Modeling protein synthesis from a physicist's perspective: a toy model
arXiv:physics/0702149 · doi:10.1119/1.2757628
Abstract
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell biology, important quantitative models of protein synthesis have been reported in research journals devoted to statistical physics and related interdisciplinary topics. From the perspective of a physicist, protein synthesis is the classical transport of interacting ribosomes on a messenger RNA (mRNA) template that dictates the sequence of the amino acids on the protein. We discuss appropriate simplification of the models and methods. In particular, we develop and analyze a simple toy model using some elementary techniques of non-equilibrium statistical mechanics and predict the average rate of protein synthesis and the spatial organization of the ribosomes in the steady state.
21 pages (including 5 EPS figures) in AJP style; Accepted for Publication in American Journal of Physics
References in corpus (17)
- Statistical Physics of Vehicular Traffic and Some Related Systems
- The totally asymmetric exclusion process with extended objects, a model for protein synthesis
- Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms
- Clustered bottlenecks in mRNA translation and protein synthesis
- Shock formation in an exclusion process with creation and annihilation
- Localization of shocks in driven diffusive systems without particle number conservation
- Local Inhomogeneity in Asymmetric Simple Exclusion Processes with Extended Objects
- Towards a model for protein production rates
- Towards a model for protein production rates
- Ribosome recycling, diffusion, and mRNA loop formation in translational regulation
- Exclusion Processes with Internal States
- Traffic of interacting ribosomes: effects of single-machine mechano-chemistry on protein synthesis
- Traffic of interacting ribosomes on mRNA during protein synthesis: effects of chemo-mechanics of individual ribosomes
- Mean field approaches to the totally asymmetric exclusion process with quenched disorder and large particles
- Car-oriented mean-field theory for traffic flow models
- Particle-hopping Models of Vehicular Traffic: Distributions of Distance Headways and Distance Between Jams
- Shocks in the asymmetric exclusion process with internal degree of freedom
Cited by in corpus (6)
- Stochastic kinetics of ribosomes: single motor properties and collective behavior
- Dynamical modeling of microRNA action on the protein translation process
- Intra-cellular traffic: bio-molecular motors on filamentary tracks
- Stochastic thermodynamics and modes of operation of a ribosome: a network theoretic perspective
- Molecular motors: design, mechanism and control
- Resource Letter: Bio-molecular Nano-machines: where Physics, Chemistry, Biology and Technology meet