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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...
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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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 Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: Jun 23, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Computational methods for predicting sites of functionally important dynamics.

Adam D Schuyler1, Heather A Carlson, Eva L Feldman

  • 1Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, USA. aschuyle@umich.edu

The Journal of Physical Chemistry. B
|April 22, 2009
PubMed
Summary
This summary is machine-generated.

Two new deterministic methods predict protein dynamic control sites by analyzing atomic connectivity and normal mode analysis. These computational tools enhance understanding of allosteric mechanisms and protein function.

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Published on: December 7, 2021

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Allosteric mechanisms are crucial for controlling protein biological function at the atomic level.
  • Current methods for identifying functionally relevant mutations often rely on random sampling, lacking mechanistic insight.
  • Understanding protein dynamics is key to deciphering allosteric regulation.

Purpose of the Study:

  • To develop deterministic computational methods for predicting dynamic control sites in proteins.
  • To identify locations experiencing correlated motions due to altered protein dynamics.
  • To provide tools for enhancing allosteric investigations and protein engineering.

Main Methods:

  • A "static" method using graph theory on a single protein structure to map atomic connectivity and identify flexible regions.
  • A "dynamic" method comparing normal modes of wild-type and mutant protein structures using a mapping function to quantify motion changes.
  • Application of both methods to dihydrofolate reductase (DHFR) as a model system.

Main Results:

  • Both methods accurately predicted known dynamic control sites in DHFR with high statistical significance (p<0.005).
  • The "static" method identified flexible locations susceptible to altered dynamics based on atomic interactions.
  • The "dynamic" method revealed altered motion correlations and proposed a novel mechanism for DHFR hyperactivity.

Conclusions:

  • The developed deterministic methods offer a structure-function approach to predict dynamic control sites.
  • These computational tools can significantly accelerate and improve the efficiency of allosteric mechanism studies.
  • The methods are broadly applicable to protein dynamics analysis and functional site prediction.