A mini-review of the diffusion dynamics of DNA-binding proteins: Experiments and models
arXiv:2011.00219 · doi:10.1007/s40042-021-00060-y
Abstract
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet, investigations over recent decades have found that the diffusion dynamics of DNA-binding proteins are generally complicated and, further, protein-specific. In this review, we collect the experimental and theoretical studies that quantify the diffusion dynamics of DNA-binding proteins and review them from the viewpoint of diffusion processes.
References in corpus (24)
- Superstatistics
- Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential
- Dynamical foundations of nonextensive statistical mechanics
- Universal nature of particle displacements close to glass and jamming transitions
- "Diffusing diffusivity": A model for anomalous and "anomalous yet Brownian" diffusion
- Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes
- Random diffusivity from stochastic equations: comparison of two models for Brownian yet non-Gaussian diffusion
- Distance matters: the impact of gene proximity in bacterial gene regulation
- Inequivalence of time and ensemble averages in ergodic systems: exponential versus power-law relaxation in confinement
- Population splitting, trapping, and non-ergodicity in heterogeneous diffusion processes
- Non-ergodicity, fluctuations, and criticality in heterogeneous diffusion processes
- Infinite Ergodic Theory for Heterogeneous Diffusion Processes
- In vivo facilitated diffusion model
- Langevin equation with fluctuating diffusivity: a two-state model
- Non-specific DNA-protein interaction: Why proteins can diffuse along DNA
- Tracer diffusion in a sea of polymers with binding zones: mobile vs frozen traps
- Anomalous features of diffusion in corrugated potentials with spatial correlations: faster than normal, and other surprises
- Localization and universal fluctuations in ultraslow diffusion processes
- Brownian motion with alternately fluctuating diffusivity: Stretched-exponential and power-law relaxation
- Base sequence dependent sliding of proteins on DNA
- Viscoelastic subdiffusion in a random Gaussian environment
- Persistent Sinai type diffusion in Gaussian random potentials with decaying spatial correlations
- Subdiffusive rocking ratchets in viscoelastic media: transport optimization and thermodynamic efficiency in overdamped regime
- Normal and anomalous diffusion of Brownian particles on disordered potentials