensions

Consider a particle moving under the action of a conservative force that has components along each coordinate axis. Each component of force is a function of the coordinates. The potential energy function U is also a function of all three spatial coordinates. Force in one dimension can be written as the negative ratio of potential energy change to the displacement along that coordinate. For minimal displacement, the ratios become derivatives. If a function has many variables, the derivative only...

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Path finding on high-dimensional free energy landscapes.

Grisell Díaz Leines1, Bernd Ensing

  • 1Van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.

Physical Review Letters
|October 4, 2012
PubMed
Summary

We developed a new method to calculate the average transition path and free energy using collective variables. This approach efficiently samples conformational changes, like in alanine dipeptide, for better molecular understanding.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Biophysics

Background:

  • Determining transition paths and free energy landscapes is crucial for understanding molecular processes.
  • Existing methods can be computationally expensive, especially with multiple collective variables.

Purpose of the Study:

  • To present a novel, efficient method for calculating average transition paths and associated free energies.
  • To apply this method to analyze conformational transitions in molecular systems.

Main Methods:

  • A history-dependent bias within the metadynamics framework is employed.
  • The method utilizes selected collective variables and controls orthogonal mode sampling.
  • The computational cost scales trivially with the number of collective variables.

Main Results:

  • The method successfully determines the average transition path and free energy.
  • It recovers the minimum free energy path in a limiting case.
  • The conformational transition of alanine dipeptide was resolved, including its path and free energy.

Conclusions:

  • The developed method offers an efficient approach to characterize molecular transitions.
  • It provides valuable insights into free energy landscapes and reaction pathways.
  • This technique is applicable to various molecular systems and conformational changes.