  Translation is a central biological process by which proteins are synthesized
from genetic information contained within mRNAs. Here we study the kinetics of
translation at molecular level through a stochastic simulation model. The model
explicitly include RNA sequences, ribosome dynamics, tRNA pool and biochemical
reactions in the translation elongation. The results show that the translation
efficiency is mainly limited by the available ribosome number, translation
initiation and the translation elongation time. The elongation time is
log-normal distribution with mean and variance determined by both the codon
saturation and the process of aa-tRNA selection at each codon binding.
Moreover, our simulations show that the translation accuracy exponentially
decreases with the sequence length. These results suggest that aa-tRNA
competition is crucial for both translation elongation, translation efficiency
and the accuracy, which in turn determined the effective protein production
rate of correct proteins. Our results improve the dynamical equation of protein
production with a delay differential equation which is dependent on sequence
informations through both the effective production rate and the distribution of
elongation time.
