Related Experiment Video
Updated: May 7, 2026
06:48
Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
Published on: January 5, 2024
DNA-binding-protein inhomogeneity in E. coli modeled as biphasic facilitated diffusion
Thomas E Kuhlman1, Edward C Cox
1Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3080, USA.
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|September 17, 2013
Summary
Nonspecifically bound lac repressors show spatial inhomogeneity in E. coli cells. This is modeled as diffusion between DNA and cytoplasm, impacting target search.
Area of Science:
- Molecular Systems Biology
- Microbiology
- Biophysics
Background:
- Nonspecifically bound lac repressors exhibit spatial inhomogeneity within E. coli.
- This distribution is influenced by the encoding gene's location and DNA compaction.
Purpose of the Study:
- To model the spatial inhomogeneity of lac repressors in E. coli.
- To understand the role of intracellular diffusion and compartmentalization in protein distribution.
- To explore the implications for DNA-binding protein target search efficiency.
Main Methods:
- Computational modeling of intracellular diffusion.
- Phase separation model considering condensed DNA and cytoplasm.
- Analysis of lac repressor behavior within these compartments.
Main Results:
- Lac repressor inhomogeneity arises from diffusion and exchange between DNA and cytoplasmic phases.
- The model explains observed spatial distributions based on biophysical principles.
- Compartmentalization significantly affects the accessibility and search dynamics of lac repressors.
Conclusions:
- Intracellular compartmentalization and diffusion are key determinants of lac repressor localization.
- The proposed two-phase model provides a framework for understanding non-specific protein binding and target search in bacteria.
- This work has implications for gene regulation and the dynamics of DNA-protein interactions within living cells.
Related Concept Videos
01:24Protein Diffusion in the Membrane
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...
01:13Physiological Pharmacokinetic Models: Assumption with Protein Binding
Physiological models with protein binding in pharmacokinetics offer a sophisticated approach to understanding drug disposition. These models consider drug-protein interactions, enabling them to effectively predict drug concentrations in different organs and tissues. This precision aids in accurate drug dosing, providing a significant advantage over conventional models. A key process within these models is equilibration, which ensures that drug concentrations achieve a steady state within the...
01:03Single-Strand DNA Binding Proteins
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
01:27Chemotaxis in E. coli
Chemotaxis in Escherichia coli is a sensory-driven motility mechanism that enables bacteria to navigate chemical gradients, moving toward beneficial environments while avoiding harmful conditions. This process relies on a signal transduction system integrating external chemical cues with flagellar motor control.Chemoreceptors and Signal DetectionE. coli detects chemical gradients through methyl-accepting chemotaxis proteins (MCPs), which are membrane-bound chemoreceptors that sense attractants...