Towards a model for protein production rates

Abstract

In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two ``bottlenecks'' (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel ``edge'' effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions.

8 pages, 8 figures

References in corpus (7)

• Phase transitions in an exactly soluble one-dimensional exclusion process
• The totally asymmetric exclusion process with extended objects, a model for protein synthesis
• Clustered bottlenecks in mRNA translation and protein synthesis
• Exact Results for the Asymmetric Simple Exclusion Process with a Blockage
• Local Inhomogeneity in Asymmetric Simple Exclusion Processes with Extended Objects
• Disordered asymmetric simple exclusion process: mean-field treatment
• Queuing Transitions in the Asymmetric Simple Exclusion Process

Cited by in corpus (42)

• Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport
• Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments
• Inhomogeneous exclusion processes with extended objects: The effect of defect locations
• Mixed population of competing TASEPs with a shared reservoir of particles
• Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mRNA translation
• Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis
• Far-from-equilibrium transport with constrained resources
• Competition between Multiple Totally Asymmetric Simple Exclusion Processes for a Finite Pool of Resources
• Stochastic kinetics of ribosomes: single motor properties and collective behavior
• Phase diagram and edge effects in the ASEP with bottlenecks
• Feedback and Fluctuations in a Totally Asymmetric Simple Exclusion Process with Finite Resources
• Dynamical modeling of microRNA action on the protein translation process
• Single-Bottleneck Approximation for Driven Lattice Gases with Disorder and Open Boundary Conditions
• Twenty five years after KLS: A celebration of non-equilibrium statistical mechanics
• Asymmetric Exclusion Processes with Disorder: Effect of Correlations
• Multiple phase transitions in a system of exclusion processes with limited reservoirs of particles and fuel carriers
• Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding
• Defect-induced phase transition in the asymmetric simple exclusion process
• Fluctuations in protein synthesis from a single RNA template: stochastic kinetics of ribosomes
• Nonequilibrium steady states in asymmetric exclusion processes on a ring with bottlenecks
• Collective dynamics of an inhomogeneous two-channel exclusion process: Theory and Monte Carlo simulations
• Disordered driven lattice gases with boundary reservoirs and Langmuir kinetics
• Modeling protein synthesis from a physicist's perspective: a toy model
• Entrainment and unit velocity: Surprises in an accelerated exclusion process
• Interplay between finite resources and local defect in an asymmetric simple exclusion process
• Power Spectra of a Constrained Totally Asymmetric Simple Exclusion Process
• Phase coexistences and particle non-conservation in a closed asymmetric exclusion process with inhomogeneities
• Intra-cellular traffic: bio-molecular motors on filamentary tracks
• Nonequilibrium steady states in a closed inhomogeneous asymmetric exclusion process with particle nonconservation
• Understanding the edge effect in TASEP with mean-field theoretic approaches
• Competition for finite resources
• Interference of two co-directional exclusion processes in the presence of a static bottleneck: a biologically motivated model
• Shepherd Model for Knot-Limited Polymer Ejection from a Capsid
• Asymmetric Exclusion Process with Global Hopping
• The fitness landscapes of translation
• Defect versus defect: stationary states of single file marching in periodic landscapes with road blocks
• Optimizing evacuation flow in a two-channel exclusion process
• Power spectra of TASEPs with a localized slow site
• Resource Letter: Bio-molecular Nano-machines: where Physics, Chemistry, Biology and Technology meet
• RNA polymerase interactions and elongation rate
• On the Structure of the Initiation and Elongation Rates that Maximize Protein Production in the Ribosome Flow Model
• Fluctuations in meta-population exclusion processes