Figure 1.
Modes of transcription factor motion.
A) Schematic of the four modes of transcription factor (TF) motion (modified from [117]). B) Schematic of their implementation in the Smoldyn model. Modes: a) 3D diffusion within solution by Brownian motion, b) 1D sliding of a TF non-specifically bound to DNA, c) intersegmental transfer, where a TF binds two DNA segments and moves from one to the other, and d) hopping, in which a TF makes short excursions away from DNA (simulated as a sequence of elementary unbinding, diffusion, and binding processes).
Figure 2.
Smoldyn model of the yeast nucleus.
A) Example of a Smoldyn simulation. The nuclear envelope is modelled as a perfect sphere containing one or more TFs (light blue dot), multiple stacks of DNA segments (grey bars), and one or more target genes (TG) on the DNA (orange hexagon). Individual DNA segments may be part of the same chromosome, but are separated so that 1D sliding is not possible between them. B) Target genes along a DNA filament, shown with their centres as black dots and their binding radii as orange regions. TF-TG complex formation occurs when a DNA-bound TF diffuses to within a binding radius of a TG.
Figure 3.
A) Illustration of the ‘antenna effect’: target gene finding times are reduced when TFs can get to their targets by diffusing along the DNA. The TF (light blue circle) diffuses along the antenna DNA (grey bar) to reach the TG (orange hexagon). B) Effect of antenna length on the number of TF-TG complexes at steady-state. C) Effect of antenna length on the time for the first TF to bind to the first TG in the simulation (blue) and on the time required for half of the steady-state number of TF-TG complexes (from panel B) to form (red). D) Effect of the DNA dissociation rate (koff) and antenna length on the number of steady-state TF-TG complexes. Simulation parameters: D3D = 2.72 µm2 s−1, D1D = 0.0262 µm2 s−1, kon = 1.7 µm/s, koff = 11.6 s−1 unless otherwise noted, σb = 2 nm, IST rate = 0, and specific binding was reversible with dissociation rate 0.025 s−1; 50 TFs were started at random 3D locations and there were 20 TGs, each at the centre of a DNA segment. Error bars represent one standard deviation, determined from 20 repeated simulations.
Figure 4.
The number of TF-TG complexes that formed for TFs that started at various distances away from their targets and that could not slide along the DNA. The distance dependence shown here is indicative of hopping motion, in which TFs repeatedly unbound from the DNA, diffused briefly in 3D space, and rebound to the DNA at a location close to the unbinding location. Simulation parameters: D3D = 2.72 µm2 s−1, D1D = 0, kon = 1.7 µm/s, koff = 11.6 s−1, σb = 2 nm, IST rate = 0, specific binding was irreversible, and multiple TFs binding to a single TG was allowed; on each of 20 DNA segments, 6 labeled TFs were started at 60 bp distance increments away from a single TG. Bar heights represent the number of TF-TG binding events, out of 20 possible, for each TF location after 60 minutes. Error bars represent one standard deviation, determined from 20 replicate simulations.
Figure 5.
A) Mean finding time for a single transcription factor placed at varying distances away from its target. Searching was possible by 1D sliding (green), “sequential” intersegmental transfer between adjacent DNA sections (yellow) or “concurrent” intersegmental transfer between all DNA sections in a group (red). B–D) Simulations testing the effect of the three major modes of motion. B) Arrangement of the 50 DNA segments within the simulated nucleus: shown 10× wider than in the simulation for clarity. The TF is placed at the position shown in light blue, and the time is measured until it binds the target gene (orange sphere). C) Total number of complexes formed over time for 100 different simulations, each with one transcription factor and one target, using nine different combinations of 3D diffusion, 1D sliding, and intersegmental transfer (IST). 3D diffusion was varied between low (+), standard +, and zero, 0. 1D sliding and IST was either present, +, or absent, 0. Shown adjacent are the corresponding values for the simulation parameters: σb is the binding radius for TFs in 3D space and also bound to DNA. 1D sliding or IST alone (grey or black line) did not achieve a single binding event in the time shown. D) Mean target finding time, in the same simulations as shown in C).
Figure 6.
Multimericity of protein structures by PDB class.
Bars show the percentage of proteins in different protein classes that form dimers (blue) and tetramers (red). The protein list, which is non-redundant, was obtained from the 3D complex database [118]. The first three bars represent sequence specific DNA binding proteins, the oxidoreductase bar is a control group that does not bind to DNA, and the final bar represents all proteins in the database.