Modeling dynamics of Translation

Instructions
If you don't see a picture above with mRNA and various buttons, please install newest version of Java.

PARAMETERS (Initiation):

Initiation is consists of thress steps;
(i) Binding of subunit with "on rate", which can detatch from mRNA with "off rate".
(ii) Forming stable complex which cannot detatch from mRNA with a rate "rate 1".
(iii) Start elongation with a rate "rate 2".
These 4 rates can be changed.

(Elongation):

Elongation occurs stochastically. A ribosome occupies 11 codons, and it proceeds with a rate given to each codons. One can choose;
1.) Constant rate 14 [1/s],
2.) Randomly distributed rate between 6 to 22 [1/s],
3.) Constant rate 14 [1/s] with slow sites 6 [1/s] in the middle of mRNA,
4.) Sites with rate from 6 to 22 [1/s] are distributed with some randomness, and faster site are located to be closer to the termination site.

(Termination):

The termination can take long time. One can choose the average time needed to terminate the translation in the box of "terminate".

The applet opens the possibility for changing length of mRNA. It is given in the number of codons. The maximam length that one can put now is 700 codons.

On the right top, one can see spatiotemporal plots, where spatial axis along mRNA is in horizontal direction, time axis in vertical direction, and the spatiotemporal location of ribosomes are shown as red bars. One can see the effect of queing clearly.

Philosophy

Another version: We have another version of the applet here , with additional information.

References:

J. E. Bergmann and H. F. Lodish, "A Kinetic Model of Protein Synthesis", J. Bio. Chem. 254, p.11927 (1979)

M. A. Sorensen and S. Pedersen, "Absolute in Vivo Translation Rates of Individual Codons in Escherichia coli' The Two Glutamic Acid Codons GAA and GAG Are Translated with a Threefold Difference in Rate" J. Mol. Biol. 222, p.265 (1991)