title: Modeling of ribosome dynamics on a ds-mRNA under an external load.
abstract: Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to the recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force and the translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions.
authors.affiliation: Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
authors.forename: Bahareh
authors.initials: B
authors.lastname: Shakiba
authors.affiliation: Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Dayeri
authors.affiliation: Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
authors.forename: Farshid
authors.initials: F
authors.lastname: Mohammad-Rafiee
mesh_terms: D008958:Models, Molecular; D012330:RNA, Double-Stranded / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D012343:RNA, Transfer