Theoretical modelling of protein synthesis

Asymmetric exclusion process in a system of interacting Brownian particles

We study a continuous-space version of the totally asymmetric simple exclusion process (TASEP), consisting of interacting Brownian particles subject to a driving force in a periodic array of potential wells. Particles are inserted into the leftmost well at rate α, hop to the right at unit rate, and are removed at the rightmost well at rate β. Our study is motivated by recent experiments on colloidal particles in a periodic potential generated by an optical tweezers array. Particles spend most of the time near potential minima, approximating the situation on the lattice; a short-range repulsive interaction prevents two particles from occupying the same potential well. A constant driving force, representing Stokes drag on particles suspended in a moving fluid, leads to biased motion. Our results for the density profile and current, obtained via numerical integration of the Langevin equation and dynamic Monte Carlo simulations, indicate that the continuous-space model exhibits phase transitions analogous to those observed in the lattice TASEP. The correspondence is not exact, however, due to the lack of particle-hole symmetry in our model.

Metabolic control analysis of monoclonal antibody synthesis

A general route for protein synthesis in eukaryotic cells has been proposed and applied to monoclonal antibody (MAb) synthesis. It takes into account transcription of the gene, binding of ribosomes to mRNA, and polypeptide elongation including binding to SRP (signal recognition particles) and SRP-receptor, competing translocation, folding and glycosylation, assembly of the heavy and light chains in a tetrameric protein and Golgi processing and secretion. A comprehensive model was built on the basis of the proposed pathway. The model takes into account the mechanism of each step. Metabolic control analysis (MCA) principles were applied to the general pathway using the proposed model, and control coefficients were calculated. The results show a shared flux control (of both pathway flux and flux ratio at the branch) among different steps, i.e., transcription, folding, glycosylation, translocation and building blocks synthesis. The steps sharing the control depend on the concentration of building blocks, pathway flux and levels of OST (oligosacharyl transferase), BiP (heavy chain binding protein) and PDI (protein disulfide isomerase). Model predictions compare well with experimental data for MAb synthesis, explaining the control structure of the route and the heterogeneity of the product and also addressing future targets for improvement of the production rate of MAbs.

Kinetics of interleukin 2 mRNA and protein produced in the human T-cell line Jurkat and effect of cyclosporin A

The kinetics of interleukin 2 mRNA accumulation in the leukemic T-cell line Jurkat, which can be induced with phytohemagglutinin and phorbol 12-myristate 13-acetate to produce large amounts of interleukin 2, was analyzed by a modified DNA-excess solution hybridization assay using a 5'-32P-labeled oligodeoxyribonucleotide 30 bases long as probe. Cyclosporin A was used as a valuable tool to gain more insight into the quantitative aspects of interleukin 2 production, on the basis of the assumption that transcription of the interleukin 2 gene is completely inhibited shortly after administration of cyclosporin A. The half-life of interleukin 2 mRNA was estimated to be approximately 2 h. With the aid of simple mathematical models, we have been able to relate the concentration of interleukin 2 protein in the supernatant to the interleukin 2 mRNA kinetics. This novel quantitative kinetic analysis revealed that, independent of the absence or presence of cyclosporin A, interleukin 2 protein is synthesized at a rate of approximately 1.3 molecules per molecule of interleukin 2 mRNA per second and secreted within 2 h after it is synthesized and that its half-life in the supernatant is approximately 10 h.

Movable finite automata (MFA) models for biological systems. II: Protein biosynthesis

A recently introduced class of models, the Movable Finite Automata (MFA) models, are used for simulating the elongation of the polypeptide chain in protein biosynthesis. The results of these simulations, all carried out on a microcomputer, are given.

Site dependent time optimization of protein synthesis with special regard to accuracy

The efficiency of protein synthesis is determined by its rate, accuracy, and energy consumption. With the energy consumption fixed, we optimize the system with respect to time and accuracy. Using an analytic model for a simple system and computer simulations for more complex systems, where also the possibility of errors is included, we demonstrate how different parts of the messenger RNA influence the protein production rate differently. The first part of the coding sequence is of major importance, since the availability of empty initiation sites is crucial, and queuing back to that region may interfere with initiation. The elongation rate at different positions depends on codon usage, on the concentrations of substrate and co-factors, and on the kinetic rate constants, including those of the proofreading branch(es). Ribosomal proofreading is a time consuming process and by allowing for more errors in the beginning of a protein, it is possible to increase the production rate of that protein. We calculate the mean translation time per functioning protein for various translation accuracies, and discuss the different strategies open to living cells.