Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

Abstract

To perform their functions, transcription factors and DNA-repair/modifying enzymes randomly search DNA in order to locate their specific targets on DNA. Discrete-state stochastic kinetic models have been developed to explain how the efficiency of the search process is influenced by the molecular properties of proteins and DNA as well as by other factors such as molecular crowding. These theoretical models not only offer explanations on the relation of microscopic processes to macroscopic behavior of proteins, but also facilitate the analysis and interpretation of experimental data. In this review article, we provide an overview on discrete-state stochastic kinetic models and explain how these models can be applied to experimental investigations using stopped-flow, single-molecule, nuclear magnetic resonance (NMR), and other biophysical and biochemical methods.

How Pioneer Transcription Factors Search for Target Sites on Nucleosomal DNA

“…The most critical step of all cellular processes is initiated by protein molecules, known as transcription factors (TFs), that must recognize and bind to specific sequences on DNA, eventually activating genetic expression by stimulating sequential biochemical and biophysical processes. − Yet, in eukaryotic cells, genes are tightly packed into chromatin structures, exhibiting a strong compaction of DNA molecules. , It is accomplished by creating nucleosome core particles that effectively close the regulatory sequences on DNA from interactions with external proteins. This raises a fundamental question of how the genes can be activated if they are not accessible to promoters.…”

“…The processes associated with normal transcription factors searching for their targets on naked DNA molecules have been thoroughly investigated in the last 40 years using a variety of experimental and theoretical tools. ,,− Many aspects of these complex phenomena are now well understood. It has been shown that normal TF might exhibit very fast and efficient target search dynamics by utilizing a so-called facilitated diffusion mechanism, in which the effective mobility of proteins is increased by alternating between 3D and 1D searching modes. , But the majority of protein target search investigations concentrated on in vitro studies where DNA molecules are typically found free in solutions. , The situation, however, is much more difficult for real in vivo cellular systems where a large fraction of DNA is covered by chromatin structures, preventing external proteins from easily accessing their regulatory sequences.…”

“…The processes associated with normal transcription factors searching for their targets on naked DNA molecules have been thoroughly investigated in the last 40 years using a variety of experimental and theoretical tools. ,,− Many aspects of these complex phenomena are now well understood. It has been shown that normal TF might exhibit very fast and efficient target search dynamics by utilizing a so-called facilitated diffusion mechanism, in which the effective mobility of proteins is increased by alternating between 3D and 1D searching modes. , But the majority of protein target search investigations concentrated on in vitro studies where DNA molecules are typically found free in solutions. , The situation, however, is much more difficult for real in vivo cellular systems where a large fraction of DNA is covered by chromatin structures, preventing external proteins from easily accessing their regulatory sequences. Although there have been several attempts to theoretically investigate some features of the protein target search in real cellular environment, − , the microscopic picture of how pioneer TFs can associate to their target sites that are covered by histones is mostly not understood at all. − At the same time, some experimental clues on the difference between normal TFs and pioneer TFs started to appear recently .…”

Particle-Environment Interactions In Arbitrary Dimensions: A Unifying Analytic Framework To Model Diffusion With Inert Spatial Heterogeneities

“…An example of a coalescing process is the search of a promoter region on DNA by transcription factors. These movement dynamics alternates between periods of 3D search in the cytoplasm and periods of restricted search along the 1D DNA [70]. We use our framework to study a system of relevance to the latter scenario: a first-passage process of two interacting particle in 1D.…”

Size limits sensitivity in all kinetic schemes

“…Then, the states of the system over time form a continuous-time Markov chain. Models of this form are ubiquitous in nonequilibrium physics, chemistry, and biophysics, where they are known by many names including: kinetic schemes [23], kinetic networks [24], Markov models, Markov jump processes, discrete-state kinetics [25], and linear framework graphs [13,26]. The main result we describe in this work applies to all such models.…”