title: Kinetics of self-assembly via facilitated diffusion: Formation of the transcription complex.
abstract: We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in three dimensions and one dimension. Our study is motivated by single-molecule-level observations revealing the dynamics of transcription factors that bind to the deoxyribonucleic acid at early stages of transcription. We calculate the probability that a complex made up of a given number of molecules is completely formed, as well as the distribution of completion times, upon the binding of a seed molecule at a target site on the filament (without explicitly modeling the three-dimensional diffusion that precedes binding). We compare two different mechanisms of assembly where molecules bind in sequential and random order. Our results indicate that while the probability of completion is greater for random binding, the completion time scales exponentially with the size of the complex; in contrast, it scales as a power law or slower for sequential binding, asymptotically. Furthermore, we provide model predictions for the dissociation and residence times of the seed molecule, which are observables accessible in single-molecule tracking experiments.
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, 606-8501, Kyoto, Japan.
authors.forename: Ziya
authors.initials: Z
authors.lastname: Kalay
mesh_terms: D003198:Computer Simulation; D055459:Facilitated Diffusion / Q000502:physiology*; D007700:Kinetics; D008390:Markov Chains; D008954:Models, Biological; D011336:Probability