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Related Concept Videos

Facilitated Transport01:19

Facilitated Transport

152.4K
The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a...
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Facilitated Transport01:19

Facilitated Transport

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The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a...
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Facilitated Diffusion01:16

Facilitated Diffusion

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The plasma membrane, a critical structure in cellular biology, houses an array of transporters, or carrier proteins, interspersed within its lipid bilayer. These proteins play a crucial role in solute transport through facilitated diffusion, a form of passive diffusion that uses transporters to move the molecules across the membrane.
In this process, substrates such as organic compounds and ions interact with a transporter on one side, triggering conformational changes in proteins that enable...
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Diffusion01:12

Diffusion

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Diffusion is the passive movement of substances down their concentration gradients—requiring no expenditure of cellular energy. Substances, such as molecules or ions, diffuse from an area of high concentration to an area of low concentration in the cytosol or across membranes. Eventually, the concentration will even out, with the substance moving randomly but causing no net change in concentration. Such a state is called dynamic equilibrium, which is essential for maintaining overall...
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Diffusion01:21

Diffusion

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Diffusion is a type of passive transport. In passive transport, a substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. For example, take the diffusion of substances through the air. When someone opens a perfume bottle in a room filled with people, the perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the...
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Protein Diffusion in the Membrane01:24

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Microscale Vortex-assisted Electroporator for Sequential Molecular Delivery
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Energetic funnel facilitates facilitated diffusion.

Massimo Cencini1, Simone Pigolotti2,3,4

  • 1Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, via dei Taurini 19, 00185 Rome, Italy.

Nucleic Acids Research
|December 8, 2017
PubMed
Summary
This summary is machine-generated.

Transcription factors (TFs) rapidly find DNA binding sites using facilitated diffusion, a process enhanced by an energy landscape funnel. This funnel, driven by DNA base composition gradients, significantly speeds up TF association.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Transcription factors (TFs) bind to specific DNA sequences to regulate gene expression.
  • The rate at which TFs find their binding sites often exceeds diffusion-limited speeds.
  • Facilitated diffusion, involving 3D diffusion and 1D sliding, is a proposed mechanism for rapid TF binding.

Purpose of the Study:

  • To investigate the role of DNA binding energy landscapes in TF association rates.
  • To explore the relationship between DNA base composition and TF binding efficiency.
  • To computationally model and validate the facilitated diffusion mechanism for TF-DNA interactions.

Main Methods:

  • Analysis of TF binding sites from Escherichia coli (RegulonDB) and Bacillus subtilis (DBTBS) databases.
  • Computational modeling of stochastic sliding processes along DNA.
  • Characterization of DNA binding energy landscapes and base composition gradients (AT content).

Main Results:

  • A binding energy landscape funnel was identified around TF target sequences.
  • The presence of AT-rich gradients in flanking DNA regions correlates with the funnel structure.
  • Computational simulations demonstrated that the funnel significantly enhances TF target search probability during sliding.

Conclusions:

  • The binding energy funnel, influenced by DNA base composition, accelerates transcription factor association.
  • Facilitated diffusion, aided by this funnel, explains the rapid kinetics of TF-DNA binding.
  • This mechanism provides a deeper understanding of gene regulation efficiency in prokaryotes.