How a protein searches for its site on DNA: the mechanism of facilitated diffusion

DOI10.1088/1751-8113/42/43/434013zbMath1173.92014OpenAlexW2074142433MaRDI QIDQ3643250

Anahita Tafvizi, Jason Leith, Leonid Mirny, Michael Slutsky, Zeba Wunderlich, Andrej Košmrlj

Publication date: 10 November 2009

Published in: Journal of Physics A: Mathematical and Theoretical (Search for Journal in Brave)

Full work available at URL: https://semanticscholar.org/paper/627170dfb22406b73884907305e18d40b9fe4566

Mathematics Subject Classification ID

Probabilistic models, generic numerical methods in probability and statistics (65C20) Biochemistry, molecular biology (92C40) Biophysics (92C05) Computational methods for problems pertaining to biology (92-08)

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A first-passage kinetic Monte Carlo method for reaction-drift-diffusion processes ⋮ Protein diffusion along DNA: on the effect of roadblocks and crowders ⋮ The influence of spatial variation in chromatin density determined by X-ray tomograms on the time to find DNA binding sites ⋮ Stochastic switching in biology: from genotype to phenotype ⋮ Transcription factor target site search and gene regulation in a background of unspecific binding sites ⋮ Generalized theory on the mechanism of site-specific DNA–protein interactions ⋮ First-passage processes on a filamentous track in a dense traffic: optimizing diffusive search for a target in crowding conditions ⋮ Simulation and Optimization of Mean First Passage Time Problems in 2-D Using Numerical Embedded Methods and Perturbation Theory ⋮ Theoretical study of the role of dynamic bulk crowders in the protein search for targets on DNA ⋮ Span observables: ``when is a foraging rabbit no longer hungry? ⋮ The helical structure of DNA facilitates binding ⋮ Target search of a protein on DNA in the presence of position-dependent bias ⋮ A theoretical study of the role of bulk crowders on target search dynamics of DNA binding proteins ⋮ Generalized master equation for first-passage problems in partitioned spaces

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