Stochastic model of template-directed elongation processes in biology
| Autor: | Chrystopher L. Nehaniv, Maria J. Schilstra |
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| Rok vydání: | 2010 |
| Předmět: |
Statistics and Probability
Stochastic Processes Binding Sites biology DNA polymerase Activator (genetics) Applied Mathematics Repressor Templates Genetic General Medicine Models Theoretical Ribosome General Biochemistry Genetics and Molecular Biology Receptor–ligand kinetics Kinetics chemistry.chemical_compound chemistry Transcription (biology) Modeling and Simulation RNA polymerase Biophysics biology.protein Elongation Simulation |
| Zdroj: | Biosystems. 102:55-60 |
| ISSN: | 0303-2647 |
| Popis: | We present a novel modular, stochastic model for biological template-based linear chain elongation processes. In this model, elongation complexes (ECs; DNA polymerase, RNA polymerase, or ribosomes associated with nascent chains) that span a finite number of template units step along the template, one after another, with semaphore constructs preventing overtaking. The central elongation module is readily extended with modules that represent initiation and termination processes. The model was used to explore the effect of EC span on motor velocity and dispersion, and the effect of initiation activator and repressor binding kinetics on the overall elongation dynamics. The results demonstrate that (1) motors that move smoothly are able to travel at a greater velocity and closer together than motors that move more erratically, and (2) the rate at which completed chains are released is proportional to the occupancy or vacancy of activator or repressor binding sites only when initiation or activator/repressor dissociation is slow in comparison with elongation. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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