Analysis of the dynamics and competition for resources in the system of protein translation using stochastic simulations

Protein synthesis plays an important role in biological systems since its products, proteins and enzymes, constitute most of the molecular machinery required for cell regulation, growth and function in the tissue. Understanding the mechanisms of decoding and its rate limiting steps is crucial for the development of target drugs. A deterministic model based on kinetic description of the ribosomal pathway showed that competitive tRNA behavior was a determinant of codon elongation rates, whereas a recent work proposes Watson-Crick and non-Watson-Crick types of decoding as the main determinant. We use a stochastic algorithm to model the translation process using a mechanistic model for ribosomal kinetics that accounts for both competitive tRNA behavior and Watson-Crick and non-Watson-Crick types of decoding. With this framework we simulate an E. coli translating gene pool and analyze the effects of codon usage in the exploitation of ribosomes and tRNA resources.