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STOCHASTIC MODEL OF TRANSLATION ELONGATION BASED ON CONTINUOUS TIME MONTE CARLO METHOD

Motivation: Protein synthesis is one of the most energy consuming processes in cell. As a result, there are strong evidences of optimization at different stages of mRNA translation in many organisms. In particular, for individual mRNAs their codon composition and local secondary structures are biased, resulting in high optimization of elongation. To reveal fine patterns of ribosome traffic along mRNA, development of mathematical model of mRNA translation is required. Results: A stochastic model of elongation based on continuous time Monte Carlo method has been developed. The model simulates initiation of translation, ribosome movement along mRNA, tacking into account the current codon in A-site of ribosome, rate of cognate tRNA binding to the codon, local secondary structures and ribosome size. A new effect of periodical localization of non-optimal codons in mRNA has been predicted using the model. This effect has been shown to exist in natural E. coli genes. The length of the period is equal to the ribosome size obtained in experimental studies, confirming the model validity and its applicability for solving biological problems.