title: Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation.
abstract: Messenger RNA translation is often studied by means of statistical-mechanical models based on the asymmetric simple exclusion process (ASEP), which considers hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In this work we extend this class of models and consider the two fundamental steps of the ribosome's biochemical cycle following a coarse-grained perspective. In order to achieve a better understanding of the underlying biological processes and compare the theoretical predictions with experimental results, we provide a description lying between the minimal ASEP-like models and the more detailed models, which are analytically hard to treat. We use a mean-field approach to study the dynamics of particles associated with an internal stepping cycle. In this framework it is possible to characterize analytically different phases of the system (high density, low density or maximal current phase). Crucially, we show that the transitions between these different phases occur at different parameter values than the equivalent transitions in a standard ASEP, indicating the importance of including the two fundamental steps of the ribosome's biochemical cycle into the model.
authors.affiliation: Institute for Complex Systems and Mathematical Biology, King's College, University of Aberdeen, AB24 3UE Aberdeen, United Kingdom. l.ciandrini@abdn.ac.uk
authors.forename: L
authors.initials: L
authors.lastname: Ciandrini
authors.forename: I
authors.initials: I
authors.lastname: Stansfield
authors.forename: M C
authors.initials: MC
authors.lastname: Romano
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D003062:Codon; D003198:Computer Simulation; D016681:Genome, Fungal; D008957:Models, Genetic; D015233:Models, Statistical; D008962:Models, Theoretical; D009010:Monte Carlo Method; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D012270:Ribosomes / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013314:Stress, Mechanical
chemical_list: D003062:Codon; D012333:RNA, Messenger