Driven transport on a flexible polymer with particle recycling: A model inspired by transcription and translation

Abstract

Many theoretical works have attempted to coarse grain gene expression at the level of transcription and translation via frameworks based on exclusion processes. Usually in these models the threedimensional conformation of the substrates (DNA and mRNA) is neglected, and particles move on a static unidimensional lattice in contact to an infinite reservoir. In this work we generalise the paradigmatic exclusion process and study the transport of particles along a unidimensional polymerlike flexible lattice immersed in a three-dimensional particle reservoir. We study the recycling of particles in the reservoir, how the transport is influenced by the global conformation of the lattice and, in turn, how particle density dictates the structure of the polymer. arXiv:1803.08110v4 [cond-mat.stat-mech]

Modelling the effect of ribosome mobility on the rate of protein synthesis

“…Here, we would like to focus on the physical consequences of Eqs. (8) and (9). To obtain the protein synthesis rate J, we combine Eqs.…”

“…To obtain the protein synthesis rate J, we combine Eqs. (5) and (8). In the LD phase, we obtain a secondorder algebraic equation whose solution α ∈ [0, p/2] is given by…”

“…a e-mail: izaak.neri@kcl.ac.uk (corresponding author) b e-mail: jean-charles.walter@umontpellier.fr c e-mail: andrea.parmeggiani@umontpellier.fr It has been argued that the recycling of ribosomes through Brownian diffusion in the cytosol plays an important role in the control or regulation of translation [1,[6][7][8]. When a ribosome unbinds from the mRNA after termination, it can either rebind to the same mRNA or bind to another mRNA.…”

“…Phenomena of active transport coupled to a diffusive reservoir have been studied before in the literature, see, for example, Refs. [6][7][8][17][18][19][20][21][22][23][24][25][26][27][28]. In these studies, much focus has been put on nonequilibrium phase transitions [11,22,29,30].…”

What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis

“…In fact, it is thought that some components of the translational machinery can be recycled after termination, without completely re-entering the enzyme pool in the cytoplasm, thus increasing translation efficiency [ 142 ]. To study this phenomenon, some works [ 143 , 144 ] have coupled the TASEP with ribosome diffusion in a three-dimensional medium, and these model ribosome adsorption/desorption kinetics at mRNA initiation/termination sites as well as polymer physics, which determines the spatial distribution of the termini with respect to each other ( figure 3 b (iv)). This process can be facilitated by additional mRNA-binding factors which can prompt loop formation, bringing the 3′ and 5′ ends of the transcript in proximity [ 145 – 147 ].…”