The article by Peter H. von Hippel and Otto G. Berg explores the phenomenon of facilitated target location in biological systems, particularly focusing on how protein regulators of gene expression find their regulatory DNA targets at rates faster than diffusion-controlled processes. The authors discuss the limitations of reaction rates in biological systems, which are typically limited by the rates at which diffusion can bring reactants together. They introduce the Smoluchowski equation to estimate the maximum rate of molecular association and modify it to account for factors such as molecular asymmetry, electrostatic interactions, and the interaction distance.
The article highlights the importance of inelastic collisions and the formation of intermediate complexes between nonspecific DNA sites, which can speed up target location. Two mechanisms are discussed: "sliding" and "intersegment transfer." Sliding involves the one-dimensional diffusion of the protein along the DNA contour, while intersegment transfer allows the protein to bind to two distant DNA sites transiently before separating. These processes can significantly increase the rate of target location.
The authors also provide diagnostic methods to determine whether sliding or other forms of facilitated diffusion are involved in DNA target location, emphasizing the need for careful experimental design to isolate the rate-limiting step in the interaction process. The article concludes by summarizing the overall perspective on how reduced-dimensional diffusion and nonspecifically bound states can enhance biological interactions beyond the limits set by three-dimensional diffusion processes.The article by Peter H. von Hippel and Otto G. Berg explores the phenomenon of facilitated target location in biological systems, particularly focusing on how protein regulators of gene expression find their regulatory DNA targets at rates faster than diffusion-controlled processes. The authors discuss the limitations of reaction rates in biological systems, which are typically limited by the rates at which diffusion can bring reactants together. They introduce the Smoluchowski equation to estimate the maximum rate of molecular association and modify it to account for factors such as molecular asymmetry, electrostatic interactions, and the interaction distance.
The article highlights the importance of inelastic collisions and the formation of intermediate complexes between nonspecific DNA sites, which can speed up target location. Two mechanisms are discussed: "sliding" and "intersegment transfer." Sliding involves the one-dimensional diffusion of the protein along the DNA contour, while intersegment transfer allows the protein to bind to two distant DNA sites transiently before separating. These processes can significantly increase the rate of target location.
The authors also provide diagnostic methods to determine whether sliding or other forms of facilitated diffusion are involved in DNA target location, emphasizing the need for careful experimental design to isolate the rate-limiting step in the interaction process. The article concludes by summarizing the overall perspective on how reduced-dimensional diffusion and nonspecifically bound states can enhance biological interactions beyond the limits set by three-dimensional diffusion processes.