title: Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins.
abstract: Since Robert Brown's first observations of random walks by pollen particles suspended in solution, the concept of diffusion has been subject to countless theoretical and experimental studies in diverse fields from finance and social sciences, to physics and biology. Diffusive transport of macromolecules in cells is intimately linked to essential cellular functions including nutrient uptake, signal transduction, gene expression, as well as DNA replication and repair. Advancement in experimental techniques has allowed precise measurements of these diffusion processes. Mathematical and physical descriptions and computer simulations have been applied to model complicated biological systems in which anomalous diffusion, in addition to simple Brownian motion, was observed. The purpose of this review is to provide an overview of the major physical models of anomalous diffusion and corresponding experimental evidence on the target search problem faced by DNA-binding proteins, with an emphasis on DNA repair proteins and the role of anomalous diffusion in DNA target recognition.
authors.affiliation: Department of Pharmacology and Chemical Biology, Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA 15213, United States.
authors.forename: Muwen
authors.initials: M
authors.lastname: Kong
authors.affiliation: Department of Pharmacology and Chemical Biology, Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA 15213, United States. Electronic address: vanhoutenb@upmc.edu.
authors.forename: Bennett
authors.initials: B
authors.lastname: Van Houten
mesh_terms: D000818:Animals; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D004058:Diffusion; D006801:Humans; D011487:Protein Conformation
chemical_list: D004268:DNA-Binding Proteins
keywords: Anomalous diffusion; Brownian motion; Constrained motion; Facilitated diffusion; Nucleotide excision repair; Protein-DNA interactions; Rad4-Rad23; Single-molecule imaging