Intracellular facilitated diffusion: searchers, crowders and blockers

Abstract

In bacteria, regulatory proteins search for a specific DNA binding target via "facilitated diffusion": a series of rounds of 3D diffusion in the cytoplasm, and 1D linear diffusion along the DNA contour. Using large scale Brownian dynamics simulations we find that each of these steps is affected differently by crowding proteins, which can either be bound to the DNA acting as a road block to the 1D diffusion, or freely diffusing in the cytoplasm. Macromolecular crowding can strongly affect mechanistic features such as the balance between 3D and 1D diffusion, but leads to surprising robustness of the total search time.

References in corpus (5)

• Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential
• Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
• Effects of intersegmental transfers on target location by proteins
• Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model
• Comparison of kinetic and dynamical models of DNA-protein interaction and facilitated diffusion

Cited by in corpus (12)

• Anomalous, non-Gaussian tracer diffusion in heterogeneously crowded environments
• Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects
• Optimization and universality of Brownian search in quenched heterogeneous media
• Energetic funnel facilitates facilitated diffusion
• Investigating the interplay between mechanisms of anomalous diffusion via fractional Brownian walks on a comb-like structure
• Physical constraints determine the logic of bacterial promoter architectures
• Target search on DNA by interacting molecules: First-passage approach
• Facilitated diffusion buffers noise in gene expression
• The robustness of proofreading to crowding-induced pseudo-processivity in the MAPK pathway
• Polymer brush-induced depletion interactions and clustering of membrane proteins
• The Effect of Obstacles in Multi-Site Protein Target Search with DNA Looping
• A nonequilibrium strategy for fast target search on the genome